subject:(phylogenomics)

1. Davis, Edward W. II. Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria.

Degree: PhD, 2017, Oregon State University

URL: http://hdl.handle.net/1957/61588

► Gall-associated phytopathogens have unique evolutionary histories that have shaped both their modes of infection and genomic structures. Pathogenicity of the gall- associated plant pathogens of… (more)

▼ Gall-associated phytopathogens have unique evolutionary histories that have shaped both their modes of infection and genomic structures. Pathogenicity of the gall- associated plant pathogens of the Rhodococcus, Agrobacterium, and Rathayibacter genera is mediated by horizontally acquired virulence loci. The relative ease of gain and loss of the virulence loci has confounded accurate characterization of these bacteria, especially those characterizations made prior to the use of molecular markers for genotyping. Work presented in this thesis uses whole genome guided approaches to discern the intra- and inter- species genetic diversity in the three genera described. Rhodococcus fascians is the causal agent of leafy gall disease. We tested the hypothesis that R. fascians is comprised of a single species level group and show that two distinct clades with up to six species level groups are able to cause symptoms consistent with leafy gall disease. These data reveal previously unknown chromosomal diversity within this group of phytopathogenic bacteria. Four lines of evidence that make use of whole genome sequences indicate that the species are acted on by distinct selective pressures and have unique evolutionary histories. Further, a set of horizontally acquired virulence loci is correlated with the pathogenic phenotype, regardless of chromosomal lineage. These data suggest that delimitation of phytopathogenic Rhodococcus isolates requires careful consideration with respect to both the chromosomal genotype as well as the presence of virulence loci. Rathayibacter spp. are vector mediated plant pathogens that infect nematode galls in the seed heads of several grass species. Rathayibacter toxicus, a Select Agent in the U.S., has been shown to produce corynetoxins, nucleoside antibiotics that also cause neurotoxic effects in mammals, when infected by a bacteriophage. As R. toxicus encodes a clustered regularly interspersed short palindromic repeats (CRISPR) system that acts as an adaptive immune system against foreign DNA in bacteria, we studied the CRISPR array evolution for insights into the ecology of bacteria-phage interactions. We predicted that over half of the spacers encoded in R. toxicus are functional in targeting the phage, while the bacteria still show susceptibility to the phage. These data suggest a complex homeostatic interaction whereby neither bacteria nor phage populations are eliminated. Further, our results challenge past conclusions on the efficacy of CRISPR-mediated immunity. Lastly, we generated a set of tools to facilitate comparative genomics research and accurate species and strain identification. Data are integrated into a website (http://gall-id.cgrb.oregonstate.edu/) to facilitate their use by all researchers, regardless of computational proclivity. Advisors/Committee Members: Chang, Jeff H. (advisor), Mahmud, Taifo (committee member).

Subjects/Keywords: phylogenomics

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APA (6^th Edition):

Davis, E. W. I. (2017). Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/61588

Chicago Manual of Style (16^th Edition):

Davis, Edward W II. “Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria.” 2017. Doctoral Dissertation, Oregon State University. Accessed January 25, 2021. http://hdl.handle.net/1957/61588.

MLA Handbook (7^th Edition):

Davis, Edward W II. “Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria.” 2017. Web. 25 Jan 2021.

Vancouver:

Davis EWI. Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria. [Internet] [Doctoral dissertation]. Oregon State University; 2017. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/1957/61588.

Council of Science Editors:

Davis EWI. Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria. [Doctoral Dissertation]. Oregon State University; 2017. Available from: http://hdl.handle.net/1957/61588

University of California – San Diego

2. Millan Aguinaga, Natalie. The genus Salinispora as a model organism for species concepts and natural products discovery.

Degree: Marine biology, 2016, University of California – San Diego

URL: http://www.escholarship.org/uc/item/0rf2h9n2

► My dissertation project focuses on the bacterial genus Salinispora, a marine actinomycete and an important producer of diverse secondary metabolites including anticancer and antibiotic compounds.… (more)

▼ My dissertation project focuses on the bacterial genus Salinispora, a marine actinomycete and an important producer of diverse secondary metabolites including anticancer and antibiotic compounds. This genus is comprised of 3 named species (S. tropica, S. arenicola, and S. pacifica) that are closely related based on the highly conserved 16S rRNA gene. Multilocus sequence analyses (MLSA) of 5 housekeeping genes revealed a well-supported concatenated tree providing strong support for the delineation of the three species and the ancestral relationship of S. arenicola to the more recently diverged sister taxa S. tropica and S. pacifica. Recently, our laboratory obtained 119 draft Salinispora genomes, which provide an unprecedented opportunity for comparative genomic analysis. Genome analyses revealed that all 119 strains share 2362 single-copy genes. This represents the Salinispora core genome, which comprises on average 46% of the gene content of each strain. Calculation of the genome-wide Average Nucleotide Identity (gANI) and Alignment Fraction (AF) provided a new perspective of Salinispora diversity and suggested that the three currently named species would be better represented by at least five additional species. The presence/absence of predicted biosynthetic gene clusters also revealed clustering patterns that were congruent with the species phylogeny, indicating that secondary metabolism represents important functional traits that help delineate species in this lineage. The genome sequences are also being used to identify shared genes that have been duplicated or occur near or within biosynthetic gene clusters (BGCs). One hypothesis is that antibiotic-resistance genes have co-evolved with antibiotic biosynthesis as a self-protection mechanism. This new approach called Target-directed genome mining identified duplicated genes from the core genome that occur near or within biosynthetic gene clusters (BGC), with the hypothesis that the products of these genes are the targets of the compounds produced by the clusters. This new method was validated with the correlation of a candidate resistance gene (fabF/B) with the orphan BGC named as PKS44 that expressed the compound thiolactomycin. This new approach may open new avenues for the discovery of novel antibiotics.

Subjects/Keywords: Microbiology; Genomics; Phylogenomics

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APA (6^th Edition):

Millan Aguinaga, N. (2016). The genus Salinispora as a model organism for species concepts and natural products discovery. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/0rf2h9n2

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):

Millan Aguinaga, Natalie. “The genus Salinispora as a model organism for species concepts and natural products discovery.” 2016. Thesis, University of California – San Diego. Accessed January 25, 2021. http://www.escholarship.org/uc/item/0rf2h9n2.

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

MLA Handbook (7^th Edition):

Millan Aguinaga, Natalie. “The genus Salinispora as a model organism for species concepts and natural products discovery.” 2016. Web. 25 Jan 2021.

Vancouver:

Millan Aguinaga N. The genus Salinispora as a model organism for species concepts and natural products discovery. [Internet] [Thesis]. University of California – San Diego; 2016. [cited 2021 Jan 25]. Available from: http://www.escholarship.org/uc/item/0rf2h9n2.

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

Council of Science Editors:

Millan Aguinaga N. The genus Salinispora as a model organism for species concepts and natural products discovery. [Thesis]. University of California – San Diego; 2016. Available from: http://www.escholarship.org/uc/item/0rf2h9n2

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

Massey University

3. Zhong, Bojian. Phylogenomics and plant evolution.

Degree: PhD, Genetics, 2013, Massey University

URL: http://hdl.handle.net/10179/5348

► Phylogenomics, the study of evolutionary relationships among groups of organisms using genome-scale data, is central to our understanding of the evolution of life. While large… (more)

▼ Phylogenomics, the study of evolutionary relationships among groups of organisms using genome-scale data, is central to our understanding of the evolution of life. While large amounts of data are available and methodological developments are increasing at a fast pace, there are basic problems that are overlooked in phylogenomic analyses of molecular sequences, which may impede the accuracy and reliability of tree reconstruction. These problems include: How can we detect the non-phylogenetic signals from genomic data? How can we offer a better statistical fitness between the evolutionary model and data? How can we improve the phylogenetic inference using sophisticated and realistic models? How can we accurately infer the species trees? How can we quantitatively confirm the evolutionary theory? With these goals, this thesis concentrates on phylogenomics of land plants (and their origin) and evolution in general. • Resolving the phylogenetic position of Gnetales. We show that non-time reversible properties of positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction, and highlight that the goodness of fit between substitution model and data should be taken into account when performing phylogenomic analyses. • Resolving the origin of land plants: 1). The multispecies coalescent model is applied to estimate the species tree of origin of land plants, and it is proved to be able to estimate accurate and congruent species tree in the presence of ancient incomplete lineage sorting from nuclear genes. 2). The chloroplast phylogenomic analyses are conducted using sophisticated and realistic evolutionary models that can account for site-heterogeneity and compositional heterogeneity. These chloroplast phylogenomic results confirm the previous nuclear data analyses. • We develop a statistical test and demonstrate that evolutionary theory could be tested by convergence of molecular data. It also indicates that the reality of evolution can be tested using standard methods and tools.

