subject:(introgression)

Rice University

1. Elshahat, Eslam. Functional divergence and natural selection underlying genome wide introgressive hybridization of protein coding genes between the Algerian mouse (Mus spretus) and the house mouse (Mus musculus domesticus).

Degree: PhD, Natural Sciences, 2019, Rice University

URL: http://hdl.handle.net/1911/105346

► Genome wide introgression was recently reported between two mice species in Europe, Mus musculus domesticus (West European house mouse) and Mus spretus (the Algerian mouse).… (more)

▼ Genome wide introgression was recently reported between two mice species in Europe, Mus musculus domesticus (West European house mouse) and Mus spretus (the Algerian mouse). Introgression was found outside the area of sympatry between the two species. My dissertation is an attempt to understand introgression in good biological species, and how introgression affects genome evolution using the house mouse as a study system. I used genome wide array data from 45 M. m. domesticus and 6 M. spretus, as well as 67 whole genome sequences from Mus genus mice. I calculated the molecular evolution rates of protein coding genes between the two mice species, and studied functionality of introgressed genes. I investigated if introgression in mice is a rare or frequent phenomenon. Introgression between the two species affected large portions of the M. m. domesticus genome, almost 135 Mb. I studied the directionality of introgression, and concluded it is a bidirectional process; and the genetic material flow favored from M. spretus to M. m. domesticus. I investigated the geographical distribution of introgressions, and the genic content of introgressed fragments. Most introgressions occur in gene carrying regions, and most introgressed genes contain protein changing mutations. Introgressed gene have a wide range of biological functions. Olfactory receptors and immune response were some of the frequent introgressed functions. One of the largest introgressed fragments was found in chromosome 7 which contains Vkorc1 gene; a gene responsible of anti-coagulants poisons resistance. I explored the genetic polymorphism of the introgressed fragments between M. spretus, M. m. domesticus, M. m. musculus, and M. m. castaneus. I concluded that the species history of mice is complicated and could affect the study of introgression. Introgressive hybridization plays an important role in introducing adaptive genetic mutations under different conditions. Understanding how species hybridize and exchange genes in nature will help us better understand adaptation and evolution. Advisors/Committee Members: Kohn, Micheal (advisor).

Subjects/Keywords: Introgression; house mouse; gene introgression

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APA (6^th Edition):

Elshahat, E. (2019). Functional divergence and natural selection underlying genome wide introgressive hybridization of protein coding genes between the Algerian mouse (Mus spretus) and the house mouse (Mus musculus domesticus). (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/105346

Chicago Manual of Style (16^th Edition):

Elshahat, Eslam. “Functional divergence and natural selection underlying genome wide introgressive hybridization of protein coding genes between the Algerian mouse (Mus spretus) and the house mouse (Mus musculus domesticus).” 2019. Doctoral Dissertation, Rice University. Accessed March 06, 2021. http://hdl.handle.net/1911/105346.

MLA Handbook (7^th Edition):

Elshahat, Eslam. “Functional divergence and natural selection underlying genome wide introgressive hybridization of protein coding genes between the Algerian mouse (Mus spretus) and the house mouse (Mus musculus domesticus).” 2019. Web. 06 Mar 2021.

Vancouver:

Elshahat E. Functional divergence and natural selection underlying genome wide introgressive hybridization of protein coding genes between the Algerian mouse (Mus spretus) and the house mouse (Mus musculus domesticus). [Internet] [Doctoral dissertation]. Rice University; 2019. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1911/105346.

Council of Science Editors:

Elshahat E. Functional divergence and natural selection underlying genome wide introgressive hybridization of protein coding genes between the Algerian mouse (Mus spretus) and the house mouse (Mus musculus domesticus). [Doctoral Dissertation]. Rice University; 2019. Available from: http://hdl.handle.net/1911/105346

University of Windsor

2. Munholland, Seth. Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean).

Degree: PhD, Biological Sciences, 2020, University of Windsor

URL: https://scholar.uwindsor.ca/etd/8323

► Phaseolus vulgaris is a major food crop grown and consumed around the world. A new world vegetable, the common bean underwent two separate domestication events,… (more)

▼ Phaseolus vulgaris is a major food crop grown and consumed around the world. A new world vegetable, the common bean underwent two separate domestication events, both pre-Columbus. These events generated two different land races, the Mesoamerican and Andean, named for the area where the domestication took place. Since the initial domestications the land races have been generally evenly cultivated, but despite its popularity the common bean has only very recently been fully sequenced. One of the issues faced by bean growers worldwide is Common Bacterial Blight (CBB). A disease caused by Xanthomonas axonopodis, CBB causes crop loses ranging from 20–40% every year but does not affect all species within Phaseolus evenly; P. acutifolius, for example, shows an innate resistance to CBB. To leverage this advantage, researchers at the University of Guelph, in partnership with the Ontario Agricultural College, developed a cultivar of Mesoamerican P. vulgaris that was introgressed with PI440795, a P. acutifolius accession, and backcrossed repeatedly with several other Mesoamerican P. vulgaris accessions to generate ‘OAC-Rex’, a plant that displays the crop-desired traits of P. vulgaris and the disease resistance traits of P. acutifolius. Genetic introgression is the process of crossing distantly related organisms followed by repeated backcrossing, resulting in a viable offspring that displays characteristics of each parent. Though rarely occurring, it can be observed in both plants and animals and is often exploited in a crop development context to generate new cultivars. Unfortunately, though regularly observed, introgression has been followed on a predominantly phenotypic level, usually many generations after the event, and as such molecular aspects of this phenomenon are largely unknown.By studying OAC-Rex, PI440795, and G-19833 (an Andean cultivar whose whole-genome has been published) introgression was examined directly and a method for the detection of regions within the introgressed genome uniquely donated from either parent Advisors/Committee Members: William Crosby.

Subjects/Keywords: Genomics; Introgression; Phaseolus

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APA (6^th Edition):

Munholland, S. (2020). Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean). (Doctoral Dissertation). University of Windsor. Retrieved from https://scholar.uwindsor.ca/etd/8323

Chicago Manual of Style (16^th Edition):

Munholland, Seth. “Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean).” 2020. Doctoral Dissertation, University of Windsor. Accessed March 06, 2021. https://scholar.uwindsor.ca/etd/8323.

MLA Handbook (7^th Edition):

Munholland, Seth. “Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean).” 2020. Web. 06 Mar 2021.

Vancouver:

Munholland S. Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean). [Internet] [Doctoral dissertation]. University of Windsor; 2020. [cited 2021 Mar 06]. Available from: https://scholar.uwindsor.ca/etd/8323.

Council of Science Editors:

Munholland S. Organization And Introgression Mechanics Of Phaseolus Vulgaris (Common Bean). [Doctoral Dissertation]. University of Windsor; 2020. Available from: https://scholar.uwindsor.ca/etd/8323

University of Alberta

3. Bowles, Victoria. Relationships and introgression within Carthamus (Asteraceae), with an emphasis on safflower (Carthamus tinctorius).

Degree: MS, Department of Biological Sciences, 2010, University of Alberta

URL: https://era.library.ualberta.ca/files/2f75r956w

► Carthamus (Asteraceae) contains both crop species (C. tinctorius, safflower) and weedy species, increasing the need for a better understanding of the genus. Despite previous studies,… (more)

Subjects/Keywords: introgression; microsatellite; Carthamus; relationships; phylogenetics

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APA (6^th Edition):

Bowles, V. (2010). Relationships and introgression within Carthamus (Asteraceae), with an emphasis on safflower (Carthamus tinctorius). (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/2f75r956w

Chicago Manual of Style (16^th Edition):

Bowles, Victoria. “Relationships and introgression within Carthamus (Asteraceae), with an emphasis on safflower (Carthamus tinctorius).” 2010. Masters Thesis, University of Alberta. Accessed March 06, 2021. https://era.library.ualberta.ca/files/2f75r956w.

MLA Handbook (7^th Edition):

Bowles, Victoria. “Relationships and introgression within Carthamus (Asteraceae), with an emphasis on safflower (Carthamus tinctorius).” 2010. Web. 06 Mar 2021.

Vancouver:

Bowles V. Relationships and introgression within Carthamus (Asteraceae), with an emphasis on safflower (Carthamus tinctorius). [Internet] [Masters thesis]. University of Alberta; 2010. [cited 2021 Mar 06]. Available from: https://era.library.ualberta.ca/files/2f75r956w.

Council of Science Editors:

Bowles V. Relationships and introgression within Carthamus (Asteraceae), with an emphasis on safflower (Carthamus tinctorius). [Masters Thesis]. University of Alberta; 2010. Available from: https://era.library.ualberta.ca/files/2f75r956w

University of Alberta

4. Rahman, Md Mostafizur. Introgression of Blackleg Resistance into Brassica napus from Brassica carinata.

Degree: MS, Department of Agricultural, Food, and Nutritional Science, 2011, University of Alberta

URL: https://era.library.ualberta.ca/files/9g54xk22j

► Blackleg, caused by Leptosphaeria maculans, is one of the most damaging diseases of oilseed rape, Brassica napus. Interspecific hybridization between B. napus and B. carinata… (more)

Subjects/Keywords: Introgression, blackleg, ovule culture, backcross

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APA (6^th Edition):

Rahman, M. M. (2011). Introgression of Blackleg Resistance into Brassica napus from Brassica carinata. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/9g54xk22j

Chicago Manual of Style (16^th Edition):

Rahman, Md Mostafizur. “Introgression of Blackleg Resistance into Brassica napus from Brassica carinata.” 2011. Masters Thesis, University of Alberta. Accessed March 06, 2021. https://era.library.ualberta.ca/files/9g54xk22j.

MLA Handbook (7^th Edition):

Rahman, Md Mostafizur. “Introgression of Blackleg Resistance into Brassica napus from Brassica carinata.” 2011. Web. 06 Mar 2021.

Vancouver:

Rahman MM. Introgression of Blackleg Resistance into Brassica napus from Brassica carinata. [Internet] [Masters thesis]. University of Alberta; 2011. [cited 2021 Mar 06]. Available from: https://era.library.ualberta.ca/files/9g54xk22j.

Council of Science Editors:

Rahman MM. Introgression of Blackleg Resistance into Brassica napus from Brassica carinata. [Masters Thesis]. University of Alberta; 2011. Available from: https://era.library.ualberta.ca/files/9g54xk22j

University of Alberta

5. Navabi, Zahra. Genetic analysis of the B-genome chromosomes in the Brassica species.

Degree: PhD, Department of Agricultural, Food and Nutritional Science, 2009, University of Alberta

URL: https://era.library.ualberta.ca/files/cr56n188v

► The family Brassicaceae includes a number of important species used as vegetables, oilseeds and medicine. The Brassica B-genome is significantly diverged from the A- and… (more)

▼ The family Brassicaceae includes a number of important species used as vegetables, oilseeds and medicine. The Brassica B-genome is significantly diverged from the A- and C-genomes, and species containing the B-genome possess many valuable agronomic and disease resistance traits. In this thesis, two populations of interspecific crosses between Brassica napus (AACC) and Brassica carinata (BBCC) were studied, and microsatellite (SSR) markers and genomic in situ hybridization (GISH) techniques were applied to characterize the B-genome chromosome introgressions in the advanced backcross populations and their effect on disease resistance, morphological and seed quality traits. A BC2S3 derived doubled haploid (DH) population was genotyped with 184 SSR markers and DH lines carrying stable B-genome chromosomal segments were identified. The GISH assay demonstrated that three of the 60 DHs were substitution lines in which the B-genome chromosome J13 was common to all. The lines with B-genome chromosomes, “B+”, were significantly different (P <0.01) from the lines without B-genome chromosomes, “B-” for some morphological and seed quality traits, such as days to flowering, days to maturity and erucic acid content. Further study revealed that resistance to Sclerotinia stem rot (caused by Sclerotinia sclerotiorum) has been inherited from the B or C genomes of B. carinata in some of the DH lines. Several BC3S1 families of another cross, derived from well-characterized BC3 plants containing introgressed B-genome chromosomes, were analyzed using SSR markers and the GISH assay to study the inheritance of the B-genome chromosome(s) and their association with morphological traits. This study revealed that the B-genome chromosomes tend to transfer through generations, either as whole chromosome(s) or as chromosomes without small terminal segments, as evidenced by low recombination frequencies (~ 0%) between the B and A/C-genome chromosomes. These results were supported by the GISH assay and chromosomes counts, and revealed that many of the BC3S1 lines were addition lines carrying extra B-genome chromosomes.