Subjects/Keywords: Phylogenomics; Plant evolution

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

APA (6^th Edition):

Zhong, B. (2013). Phylogenomics and plant evolution. (Doctoral Dissertation). Massey University. Retrieved from http://hdl.handle.net/10179/5348

Chicago Manual of Style (16^th Edition):

Zhong, Bojian. “Phylogenomics and plant evolution.” 2013. Doctoral Dissertation, Massey University. Accessed January 25, 2021. http://hdl.handle.net/10179/5348.

MLA Handbook (7^th Edition):

Zhong, Bojian. “Phylogenomics and plant evolution.” 2013. Web. 25 Jan 2021.

Vancouver:

Zhong B. Phylogenomics and plant evolution. [Internet] [Doctoral dissertation]. Massey University; 2013. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10179/5348.

Council of Science Editors:

Zhong B. Phylogenomics and plant evolution. [Doctoral Dissertation]. Massey University; 2013. Available from: http://hdl.handle.net/10179/5348

Penn State University

4. Jiao, Yuannian. Phylogenomic analysis of ancient genome duplications in the history of plants .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/12393

► Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization, has generally been viewed as a primary source of material for the origin of… (more)

▼ Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization, has generally been viewed as a primary source of material for the origin of evolutionary novelties. Most flowering plants have been shown to be ancient polyploids that have undergone one or more rounds of WGDs early in their evolution, and many lineages have since undergone additional, independent and more recent genome duplications. It was suggested that the paleopolyploidy events were crucial to the radiation and success of angiosperms, but evidence for proposed ancient genome duplications remains equivocal. Plant genomes are highly dynamic and usually go through intense structural rearrangements and gene loss following duplication. Old(er) WGDs can not be detected using within-genome colinearity method. Although the occurrence of WGD event(s) is well accepted, the actual number, phylogenetic timing, and age of the event(s) remain equivocal. Here we mainly employed phylogenomic approach to address following questions: 1) To more precisely time and evaluate the fates of genes following genome duplications in eudicots, we built a phylogenomic pipeline to reconstruct the evolutionary relationships of 4433 gene families from the complete gene sets of Arabidopsis, Populus, Vitis, and Oryza. For each family, we determined the gene duplications relative to the evolutionary tree of the organisms, and also matched gene pairs of specific WGD events for later synonymous substitution (Ks) analysis. Concentrations of duplication events at shared branch points in the gene family phylogenies confirmed some of the results of earlier studies, and also indicated new interesting signals for polyploidy events. 2) To track more ancient WGDs pre-dating the divergence of monocots and eudicots, we used comprehensive phylogenomic analyses of nine sequenced plant genomes and more than 12.6 million new expressed-sequence-tag (EST) sequences from phylogenetically pivotal lineages. Two additional, previously unnoticed ancient WGDs have been elucidated in the common ancestor of extant seed plants dated at ~ 319 million years ago (mya) and extant angiosperms dated at ~ 192 mya, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms. 3) To precisely time the γ event, which was proposed before the separation of all rosids, we mapped the duplication events onto phylogenetic trees that include the paralogs created by the γ event and orthologous genes from other species. The overwhelming majority of well-resolved Vitis duplications were placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing evidence for the WGD (γ) early in eudicot evolution. A large proportion of the Vitis duplications were placed after the divergence of basal eudicots, supporting the γ… Advisors/Committee Members: Claude Walker Depamphilis, Dissertation Advisor/Co-Advisor, Claude Walker Depamphilis, Committee Chair/Co-Chair, Hong Ma, Committee Member, John Edward Carlson, Committee Member, Webb Colby Miller, Committee Member, Naomi S Altman, Committee Member.

Subjects/Keywords: Whole genome duplication; Phylogenomics

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APA (6^th Edition):

Jiao, Y. (2011). Phylogenomic analysis of ancient genome duplications in the history of plants . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/12393

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):

Jiao, Yuannian. “Phylogenomic analysis of ancient genome duplications in the history of plants .” 2011. Thesis, Penn State University. Accessed January 25, 2021. https://submit-etda.libraries.psu.edu/catalog/12393.

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

MLA Handbook (7^th Edition):

Jiao, Yuannian. “Phylogenomic analysis of ancient genome duplications in the history of plants .” 2011. Web. 25 Jan 2021.

Vancouver:

Jiao Y. Phylogenomic analysis of ancient genome duplications in the history of plants . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Jan 25]. Available from: https://submit-etda.libraries.psu.edu/catalog/12393.

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

Council of Science Editors:

Jiao Y. Phylogenomic analysis of ancient genome duplications in the history of plants . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/12393

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

University of Edinburgh

5. Koutsovoulos, Georgios D. Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes.

Degree: PhD, 2015, University of Edinburgh

URL: http://hdl.handle.net/1842/10558

► Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several… (more)

Subjects/Keywords: 592; nematodes; evolution; bioinformatics; phylogenomics

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APA (6^th Edition):

Koutsovoulos, G. D. (2015). Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/10558

Chicago Manual of Style (16^th Edition):

Koutsovoulos, Georgios D. “Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed January 25, 2021. http://hdl.handle.net/1842/10558.

MLA Handbook (7^th Edition):

Koutsovoulos, Georgios D. “Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes.” 2015. Web. 25 Jan 2021.

Vancouver:

Koutsovoulos GD. Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/1842/10558.

Council of Science Editors:

Koutsovoulos GD. Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/10558

University of Melbourne

6. Milla, Elizabeth. Evolution and ecology of the Australian Heliozelidae (Adeloidea, Lepidoptera).

Degree: 2018, University of Melbourne

URL: http://hdl.handle.net/11343/220280

► The Heliozelidae (Adeloidea: Lepidoptera) are a family of small, primitive day-flying moths with a worldwide distribution. In recent years, potentially hundreds of new species have… (more)

▼ The Heliozelidae (Adeloidea: Lepidoptera) are a family of small, primitive day-flying moths with a worldwide distribution. In recent years, potentially hundreds of new species have been collected around Australia, predominantly in the southwest region of Western Australia. Overall, our observations suggested that many Australian species have evolved independently from other groups in the family. In particular, there is one group of Australian species possessing a unique pollen-carrying abdominal cleft that have established a remarkably close association with species of the Rutaceae (Sapindales) plant genus Boronia. In order to understand the evolution of the Australian Heliozelidae, a robust phylogenetic framework of the Heliozelidae family was required. Additionally, examination of the origins and purpose of the unique morphology of pollen-carrying species and the nature of the associations with their Boronia hosts was crucial to understand their ecological role. Thus, in the first part of this thesis (Chapters Two and Three), I focused on resolving the phylogeny of the worldwide Heliozelidae family and placing the Australian species within it. In Chapter Two, I generated a preliminary phylogeny identifying the major Heliozelidae clades and identify Australia as one of the regions with high undescribed diversity. In Chapter Three, I estimated a fully resolved time-calibrated phylogeny of the major heliozelid clades, with an ancestral range estimation tracing the origins of the family to the Australian region around 96 Mya, during the Late Miocene. In the second part of the thesis (Chapters Four and Five), I focused on the group of Western Australian species that has formed a remarkable association with species in the plant genus Boronia. In Chapter Four, I presented a molecular phylogeny of the Boronia pollinator moths and found preliminary evidence of cospeciation between the moths and their Boronia hosts. In Chapter Five, I described the remarkable active pollination behaviour in three different species of Boronia pollinator, and established the obligate pollination relationship between B. megastigma and its heliozelid pollinator. The findings from this thesis suggest that Heliozelidae play an important role in the Australian environment, exemplified through their close pollination association with the predominantly Australia genus Boronia. Thus, further research into this family of small day-flying moths, which has been poorly studied in Australia until now, is required to better understand their significance.

Subjects/Keywords: pollination; phylogenomics; obligate mutualism; biogeography

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APA (6^th Edition):

Milla, E. (2018). Evolution and ecology of the Australian Heliozelidae (Adeloidea, Lepidoptera). (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/220280

Chicago Manual of Style (16^th Edition):

Milla, Elizabeth. “Evolution and ecology of the Australian Heliozelidae (Adeloidea, Lepidoptera).” 2018. Doctoral Dissertation, University of Melbourne. Accessed January 25, 2021. http://hdl.handle.net/11343/220280.

MLA Handbook (7^th Edition):

Milla, Elizabeth. “Evolution and ecology of the Australian Heliozelidae (Adeloidea, Lepidoptera).” 2018. Web. 25 Jan 2021.

Vancouver:

Milla E. Evolution and ecology of the Australian Heliozelidae (Adeloidea, Lepidoptera). [Internet] [Doctoral dissertation]. University of Melbourne; 2018. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/11343/220280.

Council of Science Editors:

Milla E. Evolution and ecology of the Australian Heliozelidae (Adeloidea, Lepidoptera). [Doctoral Dissertation]. University of Melbourne; 2018. Available from: http://hdl.handle.net/11343/220280

7. Akanni, Wasiu. Developing and applying supertree methods in Phylogenomics and Macroevolution.

Degree: 2014, RIAN

URL: http://mural.maynoothuniversity.ie/4997/

► Supertrees can be used to combine partially overalapping trees and generate more inclusive phylogenies. It has been proposed that Maximum Likelihood (ML) supertrees method (SM)… (more)

Subjects/Keywords: Biology; Supertree methods; Phylogenomics; Macroevolution

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APA (6^th Edition):

Akanni, W. (2014). Developing and applying supertree methods in Phylogenomics and Macroevolution. (Thesis). RIAN. Retrieved from http://mural.maynoothuniversity.ie/4997/

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):

Akanni, Wasiu. “Developing and applying supertree methods in Phylogenomics and Macroevolution.” 2014. Thesis, RIAN. Accessed January 25, 2021. http://mural.maynoothuniversity.ie/4997/.

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

MLA Handbook (7^th Edition):

Akanni, Wasiu. “Developing and applying supertree methods in Phylogenomics and Macroevolution.” 2014. Web. 25 Jan 2021.

Vancouver:

Akanni W. Developing and applying supertree methods in Phylogenomics and Macroevolution. [Internet] [Thesis]. RIAN; 2014. [cited 2021 Jan 25]. Available from: http://mural.maynoothuniversity.ie/4997/.

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

Council of Science Editors:

Akanni W. Developing and applying supertree methods in Phylogenomics and Macroevolution. [Thesis]. RIAN; 2014. Available from: http://mural.maynoothuniversity.ie/4997/

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

University of Georgia

8. McKain, Michael Ramon. Phylogenomic placement of ancient polyploidy events within the Poales and Agavoideae (Asparagales).

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/29639

► Polyploidy has been an important component to the evolution of angiosperms. Recent studies have shown that an ancient polyploid (paleopolyploid) event can be traced to… (more)

▼ Polyploidy has been an important component to the evolution of angiosperms. Recent studies have shown that an ancient polyploid (paleopolyploid) event can be traced to the lineage leading to the diversification of all angiosperms, and it has long been known that recurring polyploid events can be found throughout the angiosperm tree of life. With the advent of high-throughput sequencing, the prominent place of paleopolyploid events in the evolutionary history of angiosperms has become increasingly clear. Polyploidy is thought to spur both diversification and trait innovation through the duplication and reworking of gene networks. Understanding the evolutionary impact of paleopolyploidy within the angiosperms requires knowing when these events occurred during angiosperm evolution. This study utilizes a high-throughput phylogenomic approach to identify the timing of paleopolyploid events by comparing the origin of paralogous genes within a gene family to a known species tree. Transcriptome data derived from taxa in lineages with previously little to no genomic data, were utilized to assess the timing of duplication events within hundreds of gene families. Previously described paleopolyploid events in the history of grasses, identified through analyses of syntenic blocks within Poaceae genomes, were placed on the Poales phylogeny and the implications of these events were considered. Additionally, a previously unverified paleopolyploidy event was found to have occurred in a common ancestor of all members of the Asparagales and commelinids (including Poales, Zingiberales, Commelinales, Arecales and Dasypogonales). The phylogeny of the Asparagaceae subfamily Agavoideae was resolved using whole chloroplast genomes, and two previously unknown paleopolyploid events were described within the context of that phylogeny. The potential effects of these paleopolyploid events on the evolution of the “Yucca-Agave” bimodal karyotype were discussed. This study demonstrates the utility of large transcriptomic sequencing projects and phylogenomic analyses of gene families to identify novel polyploid events and place them within an evolutionary context.

Subjects/Keywords: Agavoideae; Asparagaceae; paleopolyploidy; phylogenomics; Poales

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APA (6^th Edition):

McKain, M. R. (2014). Phylogenomic placement of ancient polyploidy events within the Poales and Agavoideae (Asparagales). (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/29639

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):

McKain, Michael Ramon. “Phylogenomic placement of ancient polyploidy events within the Poales and Agavoideae (Asparagales).” 2014. Thesis, University of Georgia. Accessed January 25, 2021. http://hdl.handle.net/10724/29639.

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

MLA Handbook (7^th Edition):

McKain, Michael Ramon. “Phylogenomic placement of ancient polyploidy events within the Poales and Agavoideae (Asparagales).” 2014. Web. 25 Jan 2021.

Vancouver:

McKain MR. Phylogenomic placement of ancient polyploidy events within the Poales and Agavoideae (Asparagales). [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10724/29639.

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

Council of Science Editors:

McKain MR. Phylogenomic placement of ancient polyploidy events within the Poales and Agavoideae (Asparagales). [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/29639

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

University of Vermont

9. Lopez-Osorio, Federico. Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps.

Degree: PhD, Biology, 2016, University of Vermont

URL: https://scholarworks.uvm.edu/graddis/569

► Societies where workers sacrifice their own reproduction and cooperatively nurture the offspring of a reproductive queen caste have originated repeatedly across the Tree of… (more)

▼ Societies where workers sacrifice their own reproduction and cooperatively nurture the offspring of a reproductive queen caste have originated repeatedly across the Tree of Life. The attainment of such reproductive division of labor enabled the evolution of remarkable diversity in development, behavior, and social organization in the Hymenoptera (ants, bees, and wasps). Wasps of the family Vespidae exhibit a gamut of social levels, ranging from solitary to highly social behavior. The highly social yellowjackets and hornets (Vespinae) have well developed differences in form and function between queens and workers, large colony sizes, and intricate nest architecture. Moreover, certain socially parasitic species in the Vespinae have secondarily lost the worker caste and rely entirely on the workers of a host species to ensure the survival of parasitic offspring. Understanding the evolution of behavioral traits in the Vespinae over long periods of time would be greatly enhanced by a robust hypothesis of historical relationships. In this study, I analyze targeted genes and transcriptomes to address three goals. First, infer phylogenetic relationships within yellowjackets (Vespula and Dolichovespula) and hornets (Vespa and Provespa). Second, test the hypothesis that social parasites are more closely related to their hosts than to any other species (Emery's rule). Third, test the protein evolution hypothesis, which states that accelerated evolution of protein coding genes and positive selection operated in the transition to highly eusocial behavior. The findings of this study challenge the predominant understanding of evolutionary relationships in the Vespinae. I show that yellowjacket genera are not sister lineages, instead recovering Dolichovespula as more closely related to the hornets, and placing Vespula as sister to all other vespine genera. This implies that traits such as large colony size and high paternity are mostly restricted to a particular evolutionary trajectory (Vespula) from an early split in the Vespinae. I demonstrate that obligate and facultative social parasites do not share immediate common ancestry with their hosts, indicating that socially parasitic behavior likely evolved independently of host species. Moreover, obligate social parasites share a unique evolutionary history, suggesting that their parasitic behavior might have a genetic component. Lastly, I analyze transcriptomic data to infer a phylogeny of vespid wasps and use this phylogeny to discover lineage-specific signatures of positive selection. I identify more than two hundred genes showing signatures of positive selection on the branch leading to the highly eusocial yellowjackets and hornets. These positively selected genes involve functions related mainly to carbohydrate metabolism and mitochondrial activity, in agreement with insights from studies of bees and ants. Parallels of functional categories for genes under positive selection suggests that at the molecular level the evolution of highly eusocial behavior across… Advisors/Committee Members: Ingi Agnarsson.

Subjects/Keywords: Hymenoptera; Phylogenomics; Phylogeny; Sociality; Transcriptome; Wasp; Biology

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APA (6^th Edition):

Lopez-Osorio, F. (2016). Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps. (Doctoral Dissertation). University of Vermont. Retrieved from https://scholarworks.uvm.edu/graddis/569

Chicago Manual of Style (16^th Edition):

Lopez-Osorio, Federico. “Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps.” 2016. Doctoral Dissertation, University of Vermont. Accessed January 25, 2021. https://scholarworks.uvm.edu/graddis/569.