Subjects/Keywords: Genetics, brassica species, introgression

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Navabi, Z. (2009). Genetic analysis of the B-genome chromosomes in the Brassica species. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/cr56n188v

Chicago Manual of Style (16^th Edition):

Navabi, Zahra. “Genetic analysis of the B-genome chromosomes in the Brassica species.” 2009. Doctoral Dissertation, University of Alberta. Accessed March 06, 2021. https://era.library.ualberta.ca/files/cr56n188v.

MLA Handbook (7^th Edition):

Navabi, Zahra. “Genetic analysis of the B-genome chromosomes in the Brassica species.” 2009. Web. 06 Mar 2021.

Vancouver:

Navabi Z. Genetic analysis of the B-genome chromosomes in the Brassica species. [Internet] [Doctoral dissertation]. University of Alberta; 2009. [cited 2021 Mar 06]. Available from: https://era.library.ualberta.ca/files/cr56n188v.

Council of Science Editors:

Navabi Z. Genetic analysis of the B-genome chromosomes in the Brassica species. [Doctoral Dissertation]. University of Alberta; 2009. Available from: https://era.library.ualberta.ca/files/cr56n188v

Texas A&M University

6. Kyanam, Ammani Naidu. Development of Multiplex and Simplex Platforms for SNP-based Introgression of A2 and D1 Germplasm into Cotton Gossypium hirsutum (L.).

Degree: MS, Plant Breeding, 2016, Texas A&M University

URL: http://hdl.handle.net/1969.1/159063

► Cultivated Upland cotton, Gossypium hirsutum L., is a partially diploidized allotetraploid species with relatively low levels of genetic diversity. Genetic gain through traditional breeding approaches… (more)

▼ Cultivated Upland cotton, Gossypium hirsutum L., is a partially diploidized allotetraploid species with relatively low levels of genetic diversity. Genetic gain through traditional breeding approaches is thus impeded. The wild species of the primary and secondary gene pools of cotton are approachable sources of agronomic traits of interest, but biological, cytogenetic, genetic and reproductive incompatibilities can impede progress. Genomic markers can alleviate certain difficulties, and expedite selective transfer of exotic species germplasm into one or more elite genotypes of a crop species. Coordinated development of Chromosome Segment Substitution Lines (CSSLs) using markers can in principle lead to complete representation of an alien genome in a cultivated crop. Co-released with the CottonSNP63K Array, a BeadChip array for high-throughput genotyping of cotton, was a cluster file designed to facilitate automated genotype-calling germplasm from the primary genepool. Reported here is a new cluster file customized to germplasm from diploid species of the secondary gene pool. It significantly improves genotype call frequency and accuracy, and significantly increases the number of usable SNPs. The first high-density interspecific genetic map of SNPs between cotton and diploid species was developed. It contains 14,411 SNPs, based on segregation in an A2D1-BC1F1 population from an interspecific cross of G. hirsutum and a A2D1 synthetic tetraploid. Genotypes of 72 BC1F1 plants were based on the CottonSNP63K array and the new cluster file. Linkage analysis led to 26 linkage groups corresponding to the 26 chromosomes of cotton. Utility of the CottonSNP63K Array and its associated SNPs for research and introgression breeding were significantly enhanced by demonstrating the derivation of simplex or low-plex SNP assays. A sample set of SNP mapped markers were validated on the KASP™ based assays and the conversion rate was estimated at 44%. This indicates a potential for development of ad hoc simplex SNP assays that can be applied to large populations for marker-assisted introgression, selection and down-stream breeding. KASP assays are applicable to DNA extracted non-destructively from seed or seedling at low-cost. Thus, validated CottonSNP63K SNPs can be used for targeted purposes, such as detection of rare recombination events or rare combinations of genes. Advisors/Committee Members: Stelly, David M (advisor), Dever, Jane (committee member), Byrne, David H (committee member).

Subjects/Keywords: introgression; linkage mapping; genotyping; cotton

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APA (6^th Edition):

Kyanam, A. N. (2016). Development of Multiplex and Simplex Platforms for SNP-based Introgression of A2 and D1 Germplasm into Cotton Gossypium hirsutum (L.). (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/159063

Chicago Manual of Style (16^th Edition):

Kyanam, Ammani Naidu. “Development of Multiplex and Simplex Platforms for SNP-based Introgression of A2 and D1 Germplasm into Cotton Gossypium hirsutum (L.).” 2016. Masters Thesis, Texas A&M University. Accessed March 06, 2021. http://hdl.handle.net/1969.1/159063.

MLA Handbook (7^th Edition):

Kyanam, Ammani Naidu. “Development of Multiplex and Simplex Platforms for SNP-based Introgression of A2 and D1 Germplasm into Cotton Gossypium hirsutum (L.).” 2016. Web. 06 Mar 2021.

Vancouver:

Kyanam AN. Development of Multiplex and Simplex Platforms for SNP-based Introgression of A2 and D1 Germplasm into Cotton Gossypium hirsutum (L.). [Internet] [Masters thesis]. Texas A&M University; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1969.1/159063.

Council of Science Editors:

Kyanam AN. Development of Multiplex and Simplex Platforms for SNP-based Introgression of A2 and D1 Germplasm into Cotton Gossypium hirsutum (L.). [Masters Thesis]. Texas A&M University; 2016. Available from: http://hdl.handle.net/1969.1/159063

University of Iowa

7. Beck, Emily Abigail. Effects of protein-protein interactions on speciation: assessment of cascading positive selection and introgression.

Degree: PhD, Genetics, 2015, University of Iowa

URL: https://ir.uiowa.edu/etd/6545

► Speciation is a process by which 1 population splits into 2 distinct populations that in time acquire reproductive isolation (RI). Interestingly, the speed at… (more)

Subjects/Keywords: introgression; selection; speciation; Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Beck, E. A. (2015). Effects of protein-protein interactions on speciation: assessment of cascading positive selection and introgression. (Doctoral Dissertation). University of Iowa. Retrieved from https://ir.uiowa.edu/etd/6545

Chicago Manual of Style (16^th Edition):

Beck, Emily Abigail. “Effects of protein-protein interactions on speciation: assessment of cascading positive selection and introgression.” 2015. Doctoral Dissertation, University of Iowa. Accessed March 06, 2021. https://ir.uiowa.edu/etd/6545.

MLA Handbook (7^th Edition):

Beck, Emily Abigail. “Effects of protein-protein interactions on speciation: assessment of cascading positive selection and introgression.” 2015. Web. 06 Mar 2021.

Vancouver:

Beck EA. Effects of protein-protein interactions on speciation: assessment of cascading positive selection and introgression. [Internet] [Doctoral dissertation]. University of Iowa; 2015. [cited 2021 Mar 06]. Available from: https://ir.uiowa.edu/etd/6545.

Council of Science Editors:

Beck EA. Effects of protein-protein interactions on speciation: assessment of cascading positive selection and introgression. [Doctoral Dissertation]. University of Iowa; 2015. Available from: https://ir.uiowa.edu/etd/6545

8. Capblancq, Thibaut. La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha : Hybrid speciation : reflexions on the process and exploration of a case study in a complex of alpine butterflies.

Degree: Docteur es, Biodiversité écologie environnement, 2016, Université Grenoble Alpes (ComUE)

URL: http://www.theses.fr/2016GREAV023

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L’hybridation interspécifique est un phénomène très étudié ces dernières années et les conséquences qui lui sont attribuées dans l’évolution des espèces sont diverses. Une littérature… (more)

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L’hybridation interspécifique est un phénomène très étudié ces dernières années et les conséquences qui lui sont attribuées dans l’évolution des espèces sont diverses. Une littérature de plus en plus fournie met notamment en évidence le rôle que peut avoir l’hybridation sur l’émergence de nouveaux taxons. Mon travail de thèse s’attache à comprendre comment des croisements entre espèces peuvent impacter le processus de spéciation d’une nouvelle lignée évolutive et stimuler ainsi la diversification des organismes vivants.Une revue des différents cas d’espèces hybrides animales proposés dans la littérature a permis, dans la première partie de cette thèse, d’identifier les patrons associés de façon redondante au processus de spéciation hybride. Nous observons par exemple que, si l’apport premier de l’hybridation à la spéciation reste toujours la recombinaison de caractéristiques parentales divergentes, cela peut se traduire de manière différente lors de l’émergence de la lignée hybride. Cette synthèse a aussi été l’occasion de discuter des difficultés méthodologiques qui limitent une réelle estimation de la prévalence de ce phénomène dans l’évolution des espèces.Dans la seconde partie de ma thèse j’explore le processus de spéciation hybride chez un complexe d’espèces proches de papillons du genre Coenonympha. Je montre que, parmi les quatre lignées identifiées dans le complexe, deux sont issues de l’hybridation. Leurs caractéristiques génétiques, écologiques et morphologiques permettent de comprendre, en partie, comment leur phénotype recombinant a favorisé leur établissement en tant qu’espèces à part entière et leur isolement vis-à-vis de leurs espèces parentales.L’histoire évolutive de ces papillons est discutée en détail dans la dernière partie de mon travail de thèse. Les résultats obtenus pour ce cas particulier y sont confrontés aux autres exemples de spéciation hybride ainsi qu’aux attendus théoriques associés à ce phénomène. Les spécificités de ce système d’étude viennent ainsi enrichir les connaissances actuelles sur le processus de spéciation hybride et sur les impacts évolutifs de l’hybridation.

Interspecific hybridization is more and more studied these last years and its consequences on species evolution are diverse. The literature especially points out its potential impact on new species emergence and the number of hybrid speciation cases is increasing. My work aims at understanding how interspecific crosses can initiate the rise of a new hybrid lineage and stimulate the diversification of living organisms.Reviewing the examples of animals hybrid species described in the literature allows me, in the first part of this work, to identify the main patterns associated with the process of hybrid speciation. I observe in particular that, if the recombination of parental characteristics is always the main driver of hybrid speciation, it leads to various patterns in hybrid species establishment. I also discuss methodological issues concerning the identification of hybrid species, which limit our capacity to…

Advisors/Committee Members: Després, Laurence (thesis director).

Subjects/Keywords: Hybridation; Introgression; Spéciation; Adaptation; Lepidoptère; Hybridization; Introgression; Speciation; Adaptation; Lepidopteran; 570

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Capblancq, T. (2016). La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha : Hybrid speciation : reflexions on the process and exploration of a case study in a complex of alpine butterflies. (Doctoral Dissertation). Université Grenoble Alpes (ComUE). Retrieved from http://www.theses.fr/2016GREAV023

Chicago Manual of Style (16^th Edition):

Capblancq, Thibaut. “La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha : Hybrid speciation : reflexions on the process and exploration of a case study in a complex of alpine butterflies.” 2016. Doctoral Dissertation, Université Grenoble Alpes (ComUE). Accessed March 06, 2021. http://www.theses.fr/2016GREAV023.

MLA Handbook (7^th Edition):

Capblancq, Thibaut. “La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha : Hybrid speciation : reflexions on the process and exploration of a case study in a complex of alpine butterflies.” 2016. Web. 06 Mar 2021.

Vancouver:

Capblancq T. La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha : Hybrid speciation : reflexions on the process and exploration of a case study in a complex of alpine butterflies. [Internet] [Doctoral dissertation]. Université Grenoble Alpes (ComUE); 2016. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2016GREAV023.

Council of Science Editors:

Capblancq T. La spéciation hybride : réflexions générales et exploration d'un cas d'étude chez des papillons alpins du genre Coenonympha : Hybrid speciation : reflexions on the process and exploration of a case study in a complex of alpine butterflies. [Doctoral Dissertation]. Université Grenoble Alpes (ComUE); 2016. Available from: http://www.theses.fr/2016GREAV023

9. Méheust, Raphaël. Étude des processus introgressifs en évolution par des méthodes de réseaux : Using network-based methods to analyze introgressive events in evolution.

Degree: Docteur es, Biologie Evolutive, 2016, Université Pierre et Marie Curie – Paris VI

URL: http://www.theses.fr/2016PA066534

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L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes… (more)

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L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.

Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery…

Advisors/Committee Members: Bapteste, Éric (thesis director), Lopez, Philippe (thesis director).