MLA Handbook (7^th Edition):

Lopez-Osorio, Federico. “Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps.” 2016. Web. 25 Jan 2021.

Vancouver:

Lopez-Osorio F. Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps. [Internet] [Doctoral dissertation]. University of Vermont; 2016. [cited 2021 Jan 25]. Available from: https://scholarworks.uvm.edu/graddis/569.

Council of Science Editors:

Lopez-Osorio F. Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps. [Doctoral Dissertation]. University of Vermont; 2016. Available from: https://scholarworks.uvm.edu/graddis/569

University of Oregon

10. McCluskey, Braedan. Genome Evolution and Gene Expression Divergence in the Genus Danio.

Degree: PhD, Department of Biology, 2016, University of Oregon

URL: http://hdl.handle.net/1794/20484

► Genus Danio includes zebrafish (Danio rerio) and several other phenotypically diverse species. To understand the history of these species and how they acquired the genetic… (more)

Subjects/Keywords: Danio; Evolution; Exome; Linked selection; Phylogenomics; Zebrafish

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APA (6^th Edition):

McCluskey, B. (2016). Genome Evolution and Gene Expression Divergence in the Genus Danio. (Doctoral Dissertation). University of Oregon. Retrieved from http://hdl.handle.net/1794/20484

Chicago Manual of Style (16^th Edition):

McCluskey, Braedan. “Genome Evolution and Gene Expression Divergence in the Genus Danio.” 2016. Doctoral Dissertation, University of Oregon. Accessed January 25, 2021. http://hdl.handle.net/1794/20484.

MLA Handbook (7^th Edition):

McCluskey, Braedan. “Genome Evolution and Gene Expression Divergence in the Genus Danio.” 2016. Web. 25 Jan 2021.

Vancouver:

McCluskey B. Genome Evolution and Gene Expression Divergence in the Genus Danio. [Internet] [Doctoral dissertation]. University of Oregon; 2016. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/1794/20484.

Council of Science Editors:

McCluskey B. Genome Evolution and Gene Expression Divergence in the Genus Danio. [Doctoral Dissertation]. University of Oregon; 2016. Available from: http://hdl.handle.net/1794/20484

Southern Illinois University

11. Muell, Morgan Renee. Phylogenomic Analysis Of Evolutionary Relationships In Ranitomeya Poison Frogs (Amphibia: Dendrobatidae) Using Ultraconserved Elements.

Degree: MS, Zoology, 2020, Southern Illinois University

URL: https://opensiuc.lib.siu.edu/theses/2749

► Knowledge of phylogenetic relationships among organisms is essential for anchoring evolutionary studies. Phylogenomic studies use large amounts of genetic data in analyses, which is… (more)

▼ Knowledge of phylogenetic relationships among organisms is essential for anchoring evolutionary studies. Phylogenomic studies use large amounts of genetic data in analyses, which is particularly important for highly phenotypically variable taxa that are difficult to distinguish from one another without the use of genetic data, due to the abundance of homoplasy in morphological characters typically used in morphological classification. Use of genome-scale molecular data has thus become the gold standard for identifying these phylogenetic relationships, specifically in comparison to past studies based on fewer genes. Greater quantities of genetic data, in addition to finer taxon sampling, may lead to different conclusions about phylogenetic relationships among organisms compared to previous studies, necessitating new analyses on organisms when new discoveries of populations and new sources of genetic data arise. Ranitomeya poison frogs (Amphibia: Dendrobatidae) are an Amazonian lineage of dendrobatid frogs consisting of 16 species possessing remarkable diversity in color pattern, range size, and parental care behavior. I present the first phylogeny based on genomic data for all species in Ranitomeya, using maximum likelihood and multi-species coalescent methods. I used ultraconserved elements (UCEs), a genome-scale nuclear marker, as my source of molecular data to construct the tree. I also present divergence time estimations using the MCMCTree program. My results indicate several differences from previous analyses in terms of interspecific relationships. Notably, I find R. toraro and R. defleri constitute different species groups, and recover R. uakarii as paraphyletic. I also designate former populations of R. fantastica from Isla Pongo, Peru and Tarapoto as R. summersi, and transfer the French Guianan R. amazonica populations to R. variabilis. My study clarifies both interspecific and intraspecific relationships within Ranitomeya, and provides key insights into phylogeny that pave the way for future studies testing hypotheses on color pattern evolution and historical biogeography. Advisors/Committee Members: Brown, Jason.

Subjects/Keywords: Divergence time estimation; Phylogenomics; Ranitomeya; UCEs

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APA (6^th Edition):

Muell, M. R. (2020). Phylogenomic Analysis Of Evolutionary Relationships In Ranitomeya Poison Frogs (Amphibia: Dendrobatidae) Using Ultraconserved Elements. (Masters Thesis). Southern Illinois University. Retrieved from https://opensiuc.lib.siu.edu/theses/2749

Chicago Manual of Style (16^th Edition):

Muell, Morgan Renee. “Phylogenomic Analysis Of Evolutionary Relationships In Ranitomeya Poison Frogs (Amphibia: Dendrobatidae) Using Ultraconserved Elements.” 2020. Masters Thesis, Southern Illinois University. Accessed January 25, 2021. https://opensiuc.lib.siu.edu/theses/2749.

MLA Handbook (7^th Edition):

Muell, Morgan Renee. “Phylogenomic Analysis Of Evolutionary Relationships In Ranitomeya Poison Frogs (Amphibia: Dendrobatidae) Using Ultraconserved Elements.” 2020. Web. 25 Jan 2021.

Vancouver:

Muell MR. Phylogenomic Analysis Of Evolutionary Relationships In Ranitomeya Poison Frogs (Amphibia: Dendrobatidae) Using Ultraconserved Elements. [Internet] [Masters thesis]. Southern Illinois University; 2020. [cited 2021 Jan 25]. Available from: https://opensiuc.lib.siu.edu/theses/2749.

Council of Science Editors:

Muell MR. Phylogenomic Analysis Of Evolutionary Relationships In Ranitomeya Poison Frogs (Amphibia: Dendrobatidae) Using Ultraconserved Elements. [Masters Thesis]. Southern Illinois University; 2020. Available from: https://opensiuc.lib.siu.edu/theses/2749

University of Illinois – Urbana-Champaign

12. Mughal, Fizza. MANET and the evolution, structure and function of biological networks.

Degree: MS, 4026, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/50497

► The metabolic MANET is an online resource that incorporates data from KEGG, SCOP and structural phylogenomics. A revised version of MANET was here produced that… (more)

Subjects/Keywords: Metabolic Networks; Enzyme Evolution; Phylogenomics; Protein Domain

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APA (6^th Edition):

Mughal, F. (2014). MANET and the evolution, structure and function of biological networks. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/50497

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):

Mughal, Fizza. “MANET and the evolution, structure and function of biological networks.” 2014. Thesis, University of Illinois – Urbana-Champaign. Accessed January 25, 2021. http://hdl.handle.net/2142/50497.

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

MLA Handbook (7^th Edition):

Mughal, Fizza. “MANET and the evolution, structure and function of biological networks.” 2014. Web. 25 Jan 2021.

Vancouver:

Mughal F. MANET and the evolution, structure and function of biological networks. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/2142/50497.

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

Council of Science Editors:

Mughal F. MANET and the evolution, structure and function of biological networks. [Thesis]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/50497

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

University of Illinois – Urbana-Champaign

13. Nasir, Arshan. Origin of viruses revealed by the genomic study of protein domain structures.

Degree: MS, 4026, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34445

► The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for… (more)

Subjects/Keywords: Mimivurs; phylogenomics, protein domain, structure, evolution

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APA (6^th Edition):

Nasir, A. (2012). Origin of viruses revealed by the genomic study of protein domain structures. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34445

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):

Nasir, Arshan. “Origin of viruses revealed by the genomic study of protein domain structures.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed January 25, 2021. http://hdl.handle.net/2142/34445.

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

MLA Handbook (7^th Edition):

Nasir, Arshan. “Origin of viruses revealed by the genomic study of protein domain structures.” 2012. Web. 25 Jan 2021.

Vancouver:

Nasir A. Origin of viruses revealed by the genomic study of protein domain structures. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/2142/34445.