Subjects/Keywords: Introgression; Bioinformatique; Génomique; Evolution; Gène composite; Endosymbiose; Bioinformatics; Introgression; Eukaryotes; 576.8

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APA (6^th Edition):

Méheust, R. (2016). Étude des processus introgressifs en évolution par des méthodes de réseaux : Using network-based methods to analyze introgressive events in evolution. (Doctoral Dissertation). Université Pierre et Marie Curie – Paris VI. Retrieved from http://www.theses.fr/2016PA066534

Chicago Manual of Style (16^th Edition):

Méheust, Raphaël. “Étude des processus introgressifs en évolution par des méthodes de réseaux : Using network-based methods to analyze introgressive events in evolution.” 2016. Doctoral Dissertation, Université Pierre et Marie Curie – Paris VI. Accessed March 06, 2021. http://www.theses.fr/2016PA066534.

MLA Handbook (7^th Edition):

Méheust, Raphaël. “Étude des processus introgressifs en évolution par des méthodes de réseaux : Using network-based methods to analyze introgressive events in evolution.” 2016. Web. 06 Mar 2021.

Vancouver:

Méheust R. Étude des processus introgressifs en évolution par des méthodes de réseaux : Using network-based methods to analyze introgressive events in evolution. [Internet] [Doctoral dissertation]. Université Pierre et Marie Curie – Paris VI; 2016. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2016PA066534.

Council of Science Editors:

Méheust R. Étude des processus introgressifs en évolution par des méthodes de réseaux : Using network-based methods to analyze introgressive events in evolution. [Doctoral Dissertation]. Université Pierre et Marie Curie – Paris VI; 2016. Available from: http://www.theses.fr/2016PA066534

University of Rochester

10. Geneva, Anthony Joseph; Glor, Richard E. Integrative analyses of speciation in Anolis lizards.

Degree: PhD, 2016, University of Rochester

URL: http://hdl.handle.net/1802/30421

► Speciation is of broad interest because this process has given rise to all of earth’s biodiversity. The study of speciation does not easily fit into… (more)

▼ Speciation is of broad interest because this process has given rise to all of earth’s biodiversity. The study of speciation does not easily fit into a single discipline within the realm of evolutionary biology. The study of groups of interbreeding organisms at the onset of speciation fall firmly within the realms of classic and population genetics. As lineages diverge population-specific alleles arise and fix, reproductive barriers form, gene flow decreases, and ultimately lineages become reciprocally monophyletic. By the end of the process, phylogenetic analyses provide more power to test hypotheses in such populations. While deep insights can come from studying speciation from either a genetic or phylogenetic perspective, a greater understanding of the process of speciation can come from an integrative approach employing the tools of multiple disciplines including population genetics, classic genetics, and phylogenetics. </br> This thesis focuses on bark anoles, part of the iconic adaptive radiation of West Indian Anolis lizards. We report the results of coalescent phylogenetics, phylogenetic comparative analyses, a two-generation hybridization experiment between ecologically differentiated lineages, and the development of a new method to detect gene flow using genome-scale DNA sequence data. Using this comprehensive approach, we find evidence for introgression between these ecologically diverged lineages as well as substantial intrinsic reproductive isolation. We find that evolutionary transitions in the ecologically adaptive trait of dewlap color are associated with divergence events in bark anoles. Finally, we introduce a new method to characterize genomic regions experiencing ongoing gene flow that outperforms available approaches. </br> Although integrative, our findings currently lack a comparative component. The work reported here can therefore be considered a beachhead into understanding the process of speciation in Anolis lizards, from which myriad comparative analyses can be launched.

Subjects/Keywords: Anolis; Anolis distichus; Gmin; Hybridization; Introgression; Speciation

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APA (6^th Edition):

Geneva, Anthony Joseph; Glor, R. E. (2016). Integrative analyses of speciation in Anolis lizards. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/30421

Chicago Manual of Style (16^th Edition):

Geneva, Anthony Joseph; Glor, Richard E. “Integrative analyses of speciation in Anolis lizards.” 2016. Doctoral Dissertation, University of Rochester. Accessed March 06, 2021. http://hdl.handle.net/1802/30421.

MLA Handbook (7^th Edition):

Geneva, Anthony Joseph; Glor, Richard E. “Integrative analyses of speciation in Anolis lizards.” 2016. Web. 06 Mar 2021.

Vancouver:

Geneva, Anthony Joseph; Glor RE. Integrative analyses of speciation in Anolis lizards. [Internet] [Doctoral dissertation]. University of Rochester; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1802/30421.

Council of Science Editors:

Geneva, Anthony Joseph; Glor RE. Integrative analyses of speciation in Anolis lizards. [Doctoral Dissertation]. University of Rochester; 2016. Available from: http://hdl.handle.net/1802/30421

Cornell University

11. Larson, Erica. Pattern And Process In A Mosaic Hybrid Zone: From Phenotype To Genotype.

Degree: PhD, Evolutionary Biology, 2013, Cornell University

URL: http://hdl.handle.net/1813/33848

! Speciation!is!the!process!of!a!single!lineage!splitting!into!two!or!more!daughter! lineages!over!time.!!The!evolution!of!barriers!to!gene!exchange!mark!the!point!in!splitting! where!diverging!lineages!represent!unique!entities!with!independent!evolutionary! trajectories.!!By!identifying!the!genes!that!contribute!to!barriers!between!recently!diverged! species!we!can!begin!to!understand!the!evolutionary!forces!that!led!to!their!divergence,! and!ultimately,!speciation.!!This!dissertation!focuses!on!two!recently!diverged!species!of! field!cricket,!Gryllus'firmus!and!G.'pennsylvanicus,!which!hybridize!in!zone!stretching!from! Connecticut!to!Virginia.!!We![1]!characterize!the!nature!of!understudied!barriers!that!occur! after!mating,!but!before!fertilization,![2]!define!the!role!of!proteins!secreted!from!the!male! accessory!glands!in!those!barriers,!and![3]!describe!patterns!of!variation!and!introgression! within!the!hybrid!zone!for!genes!expressed!in!the!male!accessory!gland.!!Chapter!1!finds! that!there!are!no!postXmating!prezygotic!barriers!between!G.'pennsylvanicus!females!and!G.' firmus!males,!but!that!the!reciprocal!crosses!are!isolated!by!barriers!that!occur!after!sperm! are!released!from!storage,!but!before!fertilization.!!Chapter!2!finds!that!seminal!fluid! proteins!secreted!from!the!male!accessory!glands!induce!a!shortXterm!eggXlaying!response,! but!alone!cannot!explain!the!normal!induction!of!eggXlaying!or!unsuccessful!fertilization!in! ! heterospecific!crosses.!!Chapter!3!lays!the!foundation!for!Chapters!4!and!5!by!describing! patterns!of!admixture!and!the!influence!of!environmental!variables!on!species!distributions! in!a!previously!uncharacterized!region!of!the!hybrid!zone!in!Pennsylvania.!!Chapter!4! compares!patterns!of!introgression!in!Pennsylvania!for!genes!known!to!encode!seminal! fluid!proteins!and!other!genes!expressed!in!the!male!accessory!gland.!!We!find!no!evidence! that!seminal!fluid!proteins!contribute!to!barriers!operating!within!the!hybrid!zone,!but! identify!a!number!of!other!candidate!barrier!genes.!!Chapter!5!compares!the!patterns!we! see!in!Pennsylvania!with!an!independent!transect!of!the!hybrid!zone!in!Connecticut.!!We! find!the!same!genes!under!selection!in!both!regions!of!the!hybrid!zone,!suggesting!that! these!genomic!regions!contribute!to!maintaining!species!boundaries.! ! Advisors/Committee Members: Harrison, Richard Gerald (chair), Lazzaro, Brian (committee member), Shaw, Kerry L (committee member).

Subjects/Keywords: speciation; barriers to gene exchange; introgression

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Larson, E. (2013). Pattern And Process In A Mosaic Hybrid Zone: From Phenotype To Genotype. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/33848

Chicago Manual of Style (16^th Edition):

Larson, Erica. “Pattern And Process In A Mosaic Hybrid Zone: From Phenotype To Genotype.” 2013. Doctoral Dissertation, Cornell University. Accessed March 06, 2021. http://hdl.handle.net/1813/33848.

MLA Handbook (7^th Edition):

Larson, Erica. “Pattern And Process In A Mosaic Hybrid Zone: From Phenotype To Genotype.” 2013. Web. 06 Mar 2021.

Vancouver:

Larson E. Pattern And Process In A Mosaic Hybrid Zone: From Phenotype To Genotype. [Internet] [Doctoral dissertation]. Cornell University; 2013. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1813/33848.

Council of Science Editors:

Larson E. Pattern And Process In A Mosaic Hybrid Zone: From Phenotype To Genotype. [Doctoral Dissertation]. Cornell University; 2013. Available from: http://hdl.handle.net/1813/33848

Texas A&M University

12. Culumber, Zachary Wyatt. Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones.

Degree: PhD, Biology, 2012, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10446

► Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. Additionally, investing the structure… (more)

▼ Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. Additionally, investing the structure of hybrid zones can provide valuable insight in the ecology and evolution of species. The present dissertation approaches the investigation of natural hybrid zones between Xiphophorus birchmanni and X. malinche from a population genetics perspective. The goal of the chapters herein are to investigate the genetic structure of these natural hybrid zones overall and the genetic structure of the populations within them in an effort to better understand the factors producing and maintaining spatial genetic patterns among this species pair and their hybrids. Using informative single nucleotide polymorphisms (SNPs) in one mitochondrial and three nuclear intron loci, I show that hybrid zones occur in replicated fashion in multiple stream reaches along a gradient from high to low elevation. Tests of FIS and linkage disequilibrium (LD) revealed significant genetic structure within a small subset of populations. Specifically, parentals and hybrids all three occur in some locations while other locations appear to be hybrid swarms. I then investigated a behavioral mechanism of reproductive isolation - social association, which might affect population structure. In clean water, individuals shoaled significantly more closely with conspecifics. Additionally, genotyping of females and their embryos revealed signatures of non-random mating in structured populations. Taken together, assortative social grouping, which may translate to assortative female mate choice, likely plays a role in maintaining population structure. Finally, I show that fluctuating asymmetry is significantly higher in unstructured than structure populations. This is a further indication that some form of non-random mating occurs in structured populations and has effects on male phenotypes. Advisors/Committee Members: Rosenthal, Gil (advisor), Criscione, Charles (committee member), Jones, Adam (committee member), Winemiller, Kirk (committee member).

Subjects/Keywords: Hybrid zone; population genetics; introgression; population structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Culumber, Z. W. (2012). Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10446

Chicago Manual of Style (16^th Edition):

Culumber, Zachary Wyatt. “Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones.” 2012. Doctoral Dissertation, Texas A&M University. Accessed March 06, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10446.

MLA Handbook (7^th Edition):

Culumber, Zachary Wyatt. “Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones.” 2012. Web. 06 Mar 2021.

Vancouver:

Culumber ZW. Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones. [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10446.

Council of Science Editors:

Culumber ZW. Mate Choice, Genetic Variation, and Population Structure in Hybrid Zones. [Doctoral Dissertation]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2011-12-10446

University of New Mexico

13. Beckman, Elizabeth Jane. BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus).

Degree: UNM Biology Department, 2016, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/151

► Landscape features, interspecific introgression, and adaptation work in concert to shape the evolutionary history of a clade. Understanding the independent and cumulative consequences of… (more)

▼ Landscape features, interspecific introgression, and adaptation work in concert to shape the evolutionary history of a clade. Understanding the independent and cumulative consequences of these evolutionary processes on diversification is critical to revealing the origins of extant biodiversity. Studying these processes within rapid radiations, a significant contributor to global biodiversity, can provide powerful insight into the process of diversification. To assess how diversification is shaped by these evolutionary forces, I examined the biogeographic history, patterns of interspecific introgression and adaptation to high elevation in a recent, rapid radiation of finches, the South American siskins (Fringillidae: Spinus). I found that this continental radiation colonized South America from North America and subsequently diversified at an exceptional rate in the high Andes. Further, my results show that sympatric siskin species within the high Andes form a monophyletic clade. I hypothesized that the close proximity of near relatives at high elevation could challenge species limits in Spinus. I investigated this hypothesis using a genome-wide SNP dataset to construct phylogenetic trees and performed formal tests of introgression among high elevation species. I developed an approach for assessing introgression despite persistent phylogenetic uncertainty, and discovered evidence for multiple introgressive events among different high elevation Spinus species. Cold temperatures and decreased partial pressure of oxygen are chronic stressors on organisms living at high elevation. Finally, to understand the consequences of high elevation on adaptive divergence in Spinus , I sequenced all genes which encode the oxygen-transport protein hemoglobin across the Spinus clade and among several populations of a species with a wide elevational range. I identified multiple instances of non-synonymous mutations at the inter- and intra-specific level in both adult and embryonic hemoglobin proteins. These patterns of genetic variation within functionally significant loci across elevation suggest that hemoglobin genes have had a significant impact on adaptation and potentially diversification within the South American siskins. Advisors/Committee Members: Christopher C. Witt, Jeffrey C. Long, Zachary A. Cheviron, Michael J. Andersen.

Subjects/Keywords: Fringillidae; Biogeography; hemoglobin; adaptation; Spinus; introgression; Biology

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APA (6^th Edition):

Beckman, E. J. (2016). BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus). (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/151

Chicago Manual of Style (16^th Edition):

Beckman, Elizabeth Jane. “BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus).” 2016. Doctoral Dissertation, University of New Mexico. Accessed March 06, 2021. https://digitalrepository.unm.edu/biol_etds/151.

MLA Handbook (7^th Edition):

Beckman, Elizabeth Jane. “BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus).” 2016. Web. 06 Mar 2021.

Vancouver:

Beckman EJ. BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus). [Internet] [Doctoral dissertation]. University of New Mexico; 2016. [cited 2021 Mar 06]. Available from: https://digitalrepository.unm.edu/biol_etds/151.

Council of Science Editors:

Beckman EJ. BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus). [Doctoral Dissertation]. University of New Mexico; 2016. Available from: https://digitalrepository.unm.edu/biol_etds/151

14. Lambert, Shea Maddock. Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) .

Degree: 2018, University of Arizona

URL: http://hdl.handle.net/10150/630229

► This dissertation consists of three works of phylogenetic biology. In each case, my collaborators and I contribute to the field by providing novel empirical results… (more)

▼ This dissertation consists of three works of phylogenetic biology. In each case, my collaborators and I contribute to the field by providing novel empirical results germane to each topic and study system, but also in a broader sense by facilitating the use and understanding of modern phylogenetic methods. In appendix A, I investigate the evolution of viviparity in phylogenetic test of the cold-climate hypothesis. This long-standing hypothesis states that the evolution of viviparity is an adaptation that prevents egg and/or juvenile mortality in cold climates. I apply a suite of cutting-edge phylogenetic comparative methods to phylogenetic, climatic, and life history data from the lizard family Phrynosomatidae. The results strongly support the cold-climate hypothesis, and help to explain two counter-intuitive patterns in Phrynosomatidae. In appendix B, I examine discordance in phylogenetic reconstruction in order to answer an unresolved question with significant practical implications for phylogeneticists: can disagreement between concatenated and multi-species coalescent estimates be predicted? Using an empirical example in higher-level scincid lizard relationships, I find that discordance between these methods is related to short, weakly supported branches, and the presence of conflicting gene trees. These results suggest that concatenation may provide a reasonable approximation of theoretically preferable species-tree methods under most circumstances. Moreover, standard methods for incorporating phylogenetic uncertainty may be sufficient to account for disagreements by species-tree method estimates. In appendix C, I demonstrate a novel workflow for the detection of nuclear introgression in an empirical case study of closely related spiny lizard (Sceloporus) species. I first show that mitochondrial data independently suggests a repeated history of introgression between the focal taxa. I then show that an exhaustive application of the DFOIL method to double-digest RADseq data from many individuals is effective at identifying introgression in the nuclear genome. This novel approach also reveals intra-specific geographic variation in in patterns of introgression, without the need to determine population structure. Finally, I find that that batch effects in ddRADseq data may mislead D-statistics (and DFOIL) under certain circumstances. Advisors/Committee Members: Wiens, John J (advisor), Barker, Michael (committeemember), Sanderson, Michael (committeemember), Whiteman, Noah (committeemember).

Subjects/Keywords: Concatenation; Introgression; Phylogenetics; Species Trees; Squamata; Viviparity

7 more images…

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APA (6^th Edition):

Lambert, S. M. (2018). Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/630229

Chicago Manual of Style (16^th Edition):

Lambert, Shea Maddock. “Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) .” 2018. Doctoral Dissertation, University of Arizona. Accessed March 06, 2021. http://hdl.handle.net/10150/630229.

MLA Handbook (7^th Edition):

Lambert, Shea Maddock. “Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) .” 2018. Web. 06 Mar 2021.

Vancouver:

Lambert SM. Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) . [Internet] [Doctoral dissertation]. University of Arizona; 2018. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/10150/630229.

Council of Science Editors:

Lambert SM. Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) . [Doctoral Dissertation]. University of Arizona; 2018. Available from: http://hdl.handle.net/10150/630229

University of Georgia

15. Heesacker, Adam Francis. Comparative mapping in common and silver-leaf sunflower.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/23641

► Several wild sunflower (Helianthus) species important sources of genetic diversity for enhancing the performance of cultivars and single-cross hybrids of common sunflower (H. annuus =… (more)

Subjects/Keywords: Comparative mapping; Introgression; Inversion; Sunflower; Synteny; Translocation

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APA (6^th Edition):

Heesacker, A. F. (2014). Comparative mapping in common and silver-leaf sunflower. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/23641

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Heesacker, Adam Francis. “Comparative mapping in common and silver-leaf sunflower.” 2014. Thesis, University of Georgia. Accessed March 06, 2021. http://hdl.handle.net/10724/23641.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Heesacker, Adam Francis. “Comparative mapping in common and silver-leaf sunflower.” 2014. Web. 06 Mar 2021.

Vancouver:

Heesacker AF. Comparative mapping in common and silver-leaf sunflower. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/10724/23641.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Heesacker AF. Comparative mapping in common and silver-leaf sunflower. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/23641

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Université Montpellier II

16. Oueslati, Soumaya. Caractérisation génétique du complexe d’espèces des anchois du genre Engraulis en Méditerranée et dans le proche Atlantique : Genetic characterization of species complex of anchovy Engraulis in the Mediterranean and the near Atlantic sea.

Degree: Docteur es, Evolution, Ecologie, Ressources génétiques, Paléontologie, 2013, Université Montpellier II

URL: http://www.theses.fr/2013MON20195

►

La question abordée est celle de la structure génétique des anchois Atlanto-méditerranéens analysée grâce à 6 locus microsatellites et un gène du cytochrome b de… (more)

Subjects/Keywords: Anchois; Différenciation génétique; Hybridation; Introgression; Contact secondaire; Anchovy; Genetic differenciation; Hybridation; Introgression; Secondary contact

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APA (6^th Edition):

Oueslati, S. (2013). Caractérisation génétique du complexe d’espèces des anchois du genre Engraulis en Méditerranée et dans le proche Atlantique : Genetic characterization of species complex of anchovy Engraulis in the Mediterranean and the near Atlantic sea. (Doctoral Dissertation). Université Montpellier II. Retrieved from http://www.theses.fr/2013MON20195

Chicago Manual of Style (16^th Edition):

Oueslati, Soumaya. “Caractérisation génétique du complexe d’espèces des anchois du genre Engraulis en Méditerranée et dans le proche Atlantique : Genetic characterization of species complex of anchovy Engraulis in the Mediterranean and the near Atlantic sea.” 2013. Doctoral Dissertation, Université Montpellier II. Accessed March 06, 2021. http://www.theses.fr/2013MON20195.

MLA Handbook (7^th Edition):

Oueslati, Soumaya. “Caractérisation génétique du complexe d’espèces des anchois du genre Engraulis en Méditerranée et dans le proche Atlantique : Genetic characterization of species complex of anchovy Engraulis in the Mediterranean and the near Atlantic sea.” 2013. Web. 06 Mar 2021.

Vancouver:

Oueslati S. Caractérisation génétique du complexe d’espèces des anchois du genre Engraulis en Méditerranée et dans le proche Atlantique : Genetic characterization of species complex of anchovy Engraulis in the Mediterranean and the near Atlantic sea. [Internet] [Doctoral dissertation]. Université Montpellier II; 2013. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2013MON20195.

Council of Science Editors:

Oueslati S. Caractérisation génétique du complexe d’espèces des anchois du genre Engraulis en Méditerranée et dans le proche Atlantique : Genetic characterization of species complex of anchovy Engraulis in the Mediterranean and the near Atlantic sea. [Doctoral Dissertation]. Université Montpellier II; 2013. Available from: http://www.theses.fr/2013MON20195

17. Simon, Alexis. Génomique de l’hybridation anthropogénique chez les moules Mytilus spp. et valeur sélective des hybrides : Genomics of anthropogenic hybridisation in Mytilus spp. mussels and hybrid fitness.

Degree: Docteur es, Sciences de l'évolution et de la Biodiversité, 2019, Montpellier

URL: http://www.theses.fr/2019MONTG032

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Les activités anthropiques sont en train de créer de nouveaux contacts entre des lignées génétiques différenciées, nous donnant accès à la phase initiale et à… (more)

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Les activités anthropiques sont en train de créer de nouveaux contacts entre des lignées génétiques différenciées, nous donnant accès à la phase initiale et à des réplicats de contacts secondaires. Le complexe M. edulis est composé d’un ensemble d’espèces et de lignées partiellement isolées reproductivement, présentant une grande diversité de contacts secondaires et de flux de gènes, constituant un modèle de choix pour l’étude de l’hybridation et de la spéciation. Nous avons profité de plusieurs évènements de contact secondaires, à la fois naturels, anthropiques, et expérimentaux, pour étudier leurs effets sur les patrons génomiques d’admixture. En effet, plusieurs évènements d’introduction de l’espèce M. galloprovincialis dans plusieurs ports français mais aussi en Norvège, provenant de lignées différentes et s’étant admixées avec les espèces locales, ont été identifiés d’abord à l’aide d’une centaine de marqueurs génétiques informatifs. Les populations portuaires forment des zones de contact à très fine échelle entre les populations introduites à l’intérieur des ports et les populations locales à l’extérieur. Ces populations portuaires présentent une introgression importante de gènes des lignées locales avec lesquelles elles sont en contact. La comparaison de ces évènements d’admixture anthropiques avec des cas impliquant d’autres lignées mais aussi avec des croisements expérimentaux ont permis d’identifier des parallélismes dans la distorsion des fréquences alléliques lorsque les mêmes lignées sont impliquées. Afin d’explorer les patrons génomiques produits par ces évènements, nous analysons 156 génomes de populations de référence et d’individus admixés. Cette analyse permet de montrer que les corrélations de distorsions entre évènements d’admixture sont conservés à l’échelle génomique. Enfin, un modèle théorique permettant de prédire la valeur sélective des hybrides a été développé en utilisant le cadre du modèle géométrique de Fisher. Ce modèle considère les interactions épistatiques à l’échelle du génome, émergeant de la co-adaptation des mutations produites lors de la divergence. Il permet entre autres de s’affranchir des limitations des modèles classiques d’incompatibilités génétiques tout en conservant des prédictions en accord avec la théorie et les données de l’isolement post-zygotique. Ce modèle, simple et flexible, permet de prédire de nombreuses observations empiriques de l’étude de l’hybridation, dont les distorsions de ségrégation chez les moules.Il permet enfin d'expliquer que les populations admixées retrouvent une valeur sélective élevée bien qu'aillant une combinaison d'allèles provenant des deux génomes parentaux.

Anthropogenic activities are creating new contacts between genetically differentiated lineages, providing access to the initial phase and replicates of secondary contacts. The complex M. eduliscontains several species and lineages partially reproductively isolated, exhibiting a large diversity ofsecondary contacts and levels of gene flow. It constitutes therefore a good model for the…

Advisors/Committee Members: Bierne, Nicolas (thesis director).