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

Council of Science Editors:

Nasir A. Origin of viruses revealed by the genomic study of protein domain structures. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34445

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

14. Provencher, Curtis. Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins.

Degree: MS, 2018, University of New Hampshire

URL: https://scholars.unh.edu/thesis/1248

► Phylogenetic analyses of gene trees commonly begin by searching large molecular datasets from the taxa of interest using some known query sequence. Resulting sequences that… (more)

Subjects/Keywords: Bioinformatics; Cnidaria; Evolution; Genomics; Opsin; Phylogenomics

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APA (6^th Edition):

Provencher, C. (2018). Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins. (Thesis). University of New Hampshire. Retrieved from https://scholars.unh.edu/thesis/1248

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):

Provencher, Curtis. “Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins.” 2018. Thesis, University of New Hampshire. Accessed January 25, 2021. https://scholars.unh.edu/thesis/1248.

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

MLA Handbook (7^th Edition):

Provencher, Curtis. “Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins.” 2018. Web. 25 Jan 2021.

Vancouver:

Provencher C. Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins. [Internet] [Thesis]. University of New Hampshire; 2018. [cited 2021 Jan 25]. Available from: https://scholars.unh.edu/thesis/1248.

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

Council of Science Editors:

Provencher C. Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins. [Thesis]. University of New Hampshire; 2018. Available from: https://scholars.unh.edu/thesis/1248

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

Louisiana State University

15. Ludt, William Benton. Determining the Drivers of Anti-Tropical Distributions Across the Fish Tree of Life.

Degree: PhD, Evolution, 2018, Louisiana State University

URL: https://digitalcommons.lsu.edu/gradschool_dissertations/4649

► Anti-tropical distributions are those where populations of a single species, or multiple closely related taxa, are distributed outside of, and on opposing sides of,… (more)

▼ Anti-tropical distributions are those where populations of a single species, or multiple closely related taxa, are distributed outside of, and on opposing sides of, the tropics. These latitudinally disjunct distributions have been noted for over a century. Despite this long history of interest, little has been concluded regarding the actual mechanisms that drive this pattern, with several prominent hypotheses competing with one another in the literature. Here I review the proposed drivers of anti-tropicality, and subsequently test them using fishes with a variety of life history and taxonomic differences. This includes (1) a temperately restricted family with anti-tropical distributions – Cheilodactylidae, (2) a tropical reef fish family with a single temperate anti-tropical genus – Prionurus, and (3) a variety of fishes from across the fish tree of life that have populations split by the tropics. Using complete taxonomic sampling, and phylogenomic approaches coupled with fossil calibration points, I find evidence for recent equatorial divergence events in the Pleistocene and Pliocene, as well as divergence events dating to the Miocene for both Cheilodactylidae and Prionurus. Furthermore, taxonomic issues were detected, and explored within both of these groups. To disentangle the multiple hypotheses that can explain recent transitions, I used ecological niche models coupled with extant distributional data for a variety of species across the fish tree of life that exhibit intra-specific anti-tropicality. These data reveal distinct support for both glacial dispersal, and biotic exclusion from the tropics. These results are then interpreted in a comprehensive framework to determine what drives anti-tropical distributions in marine systems. Overall, multiple mechanisms seem responsible that act in concert over time to produce these distributions. Certain equatorial divergence events are recovered in time periods currently not associated with any anti-tropical hypotheses. It seems likely that stochastic crossing events may be important in the initial colonization of a new hemisphere.

Subjects/Keywords: Ichthyology; Biogeography; Phylogenomics; Vicariance; Dispersal; ENM

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APA (6^th Edition):

Ludt, W. B. (2018). Determining the Drivers of Anti-Tropical Distributions Across the Fish Tree of Life. (Doctoral Dissertation). Louisiana State University. Retrieved from https://digitalcommons.lsu.edu/gradschool_dissertations/4649

Chicago Manual of Style (16^th Edition):

Ludt, William Benton. “Determining the Drivers of Anti-Tropical Distributions Across the Fish Tree of Life.” 2018. Doctoral Dissertation, Louisiana State University. Accessed January 25, 2021. https://digitalcommons.lsu.edu/gradschool_dissertations/4649.

MLA Handbook (7^th Edition):

Ludt, William Benton. “Determining the Drivers of Anti-Tropical Distributions Across the Fish Tree of Life.” 2018. Web. 25 Jan 2021.

Vancouver:

Ludt WB. Determining the Drivers of Anti-Tropical Distributions Across the Fish Tree of Life. [Internet] [Doctoral dissertation]. Louisiana State University; 2018. [cited 2021 Jan 25]. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/4649.

Council of Science Editors:

Ludt WB. Determining the Drivers of Anti-Tropical Distributions Across the Fish Tree of Life. [Doctoral Dissertation]. Louisiana State University; 2018. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/4649

University of Minnesota

16. Razuri Gonzales, Luis. Phylogenomics of the Caddisfly Genus Smicridea, With A Taxonomic Revision of the S. Nigripennis Species Group (Trichoptera: Hydropsychidae).

Degree: PhD, Entomology, 2020, University of Minnesota

URL: http://hdl.handle.net/11299/216116

► The genus Smicridea McLachlan, 1871 (Hydropsychidae, Trichoptera) currently contains 242 species (Holzenthal & Calor 2017), and is by far, the largest Hydropsychidae genus in the… (more)

▼ The genus Smicridea McLachlan, 1871 (Hydropsychidae, Trichoptera) currently contains 242 species (Holzenthal & Calor 2017), and is by far, the largest Hydropsychidae genus in the Western Hemisphere. It is distributed from southwestern USA, through Mexico, Central America, the Caribbean Islands, and South America. The genus is divided into two subgenera: the nominotypical Smicridea (137 spp.) and the subgenus Rhyacophylax (105 spp.), which are distinguished based on wing venation characters. Additionally, characters of the male genitalia were used to informally define species group within both subgenera. In Chapter 1, I tested the monophyly of the genus Smicridea, its constituent subgenera, and the species groups using 200 targeted enrichment loci for 26 taxa as well as mitochondrial COI and nuclear ribosomal RNA 28S for 17 additional species to fill the tips of the backbone phylogeny, produced with the targeted enrichment loci. I used maximum likelihood, as implemented in the software IQ-TREE, to analyze the sequence supermatrix as well as the "summary" method ASTRAL-III, which takes into consideration gene tree – species tree discordance. The resulting trees from both types of analysis showed the same relationships. However, support values for some nodes in the ASTRAL-III tree were lower than those in the concatenated tree. Both subgenera in Smicridea were recovered as monophyletic as expected by morphological characters. In the subgenus Rhyacophylax, the species S. andicola, S. ventridenticulata, and S. talamanca, members of the S. peruana species group, were recovered as monophyletic, and S. radula (S. radula species group) and S. unguiculata (unplaced) were related to one another. In the subgenus Smicridea, the S. nigripennis species groups was recovered as monophyletic. Conversely, the S. fasciatella species group was recovered as paraphyletic and composed of at least 5 different clades. The clade composed of the Chilean species of Smicridea (Smicridea) and S. (S.) curvipenis diverged from the rest of the species included in this analysis. The support values for the full dataset tree (i.e., targeted enrichment loci + COI + 28S) were even lower than the support values in the ASTRAL-III for the targeted enrichment loci, and some of the relationships from the targeted enrichment loci tree were not recovered. However, the COI/28S did recover some interesting relationships such as a group of morphologically similar Brazilian species in the subgenus Rhyacophylax or the clustering of S. (R.) appendiculata and S. (R.) murina. In Chapter 2, I presented a species-level revision of the Smicridea (Smicridea) nigripennis species group. In this chapter, I discussed the morphological structure of the male genitalia and produced descriptions and illustrations for each of the species in the group. The nigripennis species group currently contains 74 species and 20 were described as new: Smicridea blahniki new species (Peru), S. chamorroi new species (Nicaragua), S. edithae new species (Peru), S. erwini new species (Peru), S.…

Subjects/Keywords: Hydropsychidae; Neotropics; Phylogenomics; Smicrideinae; Taxonomy; Trichoptera

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APA (6^th Edition):

Razuri Gonzales, L. (2020). Phylogenomics of the Caddisfly Genus Smicridea, With A Taxonomic Revision of the S. Nigripennis Species Group (Trichoptera: Hydropsychidae). (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/216116

Chicago Manual of Style (16^th Edition):

Razuri Gonzales, Luis. “Phylogenomics of the Caddisfly Genus Smicridea, With A Taxonomic Revision of the S. Nigripennis Species Group (Trichoptera: Hydropsychidae).” 2020. Doctoral Dissertation, University of Minnesota. Accessed January 25, 2021. http://hdl.handle.net/11299/216116.