Subjects/Keywords: Génétique des populations; Zone hybride; Invasion; Introgression; Génomique; Population genetics; Hybrid zone; Invasion; Introgression; Genomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Simon, A. (2019). Génomique de l’hybridation anthropogénique chez les moules Mytilus spp. et valeur sélective des hybrides : Genomics of anthropogenic hybridisation in Mytilus spp. mussels and hybrid fitness. (Doctoral Dissertation). Montpellier. Retrieved from http://www.theses.fr/2019MONTG032

Chicago Manual of Style (16^th Edition):

Simon, Alexis. “Génomique de l’hybridation anthropogénique chez les moules Mytilus spp. et valeur sélective des hybrides : Genomics of anthropogenic hybridisation in Mytilus spp. mussels and hybrid fitness.” 2019. Doctoral Dissertation, Montpellier. Accessed March 06, 2021. http://www.theses.fr/2019MONTG032.

MLA Handbook (7^th Edition):

Simon, Alexis. “Génomique de l’hybridation anthropogénique chez les moules Mytilus spp. et valeur sélective des hybrides : Genomics of anthropogenic hybridisation in Mytilus spp. mussels and hybrid fitness.” 2019. Web. 06 Mar 2021.

Vancouver:

Simon A. Génomique de l’hybridation anthropogénique chez les moules Mytilus spp. et valeur sélective des hybrides : Genomics of anthropogenic hybridisation in Mytilus spp. mussels and hybrid fitness. [Internet] [Doctoral dissertation]. Montpellier; 2019. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2019MONTG032.

Council of Science Editors:

Simon A. Génomique de l’hybridation anthropogénique chez les moules Mytilus spp. et valeur sélective des hybrides : Genomics of anthropogenic hybridisation in Mytilus spp. mussels and hybrid fitness. [Doctoral Dissertation]. Montpellier; 2019. Available from: http://www.theses.fr/2019MONTG032

18. Leitwein, Maeva. Génomique, repeuplement et conservation chez la truite (Salmo trutta) méditerranéenne : Genomic, stoking and conservation of the Mediterranean brown trout (Salmo trutta).

Degree: Docteur es, Génétique et génomique, 2017, Montpellier

URL: http://www.theses.fr/2017MONTT070

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La truite commune Salmo trutta L. est l'espèce de salmonidés la plus rependue en Europe. Cette espèce présente une grande diversité phénotypique liée à son… (more)

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La truite commune Salmo trutta L. est l'espèce de salmonidés la plus rependue en Europe. Cette espèce présente une grande diversité phénotypique liée à son histoire évolutive complexe. Chaque année, d’intenses repeuplements ont lieu afin d’augmenter les densités locales de populations, notamment pour la pêche sportive. Des truites d’origine atlantique, domestiquées depuis des décennies, et plus récemment des souches domestiques méditerranéennes, sont largement utilisées pour repeupler les populations sauvages locales d’origine méditerranéenne dans le sud de la France. Jusqu’à présent, les conséquences des interactions génétiques, telles que l’hybridation et l’introgression d’allèles domestiques dans les populations locales résultants de ces repeuplements, étaient suivies à l’aide de marqueurs allozymes et microsatellites. Cependant, en raison de leurs nombres extrêmement réduits, ces marqueurs n’offraient qu’une représentation très partielle du génome. Ainsi, leur étude ne permet pas de rendre compte fidèlement des signatures génomiques associées aux pratiques de repeuplement, nécessaires pour comprendre les conséquences évolutives de l’introgression. L’objectif de cette thèse est donc d’étudier à l’échelle génomique les conséquences des interactions génétiques induites par l’introduction d’individus domestiques d’origines atlantique et méditerranéenne dans les populations ‘sauvages’ méditerranéennes du bassin de l’Orb. La première partie de cette thèse rend compte du développement d’environ 196000 marqueurs SNPs et d’une carte de liaison génétique haute densité chez S. trutta. Dans la deuxième partie, les outils moléculaires précédemment développés sont utilisés pour détecter à l’échelle individuelle les haplotypes introgressés et ainsi décrire le paysage génomique de l’introgression dans trois populations sauvages du bassin de l’Orb. La distribution de la taille de ces haplotypes est alors utilisée en prenant en compte les variations du taux local de recombinaison pour estimer l’âge moyen de l’introgression dans chaque population locale. Finalement, la troisième partie s’intéresse aux pressions sélectives - positives ou négatives - qui modulent le paysage génomique de l’introgression d’allèles domestiques dans les populations sauvages. Les résultats suggèrent que les conséquences de l’hybridation sur la valeur sélective des individus doivent être considérées séparément entre le court et le long terme. Ces travaux montrent que la compréhension des mécanismes évolutifs impliqués présente un intérêt majeur pour la conservation et la gestion des populations naturelles.

The brown trout Salmo trutta L. is the most widely distributed salmonid species in Europe. The species presents a high level of phenotypic diversity linked to its complex evolutionary history. An Atlantic hatchery lineage, which has been domesticated for decades, and more recently a domesticated Mediterranean strain, have been largely used for restocking and enhancement of wild Mediterranean populations in southern France, especially for recreational…

Advisors/Committee Members: Guinand, Bruno (thesis director), Berrebi, Patrick (thesis director).

Subjects/Keywords: Salmo trutta; Génomique; Hybridation; Introgression; Conservation; Salmo Trutta; Genomic; Hybridization; Introgression; Conservation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Leitwein, M. (2017). Génomique, repeuplement et conservation chez la truite (Salmo trutta) méditerranéenne : Genomic, stoking and conservation of the Mediterranean brown trout (Salmo trutta). (Doctoral Dissertation). Montpellier. Retrieved from http://www.theses.fr/2017MONTT070

Chicago Manual of Style (16^th Edition):

Leitwein, Maeva. “Génomique, repeuplement et conservation chez la truite (Salmo trutta) méditerranéenne : Genomic, stoking and conservation of the Mediterranean brown trout (Salmo trutta).” 2017. Doctoral Dissertation, Montpellier. Accessed March 06, 2021. http://www.theses.fr/2017MONTT070.

MLA Handbook (7^th Edition):

Leitwein, Maeva. “Génomique, repeuplement et conservation chez la truite (Salmo trutta) méditerranéenne : Genomic, stoking and conservation of the Mediterranean brown trout (Salmo trutta).” 2017. Web. 06 Mar 2021.

Vancouver:

Leitwein M. Génomique, repeuplement et conservation chez la truite (Salmo trutta) méditerranéenne : Genomic, stoking and conservation of the Mediterranean brown trout (Salmo trutta). [Internet] [Doctoral dissertation]. Montpellier; 2017. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2017MONTT070.

Council of Science Editors:

Leitwein M. Génomique, repeuplement et conservation chez la truite (Salmo trutta) méditerranéenne : Genomic, stoking and conservation of the Mediterranean brown trout (Salmo trutta). [Doctoral Dissertation]. Montpellier; 2017. Available from: http://www.theses.fr/2017MONTT070

19. Saint-Pé, Keoni. Quantification in situ des mouvements de truite fario : In situ quantification of brown trout movements.

Degree: Docteur es, Ecologie, biodiversité et évolution, 2019, Université Toulouse III – Paul Sabatier

URL: http://www.theses.fr/2019TOU30207

► Les mouvements sont un aspect crucial de l'écologie et de l'évolution, car ils déterminent la dynamique des populations et des communautés. Les menaces anthropiques pesant… (more)

▼ Les mouvements sont un aspect crucial de l'écologie et de l'évolution, car ils déterminent la dynamique des populations et des communautés. Les menaces anthropiques pesant sur ces dynamiques sont donc une préoccupation majeure pour la conservation. Dans cette thèse, j'ai étudié les mouvements de la truite commune (Salmo trutta) dans le contexte des rempoissonnements, c'est-à-dire la supplémentation des populations sauvages à partir de souches d'élevage locales et exogènes. À cette fin, j'ai d'abord développé un nouvel outil génétique utile pour détecter la structure génétique chez la truite commune et l'hybridation avec des souches élevées en captivité. Cet outil a permis un grand succès de génotypage et a permis d'identifier les patrons d'isolement par la distance. Son intérêt réside dans sa facilité de mise en œuvre, et son universalité potentielle pour la génétique des populations de cette espèce dans son aire de répartition. J'ai ensuite développé de nouvelles méthodes d'assignation combinant des données génétiques et isotopiques, afin d'étudier les mouvements à l'échelle spatiale d'un bassin hydrographique, ce qui présente un intérêt pour des questions appliquées telles que la gestion. Cette approche, basée sur le machine learning, a révélé une grande précision et un fort pouvoir discriminant pour assigner des individus à leur population d'origine. J'ai aussi décrit les effets des rempoissonnements sur les patrons de diversité et de différenciation génétiques et constaté que les rempoissonnements ont pour effet d'augmenter la diversité et la différenciation, et que les patrons naturels attendus pouvaient être inversés dans le cas de cette pratique. Ensuite, l'hybridation entre souches sauvages et d'élevage affecte les patrons de dispersion, révélant que les deux souches diffèrent en termes de propension, de distances et de direction dans leurs dispersion, alors que les hybrides présentent des patrons de dispersion moins prononcés. Enfin, j'ai cherché à mieux comprendre l'influence des facteurs individuels, environnementaux et paysagers sur les mouvements des populations naturelles; ici, j'ai trouvé que certains déterminants étaient universels d'un bassin versant à l'autre, par exemple le fait que les gros individus étant plus enclins à se déplacer, ou encore que les sites directement reliés par le flux d'eau, et ceux ayant des similitudes en termes d'altitude et de type de cours d'eau échangeaient plus de migrant que les autres. D'autre part, d'autres facteurs dépendaient du contexte, par exemple, les relations entre patrons de mouvements et position dans les paysages fluviaux et la disponibilité de l'habitat varient entre les rivières. Cette thèse a contribué à améliorer les méthodes d'étude des mouvements et à identifier les facteurs sous-jacents aux patrons de mouvements à l'échelle du bassin hydrographique. Les implications de ma thèse sont donc à la fois fondamentales et appliquées, car une meilleure compréhension des patrons de mouvement dans le contexte de perturbations humaines est cruciale pour la… Advisors/Committee Members: Blanchet, Simon (thesis director).

Subjects/Keywords: Truite fario; Génétique; SNPs; Mouvements; Introgression; Isotopes; Brown trout; Genetics; SNPs; Movements; Introgression; Isotopes

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saint-Pé, K. (2019). Quantification in situ des mouvements de truite fario : In situ quantification of brown trout movements. (Doctoral Dissertation). Université Toulouse III – Paul Sabatier. Retrieved from http://www.theses.fr/2019TOU30207

Chicago Manual of Style (16^th Edition):

Saint-Pé, Keoni. “Quantification in situ des mouvements de truite fario : In situ quantification of brown trout movements.” 2019. Doctoral Dissertation, Université Toulouse III – Paul Sabatier. Accessed March 06, 2021. http://www.theses.fr/2019TOU30207.

MLA Handbook (7^th Edition):

Saint-Pé, Keoni. “Quantification in situ des mouvements de truite fario : In situ quantification of brown trout movements.” 2019. Web. 06 Mar 2021.

Vancouver:

Saint-Pé K. Quantification in situ des mouvements de truite fario : In situ quantification of brown trout movements. [Internet] [Doctoral dissertation]. Université Toulouse III – Paul Sabatier; 2019. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2019TOU30207.

Council of Science Editors:

Saint-Pé K. Quantification in situ des mouvements de truite fario : In situ quantification of brown trout movements. [Doctoral Dissertation]. Université Toulouse III – Paul Sabatier; 2019. Available from: http://www.theses.fr/2019TOU30207

20. Silvert, Martin. Origines et conséquences des variants régulateurs chez l'humain : Sources and consequences of regulatory variants in humans.

Degree: Docteur es, Génétique des populations humaines, 2019, Sorbonne université

URL: http://www.theses.fr/2019SORUS359

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L'expression des gènes est le résultat de nombreuses interactions. De la régulation de la transcription par les promoters et les enhancers à de nombreuses formes… (more)

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L'expression des gènes est le résultat de nombreuses interactions. De la régulation de la transcription par les promoters et les enhancers à de nombreuses formes de régulations post-transcriptionelles, chaque région régulatrice étant soumise à des pressions sélectives différentes. Dans ce contexte, l’étude de l’évolution des différentes régions régulatrices au sein des populations humaines, ainsi que l’évaluation de leurs contributions respectives à la variabilité de l’expression génique sont essentielles à la compréhension de la variabilité phénotypique humaine. Ce manuscrit se propose donc d’étudier la contribution de la variabilité génétique à la régulation de l’expression génique sous deux angles différents. Je me suis penché sur les conséquences de l'introgression néandertalienne sur la diversité au sein des régions régulatrices dans les populations eurasiennes. Pour cela, j’ai déterminé non seulement quelles sont les régions régulatrices dont la diversité provient de l'introgression néandertalienne de manière disproportionnée, mais j’ai également d'identifié si la source du probable évènement de sélection associé. Je me suis aussi intéressé plus précisément au fonctionnement d'un type de régulation particulier, la régulation par les miARN. En utilisant les résultats de séquençage des petits ARN dans les monocytes, immuno-stimulés ou non, de 100 individus d'ascendance européenne et 100 individus d'ascendance africaine, j'ai pu étudier à la fois la diversité de l'expression des miARN au sein de ces individus, mais également comment ceux-ci participent à la régulation de l'expression des gènes dans un contexte immunitaire.