MLA Handbook (7^th Edition):

Razuri Gonzales, Luis. “Phylogenomics of the Caddisfly Genus Smicridea, With A Taxonomic Revision of the S. Nigripennis Species Group (Trichoptera: Hydropsychidae).” 2020. Web. 25 Jan 2021.

Vancouver:

Razuri Gonzales L. Phylogenomics of the Caddisfly Genus Smicridea, With A Taxonomic Revision of the S. Nigripennis Species Group (Trichoptera: Hydropsychidae). [Internet] [Doctoral dissertation]. University of Minnesota; 2020. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/11299/216116.

Council of Science Editors:

Razuri Gonzales L. Phylogenomics of the Caddisfly Genus Smicridea, With A Taxonomic Revision of the S. Nigripennis Species Group (Trichoptera: Hydropsychidae). [Doctoral Dissertation]. University of Minnesota; 2020. Available from: http://hdl.handle.net/11299/216116

University of Sydney

17. Foster, Charles Stuart Piper. Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution .

Degree: 2017, University of Sydney

URL: http://hdl.handle.net/2123/17852

► Angiosperms are one of the most dominant groups on Earth, and have fundamentally changed global ecosystem patterns and function. Therefore, unravelling their evolutionary history is… (more)

▼ Angiosperms are one of the most dominant groups on Earth, and have fundamentally changed global ecosystem patterns and function. Therefore, unravelling their evolutionary history is key to understanding how the world around us was formed, and how it might change in the future. In this thesis, I use genome-scale data to investigate the evolutionary patterns and timescale of angiosperms at multiple taxonomic levels, ranging from angiosperm-wide to genus-level data sets. I begin by using the largest combination of taxon and gene sampling thus far to provide a novel estimate for the timing of angiosperm origin in the Triassic period. Through a range of sensitivity analyses, I demonstrate that this estimate is robust to many important components of Bayesian molecular dating. I then explore tactics for phylogenomic dating using multiple molecular clocks. I evaluate methods for estimating the number and assignment of molecular clock models, and strategies for partitioning molecular clock models in analyses of multigene data sets. I also demonstrate the importance of critically evaluating the precision in age estimates from molecular dating analyses. Finally, I assess the utility of plastid data sets for resolving challenging phylogenetic relationships, focusing on Pimelea Banks & Sol. ex Gaertn. Through analysis of a multigene data set, sampled from many taxa, I provide an improved phylogeny for Pimelea and its close relatives. I then generate a plastome-scale data set for a representative sample of species to further refine the Pimelea phylogeny, and characterise discordant phylogenetic signals within their chloroplast genomes. The work in this thesis demonstrates the power of genome- scale data to address challenging phylogenetic questions, and the importance of critical evaluation of both methods and results. Future progress in our understanding of angiosperm evolution will depend on broader and denser taxon sampling, and the development of improved phylogenetic methods.

Subjects/Keywords: Angiospermae; flowering plants; phylogenomics; molecular dating

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APA (6^th Edition):

Foster, C. S. P. (2017). Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/17852

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):

Foster, Charles Stuart Piper. “Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution .” 2017. Thesis, University of Sydney. Accessed January 25, 2021. http://hdl.handle.net/2123/17852.

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

MLA Handbook (7^th Edition):

Foster, Charles Stuart Piper. “Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution .” 2017. Web. 25 Jan 2021.

Vancouver:

Foster CSP. Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution . [Internet] [Thesis]. University of Sydney; 2017. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/2123/17852.

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

Council of Science Editors:

Foster CSP. Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution . [Thesis]. University of Sydney; 2017. Available from: http://hdl.handle.net/2123/17852

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

Utah State University

18. Sadler, Emily A. Historical Biogeography and Natural History of Nocturnal Wasps in the Southwestern Deserts with Special Emphasis on the Genus Chyphotes (Hymenoptera: Chyphotidae).

Degree: PhD, Biology, 2018, Utah State University

URL: https://digitalcommons.usu.edu/etd/6966

► Deserts are interesting places due to the large number of plants and animals that live there. Nocturnal wasps are extremely abundant in deserts, but… (more)

Subjects/Keywords: Hymenoptera; Desert Biogeography; Phylogenomics; Taxonomy; Systematics; Biology

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APA (6^th Edition):

Sadler, E. A. (2018). Historical Biogeography and Natural History of Nocturnal Wasps in the Southwestern Deserts with Special Emphasis on the Genus Chyphotes (Hymenoptera: Chyphotidae). (Doctoral Dissertation). Utah State University. Retrieved from https://digitalcommons.usu.edu/etd/6966

Chicago Manual of Style (16^th Edition):

Sadler, Emily A. “Historical Biogeography and Natural History of Nocturnal Wasps in the Southwestern Deserts with Special Emphasis on the Genus Chyphotes (Hymenoptera: Chyphotidae).” 2018. Doctoral Dissertation, Utah State University. Accessed January 25, 2021. https://digitalcommons.usu.edu/etd/6966.

MLA Handbook (7^th Edition):

Sadler, Emily A. “Historical Biogeography and Natural History of Nocturnal Wasps in the Southwestern Deserts with Special Emphasis on the Genus Chyphotes (Hymenoptera: Chyphotidae).” 2018. Web. 25 Jan 2021.

Vancouver:

Sadler EA. Historical Biogeography and Natural History of Nocturnal Wasps in the Southwestern Deserts with Special Emphasis on the Genus Chyphotes (Hymenoptera: Chyphotidae). [Internet] [Doctoral dissertation]. Utah State University; 2018. [cited 2021 Jan 25]. Available from: https://digitalcommons.usu.edu/etd/6966.

Council of Science Editors:

Sadler EA. Historical Biogeography and Natural History of Nocturnal Wasps in the Southwestern Deserts with Special Emphasis on the Genus Chyphotes (Hymenoptera: Chyphotidae). [Doctoral Dissertation]. Utah State University; 2018. Available from: https://digitalcommons.usu.edu/etd/6966

Dalhousie University

19. Eveleigh, Robert. Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past.

Degree: MS, Department of Computational Biology and Bioinformatics, 2012, Dalhousie University

URL: http://hdl.handle.net/10222/14412

► Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show… (more)

Subjects/Keywords: Aquifex aeolicus; Thermotogae; phylogenomics; hyperthermophily; lateral gene transfer

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APA (6^th Edition):

Eveleigh, R. (2012). Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/14412

Chicago Manual of Style (16^th Edition):

Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past.” 2012. Masters Thesis, Dalhousie University. Accessed January 25, 2021. http://hdl.handle.net/10222/14412.

MLA Handbook (7^th Edition):

Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past.” 2012. Web. 25 Jan 2021.

Vancouver:

Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past. [Internet] [Masters thesis]. Dalhousie University; 2012. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10222/14412.

Council of Science Editors:

Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past. [Masters Thesis]. Dalhousie University; 2012. Available from: http://hdl.handle.net/10222/14412

Dalhousie University

20. Gaston, Daniel. PHYLOGENOMIC APPROACHES TO THE ANALYSIS OF FUNCTIONAL DIVERGENCE AND SUBCELLULAR LOCALIZATION.

Degree: PhD, Department of Biochemistry & Molecular Biology, 2012, Dalhousie University

URL: http://hdl.handle.net/10222/14439

► With rapid advances in sequencing technologies and precipitous decreases in cost, public sequence databases have increased in size apace. However, experimental characterization of novel genes… (more)