Gene expression is the result of numerous interactions, from transcription regulation by promoters and enhancers, to several forms of post-transcriptionnal regulation. But each regulatory region is under different selective constraint. In this context, the study of the evolution of regulatory regions in human populations and their relative contribution to the variability of gene expression are vital to the understanding of the human phenotypic diversity. This thesis studies the contribution of the genetic diversity to gene regulation following to different path of investigations. I investigated the consequences of the Neanderthal introgression on diversity of regulatory regions in Eurasians populations. I identified which are the regulatory regions that which diversity is unexpectedly influenced by Neanderthal introgressed mutations, and also identified the sources of the associated selection event. I also focused on the specific case of the regulation by miRNA. Using small RNA sequencing in monocytes, either resting or immune-stimulated, of 100 individual of European ancestry and 100 individuals of African ancestry. I studied the diversity of miRNA expression within this cohort, but also how miRNA participate to the regulation of genes in an immune context.

Advisors/Committee Members: Quintana-Murci, Lluis (thesis director).

Subjects/Keywords: Génétique; Régulation génique; Introgression archaïque; MiARN; Promoters; Enhancers; Genetics; Gene regulation; Archaic introgression; 576.58; 576.54

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Silvert, M. (2019). Origines et conséquences des variants régulateurs chez l'humain : Sources and consequences of regulatory variants in humans. (Doctoral Dissertation). Sorbonne université. Retrieved from http://www.theses.fr/2019SORUS359

Chicago Manual of Style (16^th Edition):

Silvert, Martin. “Origines et conséquences des variants régulateurs chez l'humain : Sources and consequences of regulatory variants in humans.” 2019. Doctoral Dissertation, Sorbonne université. Accessed March 06, 2021. http://www.theses.fr/2019SORUS359.

MLA Handbook (7^th Edition):

Silvert, Martin. “Origines et conséquences des variants régulateurs chez l'humain : Sources and consequences of regulatory variants in humans.” 2019. Web. 06 Mar 2021.

Vancouver:

Silvert M. Origines et conséquences des variants régulateurs chez l'humain : Sources and consequences of regulatory variants in humans. [Internet] [Doctoral dissertation]. Sorbonne université; 2019. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2019SORUS359.

Council of Science Editors:

Silvert M. Origines et conséquences des variants régulateurs chez l'humain : Sources and consequences of regulatory variants in humans. [Doctoral Dissertation]. Sorbonne université; 2019. Available from: http://www.theses.fr/2019SORUS359

Université Montpellier II

21. Fraïsse, Christelle. Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis : Genetics of adaptation and speciation : theory and analysis of high-throughout sequencing data in the complex of species Mytilus edulis.

Degree: Docteur es, Ecologie, évolution, ressources génétiques, paléontologie, 2014, Université Montpellier II

URL: http://www.theses.fr/2014MON20107

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Les génomes sont affectés par des régimes de sélection conflictuels. Ceci est particulièrement bien illustré par le concept de barrière semi-perméable au flux génique, issu… (more)

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Les génomes sont affectés par des régimes de sélection conflictuels. Ceci est particulièrement bien illustré par le concept de barrière semi-perméable au flux génique, issu de la littérature des zones hybrides. Certains gènes contribuent à empêcher le mélange entre lignées génétiques différenciées, soit parce qu'ils participent à l'adaptation aux conditions environnementales locales, soit parce qu'ils sont incompatibles avec les gènes d'autres lignées. D'autres parties du génome sont soit neutres, soit soumises à une sélection qui tend à homogénéiser les différentes lignées entre elles. Dans la première partie de cette thèse, des modèles d'évolution de l'isolement reproductif sont présentés pour expliquer les patrons d'isolements observés dans les expériences d'hybridation au laboratoire. Par modélisation classique d'incompatibilités génétiques de type Dobzhansky-Muller, il est montré que l'asymétrie et la complexité des incompatibilités sont imparfaitement expliquées par un filtre évolutif, c.a.d. une vitesse d'accumulation différente entre types d'incompatibilité. Une approche complémentaire de modélisation quantitative à l'aide d'une extension du modèle géométrique de Fisher a permis de préciser quelles conditions de divergence entre lignées isolées conduisaient à un effet fortement délétère des mutations dans les génotypes hybrides. L'importance relative du niveau d'épistasie moyen, de la distribution des effets des mutations et des modalités de l'adaptation de chaque lignée est discutée. La seconde partie de cette thèse profite des avancées techniques de la génomique pour étudier l'histoire de la spéciation et de l'adaptation dans un complexe d'espèces non-modèles, les moules du genre Mytilus. Une méthode statistique d'inférence de scénarios de spéciation est présentée. Les résultats montrent que les moules Européennes ont connu une histoire complexe de divergence stricte suivie d'une période de connectivité périodique. En accord avec le concept de barrière semi-perméable au flux génique, il est montré que les taux d'introgression sont hétérogènes le long du génome. Ensuite, des scans génomiques de la différenciation ont été menés entre paires de populations du complexe d'espèces. L'analyse de la variation génétique et des généalogies d'allèles sur une échelle chromosomique localisée a permis de reconstituer l'histoire évolutive de plus de 1000 régions du génome des moules. Cette analyse a révélé qu'une cause majeure, mais insoupçonnée, de la différenciation génétique intraspécifique est l'introgression différentielle d'allèles étrangers. Globalement, cette thèse montre non seulement le rôle majeur de la biogéographie de la spéciation, c.a.d. des patrons temporels et spatiaux du flux de gènes, dans notre compréhension de la biodiversité actuelle, mais aussi sa surprenante complexité et l'étendue de ses conséquences sur l'évolution des génomes.

Genomes are affected by conflicting selective regimes. This is particularly well illustrated by the concept of semi-permeable barriers to gene flow, as found in the…

Advisors/Committee Members: Bierne, Nicolas (thesis director).

Subjects/Keywords: Evolution; Sélection; Introgression; Autostop génétique; Barrière au flux génique; Evolution; Selection; Introgression; Genetic hitchhiking; Barrier to gene flow

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fraïsse, C. (2014). Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis : Genetics of adaptation and speciation : theory and analysis of high-throughout sequencing data in the complex of species Mytilus edulis. (Doctoral Dissertation). Université Montpellier II. Retrieved from http://www.theses.fr/2014MON20107

Chicago Manual of Style (16^th Edition):

Fraïsse, Christelle. “Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis : Genetics of adaptation and speciation : theory and analysis of high-throughout sequencing data in the complex of species Mytilus edulis.” 2014. Doctoral Dissertation, Université Montpellier II. Accessed March 06, 2021. http://www.theses.fr/2014MON20107.

MLA Handbook (7^th Edition):

Fraïsse, Christelle. “Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis : Genetics of adaptation and speciation : theory and analysis of high-throughout sequencing data in the complex of species Mytilus edulis.” 2014. Web. 06 Mar 2021.

Vancouver:

Fraïsse C. Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis : Genetics of adaptation and speciation : theory and analysis of high-throughout sequencing data in the complex of species Mytilus edulis. [Internet] [Doctoral dissertation]. Université Montpellier II; 2014. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2014MON20107.

Council of Science Editors:

Fraïsse C. Génétique de l’adaptation et de la spéciation : théorie et analyse de données de séquençage haut-débit dans le complexe d’espèces Mytilus edulis : Genetics of adaptation and speciation : theory and analysis of high-throughout sequencing data in the complex of species Mytilus edulis. [Doctoral Dissertation]. Université Montpellier II; 2014. Available from: http://www.theses.fr/2014MON20107

Université Montpellier II

22. Dumas, Emilie. Interaction entre la bactérie endosymbiotique Wolbachia et les moustiques du complexe Culex pipiens : Des génomes bactériens à la structuration des populations d’hôtes : Interaction between the endosymbiotic bacteria Wolbachia and mosquitoes of the Culex pipiens complex : from bacterial genomes to host population’s structuring.

Degree: Docteur es, Evolution, Ecologie, Ressources génétiques, Paléontologie, 2013, Université Montpellier II

URL: http://www.theses.fr/2013MON20161

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Wolbachia est une bactérie endosymbiotique, intracellulaire et exclusivement transmise maternellement qui infecterait au moins 106 espèces d'insectes. Wolbachia manipule fréquemment la reproduction de ses hôte… (more)

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Wolbachia est une bactérie endosymbiotique, intracellulaire et exclusivement transmise maternellement qui infecterait au moins 106 espèces d'insectes. Wolbachia manipule fréquemment la reproduction de ses hôte à son avantage, notamment en induisant une forme de stérilité conditionnelle appelée incompatibilité cytoplasmique (IC). Chez les moustiques du complexe Culex pipiens, une grande diversité de souches de Wolbachia et de types d'IC a été précédemment identifiée, mais plusieurs aspects de la biologie de cette association restaient peu connus. Les travaux présentés dans cette thèse ont notamment permis de caractériser (i) l'impact de Wolbachia sur la structuration génétique des populations hôtes et (ii) la diversité des souches de Wolbachia et, plus précisément d'appréhender le mécanisme de l'IC. Par un suivi de populations naturelles, nous avons mis en évidence que Wolbachia induisait une forte structuration de la diversité mitochondriale, mais aussi qu'elle participait à des événements répétés d'introgression cytoplasmique entre les différents membres du complexe Cx. pipiens. Nous avons également mené une étude de génomique comparative basée sur le séquençage de quatre génomes complets de Wolbachia très proches phylogénétiquement. Pour cela, nous avons mis en place une série d'analyses approfondies utilisant un large panel d'outils bioinformatiques couplés à des vérifications moléculaires. Nous avons montré qu'il existait peu de polymorphisme entre les groupes de Wolbachia infectant Cx. pipiens. De plus, ces études nous ont permis de mettre en évidence des gènes candidats qui pourraient être directement impliqués dans le mécanisme de l'IC.

Wolbachia is an intracellular bacterial symbiont, exclusively maternally inherited, infecting at least 106 species of insects. Wolbachia commonly manipulates insect reproduction to its own advantage, as well illustrated by a phenomenon of conditional sterility called cytoplasmic incompatibility (CI). In mosquitoes of Culex pipiens complex, a great diversity of Wolbachia strains and of CI types was previously identified, but several aspects of the biology of this symbiotic association remained unknown. The aim of the studies presented in this thesis is to characterize (i) the impact of Wolbachia on the host genetic structure and (ii) the Wolbachia strains diversity in order to attempt an identification of CI molecular basis. By a survey of natural populations, we highlighted that Wolbachia deeply impacts the population structure of mitochondrial diversity, but is also associated with repeated events of cytoplasmic introgression between members of complex Cx. pipiens. We also conducted a study of comparative genomics based on the sequencing of four complete genomes of very closely related Wolbachia strains. For that purpose, we performed a series of analyses using a wide panel of bioinformatic tools coupled with molecular validations. We showed a low polymorphism between two groups of Wolbachia infecting Cx. pipiens. These studies also allowed us to highlight promising…

Advisors/Committee Members: Weill, Mylène (thesis director), Duron, Olivier (thesis director).

Subjects/Keywords: Wolbachia; Culex pipens; Incompatibilité Cytoplasmique; Génome; Introgression cytoplasmique; Wolbachia; Culex pipens; Cytoplasmic Incompatibility; Genomic; Cytoplasmic Introgression

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dumas, E. (2013). Interaction entre la bactérie endosymbiotique Wolbachia et les moustiques du complexe Culex pipiens : Des génomes bactériens à la structuration des populations d’hôtes : Interaction between the endosymbiotic bacteria Wolbachia and mosquitoes of the Culex pipiens complex : from bacterial genomes to host population’s structuring. (Doctoral Dissertation). Université Montpellier II. Retrieved from http://www.theses.fr/2013MON20161

Chicago Manual of Style (16^th Edition):

Dumas, Emilie. “Interaction entre la bactérie endosymbiotique Wolbachia et les moustiques du complexe Culex pipiens : Des génomes bactériens à la structuration des populations d’hôtes : Interaction between the endosymbiotic bacteria Wolbachia and mosquitoes of the Culex pipiens complex : from bacterial genomes to host population’s structuring.” 2013. Doctoral Dissertation, Université Montpellier II. Accessed March 06, 2021. http://www.theses.fr/2013MON20161.

MLA Handbook (7^th Edition):

Dumas, Emilie. “Interaction entre la bactérie endosymbiotique Wolbachia et les moustiques du complexe Culex pipiens : Des génomes bactériens à la structuration des populations d’hôtes : Interaction between the endosymbiotic bacteria Wolbachia and mosquitoes of the Culex pipiens complex : from bacterial genomes to host population’s structuring.” 2013. Web. 06 Mar 2021.

Vancouver:

Dumas E. Interaction entre la bactérie endosymbiotique Wolbachia et les moustiques du complexe Culex pipiens : Des génomes bactériens à la structuration des populations d’hôtes : Interaction between the endosymbiotic bacteria Wolbachia and mosquitoes of the Culex pipiens complex : from bacterial genomes to host population’s structuring. [Internet] [Doctoral dissertation]. Université Montpellier II; 2013. [cited 2021 Mar 06]. Available from: http://www.theses.fr/2013MON20161.

Council of Science Editors:

Dumas E. Interaction entre la bactérie endosymbiotique Wolbachia et les moustiques du complexe Culex pipiens : Des génomes bactériens à la structuration des populations d’hôtes : Interaction between the endosymbiotic bacteria Wolbachia and mosquitoes of the Culex pipiens complex : from bacterial genomes to host population’s structuring. [Doctoral Dissertation]. Université Montpellier II; 2013. Available from: http://www.theses.fr/2013MON20161

University of California – Riverside

23. Haisten, David. A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization.

Degree: Evolution, Ecology and Organismal Biology, 2016, University of California – Riverside

URL: http://www.escholarship.org/uc/item/6mx7f00m

► Introgressive hybridization is increasingly being detected in vertebrate taxa but was thought to be rare in mammals. Recent evidence suggests that this view might not… (more)

Subjects/Keywords: Systematic biology; Cetacea; Delphinidae; Hybridization; Introgression; Orcinus orca; Steno bredanensis

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APA (6^th Edition):

Haisten, D. (2016). A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/6mx7f00m

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Haisten, David. “A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization.” 2016. Thesis, University of California – Riverside. Accessed March 06, 2021. http://www.escholarship.org/uc/item/6mx7f00m.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Haisten, David. “A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization.” 2016. Web. 06 Mar 2021.

Vancouver:

Haisten D. A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization. [Internet] [Thesis]. University of California – Riverside; 2016. [cited 2021 Mar 06]. Available from: http://www.escholarship.org/uc/item/6mx7f00m.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Haisten D. A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization. [Thesis]. University of California – Riverside; 2016. Available from: http://www.escholarship.org/uc/item/6mx7f00m

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Alberta

24. Archibald, Catherine J. Linkage mapping, phenotypic characterization, and introgression analysis of crosses with safflower (Carthamus tinctorius).

Degree: MS, Department of Biological Sciences, 2010, University of Alberta

URL: https://era.library.ualberta.ca/files/fj236329s

► An inter-specific linkage map of a backcross (BC1) population derived from a cross between C. tinctorius and C. oxyacanthus was developed using primarily microsatellite markers.… (more)

Subjects/Keywords: Linkage mapping, introgression, safflower, Carthamus tinctorius, Carthamus oxyacanthus, oilseed

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Archibald, C. J. (2010). Linkage mapping, phenotypic characterization, and introgression analysis of crosses with safflower (Carthamus tinctorius). (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/fj236329s

Chicago Manual of Style (16^th Edition):

Archibald, Catherine J. “Linkage mapping, phenotypic characterization, and introgression analysis of crosses with safflower (Carthamus tinctorius).” 2010. Masters Thesis, University of Alberta. Accessed March 06, 2021. https://era.library.ualberta.ca/files/fj236329s.

MLA Handbook (7^th Edition):

Archibald, Catherine J. “Linkage mapping, phenotypic characterization, and introgression analysis of crosses with safflower (Carthamus tinctorius).” 2010. Web. 06 Mar 2021.

Vancouver:

Archibald CJ. Linkage mapping, phenotypic characterization, and introgression analysis of crosses with safflower (Carthamus tinctorius). [Internet] [Masters thesis]. University of Alberta; 2010. [cited 2021 Mar 06]. Available from: https://era.library.ualberta.ca/files/fj236329s.

Council of Science Editors:

Archibald CJ. Linkage mapping, phenotypic characterization, and introgression analysis of crosses with safflower (Carthamus tinctorius). [Masters Thesis]. University of Alberta; 2010. Available from: https://era.library.ualberta.ca/files/fj236329s

University of Georgia

25. Brown, Ismael Nino. Fiber quality improvement of Upland cotton (Gossypium hirsutum, L.) from targeted interspecific sources using introgression lines and exotic Upland germplasm with the aid of marker-assisted introgression.

Degree: 2018, University of Georgia

URL: http://hdl.handle.net/10724/37680

► An apparent stagnation of fiber quality improvement in Upland cotton (Gossypium hirsutum) is likely due to a limited priority by breeders to improve fiber quality,… (more)

Subjects/Keywords: Cotton; Fiber quality; Gossypium; Interspecific introgression; QTL; Upland cotton

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APA (6^th Edition):

Brown, I. N. (2018). Fiber quality improvement of Upland cotton (Gossypium hirsutum, L.) from targeted interspecific sources using introgression lines and exotic Upland germplasm with the aid of marker-assisted introgression. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/37680

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Brown, Ismael Nino. “Fiber quality improvement of Upland cotton (Gossypium hirsutum, L.) from targeted interspecific sources using introgression lines and exotic Upland germplasm with the aid of marker-assisted introgression.” 2018. Thesis, University of Georgia. Accessed March 06, 2021. http://hdl.handle.net/10724/37680.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Brown, Ismael Nino. “Fiber quality improvement of Upland cotton (Gossypium hirsutum, L.) from targeted interspecific sources using introgression lines and exotic Upland germplasm with the aid of marker-assisted introgression.” 2018. Web. 06 Mar 2021.

Vancouver:

Brown IN. Fiber quality improvement of Upland cotton (Gossypium hirsutum, L.) from targeted interspecific sources using introgression lines and exotic Upland germplasm with the aid of marker-assisted introgression. [Internet] [Thesis]. University of Georgia; 2018. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/10724/37680.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Brown IN. Fiber quality improvement of Upland cotton (Gossypium hirsutum, L.) from targeted interspecific sources using introgression lines and exotic Upland germplasm with the aid of marker-assisted introgression. [Thesis]. University of Georgia; 2018. Available from: http://hdl.handle.net/10724/37680

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Texas A&M University

26. Kuhlman, Leslie Charles. Sorghum introgression breeding utilizing S. macrospermum.

Degree: PhD, Plant Breeding, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-1598

► Sorghum has been improved by plant breeders for yield, biotic and abiotic stress resistance, as well as quality traits by using germplasm from within the… (more)

▼ Sorghum has been improved by plant breeders for yield, biotic and abiotic stress resistance, as well as quality traits by using germplasm from within the species. Interspecific hybridization can greatly increase the amount of genetic variation available to plant breeders for improvement. Interspecific hybrids between sorghum and the 19 species in the tertiary gene pool have, until recently, not been successful. The Australian species, S. macrospermum, was recently successfully hybridized with sorghum by using germplasm homozygous for the iap allele, which eliminated reproductive isolation barriers. The objectives of this research were to evaluate the potential for use of S. macrospermum in an introgression breeding program, determine the map position of the Iap locus, and backcross the iap allele into elite Texas A&M germplasm. Interspecific hybrids between S. bicolor and S. macrospermum revealed moderate levels (2.6 II per PMC) of allosyndetic recombination, indicating that introgression through genetic recombination is possible. Genomic relationships were sufficient to assign S. macrospermum the genomic formula AAB1B1YYZZ, Y and Z remain unknown. In backcrosses to S. bicolor using the female interspecific hybrid gamete and embryo rescue, BC1F1 plants were recovered. They had high chromosome numbers (2n = 35-70) and were male-sterile but three plants set backcross seed. Ninety-five percent of BC2F1 plants were 2n = 20 chromosomes and 75% of them contained S. macrospermum introgression. BC2F1 plants carried between 0-18.5% S. macrospermum introgression; in total 26% of the S. macrospermum genome was detected in the BC2 generation. Three types of introgression germplasm were created: alien addition lines; alien substitution lines; and introgression lines. Recombinant chromosomes, containing S. macrospermum introgression sites, were identified in multiple introgression lines. The Iap locus was genetically mapped to sorghum chromosome 2 (SBI-02), flanking AFLP markers were 2.1 and 2.7cM away, one AFLP marker shared the same map position (0.0cM). A genetic stock, Tx3361, was created which has iap iap genotype and improved agronomic qualities such as short plant height, white seed color, non-pigmented testa, no awns, reduced lodging, early maturity, and backcross segregation of male-sterility (ms3). This research shows that S. macrospermum is now available to plant breeders for sorghum improvement. Advisors/Committee Members: Rooney, William L. (advisor), Stelly, David M. (advisor), Burson, Byron L. (committee member), Klein, Patricia E. (committee member).

Subjects/Keywords: Sorghum; Interspecific hybrids; introgression

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kuhlman, L. C. (2009). Sorghum introgression breeding utilizing S. macrospermum. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-1598

Chicago Manual of Style (16^th Edition):

Kuhlman, Leslie Charles. “Sorghum introgression breeding utilizing S. macrospermum.” 2009. Doctoral Dissertation, Texas A&M University. Accessed March 06, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-1598.

MLA Handbook (7^th Edition):

Kuhlman, Leslie Charles. “Sorghum introgression breeding utilizing S. macrospermum.” 2009. Web. 06 Mar 2021.

Vancouver:

Kuhlman LC. Sorghum introgression breeding utilizing S. macrospermum. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1598.

Council of Science Editors:

Kuhlman LC. Sorghum introgression breeding utilizing S. macrospermum. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1598

27. MacGregor, HEA. The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions.

Degree: 2017, University of Tasmania

URL: https://eprints.utas.edu.au/23864/1/MacGregor_whole_thesis_ex_pub_mat.pdf ; https://eprints.utas.edu.au/23864/2/MacGregor_whole_thesis.pdf ; MacGregor, HEA ORCID: 0000-0001-5379-8392 <https://orcid.org/0000-0001-5379-8392> 2017 , 'The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions', PhD thesis, University of Tasmania.