▼ With rapid advances in sequencing technologies and precipitous decreases in cost, public sequence databases have increased in size apace. However, experimental characterization of novel genes and their products remains prohibitively expensive and time consuming. For these reasons, bioinformatics approaches have become increasingly necessary to generate hypotheses of biological function. Phylogenomic approaches use phylogenetic methods to place genes, chromosomes, or whole genomes within the context of their evolutionary history and can be used to predict the function of encoded proteins. In this thesis, two new phylogenomic methods and software implementations are presented that address the problems of subcellular localization prediction and functional divergence prediction within protein families respectively. Most of the widely used programs for subcellular localization prediction have been trained on model organisms and ignore phylogenetic information. As a result, their predictions are not always reliable when applied to phylogenetically divergent eukaryotes, such as unicellular protists. To address this problem, PhyloPred-HMM, a novel phylogenomic method was developed to predict sequences that are targeted to mitochondria or mitochondrion-related organelles (hydrogenosomes and mitosomes). This method was compared to existing prediction methods using an existing test dataset of mitochondrion-targeted sequences from well-studied groups, sequences from a variety of protists, and the whole proteomes of two protists: Tetrahymena thermophila and Trichomonas vaginalis. PhyloPred-HMM performed comparably to existing classifiers on mitochondrial sequences from well-studied groups such as animals, plants, and Fungi and better than existing classifiers on diverse protistan lineages. FunDi, a novel approach to the prediction of functional divergence was developed and tested on 11 biological datasets and two large simulated datasets. On the 11 biological datasets, FunDi appeared to perform comparably to existing programs, although performance measures were compromised by a lack of experimental information. On the simulated datasets, FunDi was clearly superior to existing methods. FunDi, and two other prediction programs, was then used to characterize the functional divergence in two groups of plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (GAPDH) adapted to roles in the Calvin cycle. FunDi successfully identified functionally divergent residues supported by experimental data, and identified cases of potential convergent evolution between the two groups of GAPDH sequences. Advisors/Committee Members: Dr. Marc Robinson-Rechavi (external-examiner), Dr. John Archibald (graduate-coordinator), Dr. Christian Blouin (thesis-reader), Dr. Robert Beiko (thesis-reader), Dr. Edward Susko (thesis-reader), Dr. John Archibald (thesis-reader), Dr. Andrew J. Roger (thesis-supervisor), Not Applicable (ethics-approval), Yes (manuscripts), Yes (copyright-release).

Subjects/Keywords: phylogenomics; molecular evolution; functional divergence; subcellular localization prediction; phylogenetics

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

APA (6^th Edition):

Gaston, D. (2012). PHYLOGENOMIC APPROACHES TO THE ANALYSIS OF FUNCTIONAL DIVERGENCE AND SUBCELLULAR LOCALIZATION. (Doctoral Dissertation). Dalhousie University. Retrieved from http://hdl.handle.net/10222/14439

Chicago Manual of Style (16^th Edition):

Gaston, Daniel. “PHYLOGENOMIC APPROACHES TO THE ANALYSIS OF FUNCTIONAL DIVERGENCE AND SUBCELLULAR LOCALIZATION.” 2012. Doctoral Dissertation, Dalhousie University. Accessed January 25, 2021. http://hdl.handle.net/10222/14439.

MLA Handbook (7^th Edition):

Gaston, Daniel. “PHYLOGENOMIC APPROACHES TO THE ANALYSIS OF FUNCTIONAL DIVERGENCE AND SUBCELLULAR LOCALIZATION.” 2012. Web. 25 Jan 2021.

Vancouver:

Gaston D. PHYLOGENOMIC APPROACHES TO THE ANALYSIS OF FUNCTIONAL DIVERGENCE AND SUBCELLULAR LOCALIZATION. [Internet] [Doctoral dissertation]. Dalhousie University; 2012. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10222/14439.

Council of Science Editors:

Gaston D. PHYLOGENOMIC APPROACHES TO THE ANALYSIS OF FUNCTIONAL DIVERGENCE AND SUBCELLULAR LOCALIZATION. [Doctoral Dissertation]. Dalhousie University; 2012. Available from: http://hdl.handle.net/10222/14439

University of California – Berkeley

21. Reilly, Sean Bryant. Historical Biogeography of Reptiles and Amphibians from the Lesser Sunda Islands of Indonesia.

Degree: Integrative Biology, 2016, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/5458s4k2

► The Lesser Sunda Archipelago, also known as Nusa Tenggara, lies in the southeastern portion of Indonesia and extends between Bali in the west, and New… (more)

▼ The Lesser Sunda Archipelago, also known as Nusa Tenggara, lies in the southeastern portion of Indonesia and extends between Bali in the west, and New Guinea in the east. While the Lesser Sundas themselves are oceanic islands that have never been land bridged to a continent the islands on either side do. Bali and the other Greater Sunda Islands of Java, Sumatra, and Borneo become periodically land bridged with Asia during glacial maxima forming the Sunda Shelf. New Guinea and Aru become periodically land bridged to Australia during glacial maxima and form the Sahul Shelf. Given their current orientation, the Lesser Sundas may act as ‘stepping stones’ for animals and plants dispersing between the Sunda and Sahul Shelves and may act as a two-way filter for organisms dispersing between two of the world’s great biogeographical realms. Alfred Russel Wallace’s discovery of a pattern of clinal mixture of species from different biogeographical realms was a key insight leading to his identification of the Wallace Line and to his creation of the field of biogeography. Even though the Lesser Sundas played a critical role in the development of the field, this region has received little subsequent attention from historical biogeographers and our current understanding of Lesser Sunda biogeography has only modestly improved relative to what was known at the time of Wallace. The reptiles and amphibians of the Lesser Sundas represent a particularly interesting group of vertebrates from a biogeographical standpoint because they appear to show distributional patterns that are most consistent with a stepping-stone model of island colonization caused by the two-way filter zone. In Chapter 1, I review the geological and biogeographical literature for the Lesser Sundas and use these sources to formulate hypotheses concerning the colonization of the archipelago by rafting terrestrial vertebrates. In Chapters 2 through 4, I investigate the possibility that flying lizards, forest skinks, and fanged frogs have colonized the archipelago in a stepping-stone manner using a phylogenomic approach (using sequence data from mtDNA and hundreds of nuclear loci) whereby the relationships among island-specific lineages can be used to infer the sequence of island colonization. Flying lizards of the genus Draco form a monophyletic group that colonized the western Inner Arc islands of Lombok or Sumbawa from the Sunda Shelf around 10 million years ago when Lombok and Sumbawa first became land-positive. Draco continued expanding eastward through the Inner Arc until they reached Lembata, while a series of dispersal events from Flores south to Sumba, east to Timor, north to Wetar, west to Alor, and finally west to Pantar (the island immediately west of Lembata). The islands of Sumbawa and Flores contain multiple non-sister lineages that are parapatrically distributed and are exchanging migrants within an island. Forest Skinks of the genus Sphenomorphus show relatively little morphological divergence across their range yet exhibit large levels of genetic…

Subjects/Keywords: Zoology; Systematic biology; Biology; Amphibians; Biogeography; Indonesia; Islands; Phylogenomics; Reptiles

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

APA (6^th Edition):

Reilly, S. B. (2016). Historical Biogeography of Reptiles and Amphibians from the Lesser Sunda Islands of Indonesia. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/5458s4k2

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):

Reilly, Sean Bryant. “Historical Biogeography of Reptiles and Amphibians from the Lesser Sunda Islands of Indonesia.” 2016. Thesis, University of California – Berkeley. Accessed January 25, 2021. http://www.escholarship.org/uc/item/5458s4k2.

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

MLA Handbook (7^th Edition):

Reilly, Sean Bryant. “Historical Biogeography of Reptiles and Amphibians from the Lesser Sunda Islands of Indonesia.” 2016. Web. 25 Jan 2021.

Vancouver:

Reilly SB. Historical Biogeography of Reptiles and Amphibians from the Lesser Sunda Islands of Indonesia. [Internet] [Thesis]. University of California – Berkeley; 2016. [cited 2021 Jan 25]. Available from: http://www.escholarship.org/uc/item/5458s4k2.

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

Council of Science Editors:

Reilly SB. Historical Biogeography of Reptiles and Amphibians from the Lesser Sunda Islands of Indonesia. [Thesis]. University of California – Berkeley; 2016. Available from: http://www.escholarship.org/uc/item/5458s4k2

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

UCLA

22. Sorenson, Laura. Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification.

Degree: Biology, 2014, UCLA

URL: http://www.escholarship.org/uc/item/31n0c9km

► Understanding the evolutionary factors underlying the disparity in species richness across groups is a fundamental challenge in fish evolutionary biology. A difficulty in investigating this… (more)

▼ Understanding the evolutionary factors underlying the disparity in species richness across groups is a fundamental challenge in fish evolutionary biology. A difficulty in investigating this field lies in the paucity of robust, well-sampled phylogenies that act as a necessary framework to test hypotheses about the affects of ecology on fish evolution. In chapter one I use molecular sequence data to generate a time-calibrated hypothesis of surgeonfish (Family: Acanthuridae) relationships. I found strong support that the gizzard-like stomach, an important morphological trait for benthic grazing species including some Acanthurus and all Ctenochaetus, evolved only once, contrary to a previous hypothesis of multiple, independent origins. The timetree also shows that the subfamily Nasinae (genus Naso) experienced high turnover since originating in the Miocene, and that the extant species arose much more recently (~17 Ma) than previous hypotheses. To abet creating robust phylogenies across a diverse set of species and at multiple phylogenetic levels, I developed a new genomic method capturing ultraconserved elements (UCEs). UCEs are highly conserved regions of the genome that are flanked by more variable regions, making them ideal for target enrichment. I created custom probes targeting 500 loci across fishes and used massively parallel sequencing to obtain a phylogenomic dataset both efficiently and economically. I validate this method by resolving the higher-level relationships among ray-finned fishes. The well-supported topology reveals monophyly of Amia and Lepisosteus (Holostei), and suggests that elopomorphs, then osteoglossomorphs were the first teleost lineages to diverge. The results show that sequence capture of UCE loci and their flanking regions provides an excellent approach to resolve the fish Tree of Life. In chapter three, I use molecular data to generate the most comprehensive, time-calibrated phylogeny for the sharks. This framework is then used to understand the influence of ecology (e.g. habitat preference) on the diversification of these fishes. My results show that deepwater radiations and transitions to coral reefs have played an important role in generating extant biodiversity. Coral reefs, therefore, have greatly influenced species richness across multiple fish trophic levels, from algivores to top predators like sharks.