► Reproductive characters often vary geographically within species. This has led to the suggestion that traits related to reproduction evolve rapidly and that sexual selection is… (more)

▼ Reproductive characters often vary geographically within species. This has led to the suggestion that traits related to reproduction evolve rapidly and that sexual selection is an important cause of diversification. Using the common wall lizard, Podarcis muralis, this thesis explores the consequences of interactions between reproductive characters and sexual selection in two environmental contexts: (i) following secondary contact between lineages that differ in secondary sexual characters, and (ii) following introduction to a cooler and more seasonal nonnative environment. To address this, I adopted an integrated approach, combining information on associations between reproductive characters, social behaviour, and reproductive success in an experimental setting with extensive documentation of phenotypic variation across native and non-native populations. Common wall lizards occupy a wide geographic range, spanning from western Spain to Turkey. Their phylogeographic structure is complex and composed of several genetically and phenotypically distinct lineages. In the first part of this thesis I examined how divergence in male sexual characters between two lineages – the Italian lineage, where males have highly exaggerated sexual traits, and the Western European lineage, where sexual traits in males are less expressed – mediates sexual selection and ultimately patterns of hybridization and introgression following secondary contact. Specifically, I combined an investigation of behavioural interactions and patterns of paternity in experimentally replicated mixed-lineage populations with genetic and phenotypic data from three independent zones of secondary contact. Experimentally, I show that Italian males have a significant advantage over Western European males in competition for females, leading to overall greater courtship and mating success, and consequently, asymmetric hybridization. Patterns of genetic and phenotypic introgression following secondary contact mirrored this directionality. Nuclear microsatellite markers revealed a westwards shift in the position of the hybrid cline compared to mitochondrial markers. Furthermore, clines in male visual sexual characters were shifted even further westwards into the Western European lineage, indicative of the rapid and adaptive displacement of Western European male sexual phenotypes. Combined with a lack of evidence for negative effects on hybrid offspring survival and their reproductive characters, these results demonstrate an important role for pre-copulatory sexual selection through male-male competition in shaping the genetic and phenotypic consequences of secondary contact. I then examined the consistency of these effects across different communication channels, specifically comparing the above results for visual characters with chemical characteristics of male femoral secretions used as scent marks. Despite chemical communication being considered an important feature of lizard reproductive behaviour, I find little evidence for a role of divergence between the…

Subjects/Keywords: Sexual selection; Hybridization; Introgression; Reproductive investment; Podarcis muralis

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APA (6^th Edition):

MacGregor, H. (2017). The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions. (Thesis). University of Tasmania. Retrieved from https://eprints.utas.edu.au/23864/1/MacGregor_whole_thesis_ex_pub_mat.pdf ; https://eprints.utas.edu.au/23864/2/MacGregor_whole_thesis.pdf ; MacGregor, HEA ORCID: 0000-0001-5379-8392 <https://orcid.org/0000-0001-5379-8392> 2017 , 'The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions', PhD thesis, University of Tasmania.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

MacGregor, HEA. “The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions.” 2017. Thesis, University of Tasmania. Accessed March 06, 2021. https://eprints.utas.edu.au/23864/1/MacGregor_whole_thesis_ex_pub_mat.pdf ; https://eprints.utas.edu.au/23864/2/MacGregor_whole_thesis.pdf ; MacGregor, HEA ORCID: 0000-0001-5379-8392 <https://orcid.org/0000-0001-5379-8392> 2017 , 'The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions', PhD thesis, University of Tasmania..

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

MacGregor, HEA. “The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions.” 2017. Web. 06 Mar 2021.

Vancouver:

MacGregor H. The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions. [Internet] [Thesis]. University of Tasmania; 2017. [cited 2021 Mar 06]. Available from: https://eprints.utas.edu.au/23864/1/MacGregor_whole_thesis_ex_pub_mat.pdf ; https://eprints.utas.edu.au/23864/2/MacGregor_whole_thesis.pdf ; MacGregor, HEA ORCID: 0000-0001-5379-8392 <https://orcid.org/0000-0001-5379-8392> 2017 , 'The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions', PhD thesis, University of Tasmania..

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

MacGregor H. The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions. [Thesis]. University of Tasmania; 2017. Available from: https://eprints.utas.edu.au/23864/1/MacGregor_whole_thesis_ex_pub_mat.pdf ; https://eprints.utas.edu.au/23864/2/MacGregor_whole_thesis.pdf ; MacGregor, HEA ORCID: 0000-0001-5379-8392 <https://orcid.org/0000-0001-5379-8392> 2017 , 'The consequences of sexual selection in the common wall lizard : insights following secondary contact and non-native introductions', PhD thesis, University of Tasmania.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Guelph

28. Meyer, Ann. A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays.

Degree: PhD, Department of Plant Agriculture, 2015, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8779

► Individuals in a population carry different alleles allowing them to respond uniquely to internal and external cues. Examining the effect of specific alleles and investigating… (more)

▼ Individuals in a population carry different alleles allowing them to respond uniquely to internal and external cues. Examining the effect of specific alleles and investigating genome-wide allelic expression in response to internal growth cues and external stress provides insights into agriculturally important phenomena such as heterosis. Zea mays (maize) primary roots are an ideal system for studying allelic effects as maize is genotypically diverse and the primary roots exhibit growth differences between inbreds early in development. I identified 12 QTL within the maize genome that each explained up to 22% of the variance in primary root growth between two inbreds in control, stress, and recovery conditions. Introgressing one of these loci from one inbred into the other increased root length, increased the proportion of explained variance to 66%, and changed the expression of genes associated with scavenging reactive oxygen species (ROS). I used RNA-Seq to evaluate differences in allele expression levels and the regulatory mechanisms contributing to the differences in allele expression levels in reciprocal hybrids. A major impediment to using RNA-Seq for allelic analyses is unequal mapping of allelic reads to a single reference genome. Very frequently more reads map from one allele than the other and all reads from both alleles map at only 18% of polymorphic loci. Masking polymorphic sites or replacing polymorphic sites reduces the frequency of unequal mapping genome-wide but introduces new sources of unequal mapping. To reduce unequal mapping of allelic reads, I assembled parent specific transcriptomes for two inbred lines and aligned reads to these transcriptomes. Genome-wide, more genes are trans-regulated than cis-regulated with alleles of the faster growing parent having greater abundances than alleles of the slower growing parent under cis-regulation and alleles of the slower growing parent having greater abundances than alleles of the faster growing parent under trans-regulation. Under stress conditions, the number of genes with differences in allelic expression abundances increases, the number of genes with trans-regulation increases, and the number of genes with maternal or paternal expression decreases. There are more enhancing cis- and trans-regulatory interactions than compensating interactions suggesting that breeding has increased the differences between inbreds. Advisors/Committee Members: Lukens, Lewis (advisor).

Subjects/Keywords: Allele specific analysis; Maize; QTL; introgression; microarray; RNA-Seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Meyer, A. (2015). A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8779

Chicago Manual of Style (16^th Edition):

Meyer, Ann. “A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays.” 2015. Doctoral Dissertation, University of Guelph. Accessed March 06, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8779.

MLA Handbook (7^th Edition):

Meyer, Ann. “A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays.” 2015. Web. 06 Mar 2021.

Vancouver:

Meyer A. A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays. [Internet] [Doctoral dissertation]. University of Guelph; 2015. [cited 2021 Mar 06]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8779.

Council of Science Editors:

Meyer A. A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays. [Doctoral Dissertation]. University of Guelph; 2015. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8779

Australian National University

29. Blom, Mozes. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans .

Degree: 2016, Australian National University

URL: http://hdl.handle.net/1885/118217

► Understanding the evolutionary processes that generate and maintain biodiversity is a fundamental objective in ecology and evolution. In this dissertation, I characterize phylogenetic patterns in… (more)

▼ Understanding the evolutionary processes that generate and maintain biodiversity is a fundamental objective in ecology and evolution. In this dissertation, I characterize phylogenetic patterns in a recent radiation of Australian skinks, discuss the ecological context of diversification and how this has translated into macroevolutionary change across the continent. By also reconstructing the evolutionary history of all Cryptoblepharus species globally, I shed further light on the evolutionary and biogeographic processes that have shaped the diversity of the genus. This dissertation project has generated an empirical framework for future studies into the continuous nature between micro- and macroevolutionary change. To infer the phylogeny of Australian Cryptoblepharus, I generated an exon- capture dataset and designed a bioinformatic pipeline to generate quality filtered sequence alignments (Appendix A). Multi-locus datasets are required to confidently infer species trees for rapidly speciating clades due to a high prevalence of gene tree incongruence among loci. In Chapter I, I use the Cryptoblepharus radiation as an empirical example and describe how to account for differences in gene tree resolution when employing summary-coalescent methods for species tree inference. Our study highlights the importance of phylogenetically informative loci but simultaneously demonstrates that the addition of non-informative loci does not introduce phylogenetic noise. In Chapter II, I then use comparative methods and morphological measurements for over 800 individuals, to examine the ecological context of diversification in Australian Cryptoblepharus. Specifically, I focus on whether habitat specialisation can explain current patterns of variation in ecologically relevant traits. I observed significant differences in morphology between species that occur in distinct environments (rock, arboreal and littoral) and species that occur within the same habitat are often cryptic. These findings suggest that isolated analogous habitats have provided ecological opportunity and repeatedly promoted adaptive diversification, while speciation within habitat has accrued without ecomorphological change. In contrast to well known adaptive radiations in insular environments, continental radiations are likely driven by alternative diversification processes that jointly stimulate species proliferation. In Chapter III, I explore patterns of introgression between phylogenetically divergent species. I combine population and phylogenetic tools, to quantify the extent of introgression between ecomorphologically distinct and similar taxa. I describe the frequent occurrence of mitochondrial haplotype sharing across species boundaries and the complete replacement of the mitochondrial genome in one species. Furthermore, non-sister…

Subjects/Keywords: Cryptoblepharus; Scincidae; phylogenomics; introgression; speciation; macroevolution; biogeography; continental radiation; exon capture

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Blom, M. (2016). The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . (Thesis). Australian National University. Retrieved from http://hdl.handle.net/1885/118217

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Blom, Mozes. “The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans .” 2016. Thesis, Australian National University. Accessed March 06, 2021. http://hdl.handle.net/1885/118217.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Blom, Mozes. “The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans .” 2016. Web. 06 Mar 2021.

Vancouver:

Blom M. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . [Internet] [Thesis]. Australian National University; 2016. [cited 2021 Mar 06]. Available from: http://hdl.handle.net/1885/118217.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Blom M. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . [Thesis]. Australian National University; 2016. Available from: http://hdl.handle.net/1885/118217

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge

30. Hui, Ruoyun. Investigating the genetic diversity, population structure and archaic admixture history in worldwide human populations using high-coverage genomes.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/296047

► I present the analysis on 929 high-coverage (>30x) genomes from the Human Genome Diversity Project (HGDP) panel, a collection of cell lines from 54 populations… (more)

▼ I present the analysis on 929 high-coverage (>30x) genomes from the Human Genome Diversity Project (HGDP) panel, a collection of cell lines from 54 populations across the world. Some data processing steps were necessary for downstream analysis, including lifting over resources on a different reference genome assembly, annotating the genome, and statistical phasing. Genome-wide genetic diversity conforms with previous studies using SNP arrays and microsatellites, yet haplotype information reveals fine scale structures and recent demographic history that vary between populations. This dataset also provides a valuable opportunity to explore the diversity and distribution of archaic segments in modern human populations. I implemented a hidden Markov model to detect such segments, based on patterns of allele-sharing with sequenced archaic genomes and a sub-Saharan African control panel. I also compared several variants of the model and different training methods using simulated data. Applying the model on the HGDP dataset using two Neanderthal genomes and one Denisova genome, I detected variations in the level of archaic ancestry across continental regions, populations, and individuals within each population. I further compared Neanderthal and Denisovan segments regarding their lengths, genomic distribution, divergence to the archaic genomes, nucleotide diversity, and haplotype networks to shed light on the structure of the admixture events. Neanderthal segments from all non-African populations appear largely homogeneous after accounting for the recent demographic history of modern human populations, which is consistent with a single admixture event that happened before they diverged from each other. In contrast, a distinct separation exists between Denisovan haplotypes recovered from Oceania and those from East/South Asia, whilst the complicated structure in the latter cannot be explained by a single source of gene flow. Therefore I propose that more than one episode of admixture with different Denisova groups occurred in the ancestral population of present-day East Asian, South Asian and American populations after the separation from the ancestors of present-day Oceanians, and that a separate admixture event occurred between the ancestors of Oceanians and the Denisova population.

Subjects/Keywords: population genetics; human genetics; archaic introgression; human genome diversity project

Record Details Similar Records Cite « Share

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hui, R. (2019). Investigating the genetic diversity, population structure and archaic admixture history in worldwide human populations using high-coverage genomes. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/296047

Chicago Manual of Style (16^th Edition):

Hui, Ruoyun. “Investigating the genetic diversity, population structure and archaic admixture history in worldwide human populations using high-coverage genomes.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 06, 2021. https://www.repository.cam.ac.uk/handle/1810/296047.

MLA Handbook (7^th Edition):

Hui, Ruoyun. “Investigating the genetic diversity, population structure and archaic admixture history in worldwide human populations using high-coverage genomes.” 2019. Web. 06 Mar 2021.

Vancouver:

Hui R. Investigating the genetic diversity, population structure and archaic admixture history in worldwide human populations using high-coverage genomes. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 06]. Available from: https://www.repository.cam.ac.uk/handle/1810/296047.

Council of Science Editors:

Hui R. Investigating the genetic diversity, population structure and archaic admixture history in worldwide human populations using high-coverage genomes. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/296047

Open Access Theses and Dissertations