Subjects/Keywords: Biology; Bioinformatics; Diversification; Ecology; Macroevolution; Marine Fishes; Phylogenomics

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

APA (6^th Edition):

Sorenson, L. (2014). Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/31n0c9km

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):

Sorenson, Laura. “Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification.” 2014. Thesis, UCLA. Accessed January 25, 2021. http://www.escholarship.org/uc/item/31n0c9km.

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

MLA Handbook (7^th Edition):

Sorenson, Laura. “Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification.” 2014. Web. 25 Jan 2021.

Vancouver:

Sorenson L. Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification. [Internet] [Thesis]. UCLA; 2014. [cited 2021 Jan 25]. Available from: http://www.escholarship.org/uc/item/31n0c9km.

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

Council of Science Editors:

Sorenson L. Evolution of Marine Fish Biodiversity: Phylogenomics and Ecological Processes Shaping Diversification. [Thesis]. UCLA; 2014. Available from: http://www.escholarship.org/uc/item/31n0c9km

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

23. Venkatraman, Anand. Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families.

Degree: PhD, Biochemistry, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-3112

► Prediction of functions of genes in a genome is a key step in all genome sequencing projects. Sequences that carry out important functions are likely… (more)

▼ Prediction of functions of genes in a genome is a key step in all genome sequencing projects. Sequences that carry out important functions are likely to be conserved between evolutionarily distant species and can be identified using cross-species comparisons. In the absence of completed genomes and the accompanying high-quality annotations, expressed sequence tags (ESTs) from random cDNA clones are the primary tools for functional genomics. EST datasets are fragmented and redundant, necessitating clustering of ESTs into groups that are likely to have been derived from the same genes. EST clustering helps reduce the search space for sequence homology searching and improves the accuracy of function predictions using EST datasets. This dissertation is a case study that describes clustering of Bos taurus and Sus scrofa EST datasets, and utilizes the EST clusters to make computational function predictions using a comparative genomics approach. We used a novel EST clustering method, TAMUClust, to cluster bovine ESTs and compare its performance to the bovine EST clusters from TIGR Gene Indices (TGI) by using bovine ESTs aligned to the bovine genome assembly as a gold standard. This comparison study reveals that TAMUClust and TGI are similar in performance. Comparisons of TAMUClust and TGI with predicted bovine gene models reveal that both datasets are similar in transcript coverage. We describe here the design and implementation of an annotation pipeline for predicting functions of the Bos taurus (cattle) and Sus scrofa (pig) transcriptomes. EST datasets were clustered into gene families using Ensembl protein family clusters as a framework. Following clustering, the EST consensus sequences were assigned predicted function by transferring annotations of the Ensembl vertebrate protein(s) they are grouped to after sequence homology searches and phylogenetic analysis. The annotations benefit the livestock community by helping narrow down the gamut of direct experiments needed to verify function. Advisors/Committee Members: Elsik, Christine G (advisor), Hu, James C (advisor), Krutovsky, Konstantin V (committee member), Park, William D (committee member).

Subjects/Keywords: Bioinformatics; Phylogenomics; Computational Biology

…similarities and differences came to be [1]. Phylogenomics combines evolutionary and…

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APA (6^th Edition):

Venkatraman, A. (2009). Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-3112

Chicago Manual of Style (16^th Edition):

Venkatraman, Anand. “Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families.” 2009. Doctoral Dissertation, Texas A&M University. Accessed January 25, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-3112.

MLA Handbook (7^th Edition):

Venkatraman, Anand. “Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families.” 2009. Web. 25 Jan 2021.

Vancouver:

Venkatraman A. Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-3112.

Council of Science Editors:

Venkatraman A. Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-3112

24. Adam, Panagiotis. Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean : La vie avant l’oxygène : une approche combinée entre phylogénomique et paléogeochimie pour décrypter la nature et le fonctionnement du microbiota de l’Archéen ancient.

Degree: Docteur es, Microbiologie. Evolution, 2018, Sorbonne Paris Cité

URL: http://www.theses.fr/2018USPCC153

► Les premières formes de vie sur Terre seraient apparues durant l’Archéen, il y a 4 à 2,5 milliards d’années. Durant cette période, les océans et… (more)

▼ Les premières formes de vie sur Terre seraient apparues durant l’Archéen, il y a 4 à 2,5 milliards d’années. Durant cette période, les océans et l’atmosphère étaient anoxiques. Vers la fin de cet éon, la concentration en dioxygène a brusquement augmenté grâce à la photosynthèse, contribuant à la Grande Oxygénation de la Terre. Toutefois, en raison de la rareté des microorganismes fossiles connus, les métabolismes actifs à cette époque restent mal compris. Le fractionnement des isotopes stables du carbone est souvent utilisé comme un critère de biogénicité et pour l’appréciation des voies métaboliques présentes. Ces fractionnements peuvent être le résultat d’au moins six à huit voies de fixation du carbone. Pour étudier l’histoire évolutive des voies de fixation du carbone et de déterminer leur ordre d’émergence, j’ai appliqué une approche phylogénomique sur l’importante diversité microbienne récemment découverte. Le but était d’identifier les voies responsables des signatures isotopiques du carbone datant de l’éon Archéen inférieur (>3,2 milliards d’années). Le premier chapitre constitue une revue récente sur la diversité, l’écologie et l’évolution des Archaea. J’ai construit une phylogénie de référence des Archaea, robuste et incluant un nombre important de nouveaux génomes. Cette phylogénie m’a permis de mettre en évidence de nouveaux clades d’Archaea pour lesquels j’ai proposé des nouveaux noms. De plus, j’ai examiné la distribution des gènes marqueurs classiquement utilisés dans la taxonomie des Archaea. Dans le chapitre 2, j’ai assemblé différents jeux de données pour construire des phylogénies de référence pour les bactéries. Ceci m’a permis de discuter la classification au sein de ce domaine et la position de quelques groupes proches de la racine. Ces phylogénies des Archaea et Bacteria m’ont servi de cadre pour retracer l’évolution des voies de fixation du carbone. J’ai ensuite étudié la voie de Wood-Ljungdahl (WL) qui est considérée comme la forme la plus ancienne de fixation du carbone mais dont les origines restent encore controversées. J’ai assemblé des banques de données locales englobant 6400 génomes et couvrant toute la diversité connue des archées et des bactéries. Ces banques ont été utilisées pour des recherches exhaustives des homologues des enzymes de la branche carbonyle (chapitre 3) et méthyle basée sur la tétrahydrométhanoptérine (H4MPT; chapitre 4) de la voie de WL. Ces analyses m’ont permis d’inférer la présence d’une forme fonctionnelle de la branche carbonyle chez LUCA (Last Universal Common Ancestor). Cette voie a ensuite été héritée verticalement chez les archées et bactéries en gardant la co-localisation de ses gènes, à l’exception de quelques rares transferts intra et inter-domaines. La branche méthyle-H4MPT semble être apparue chez les archées puis transférée aux bactéries chez lesquelles elle serait impliquée dans la syntrophie ou l’assimilation du carbone. A la suite de gains et de pertes de gènes au sein de cette branche, elle a ensuite été successivement adaptée pour la… Advisors/Committee Members: Gribaldo, Simonetta (thesis director).

Subjects/Keywords: Évolution; Phylogénomique; Fixation du carbone; Oxygène; Evolution; Phylogenomics; Carbon fixation; Oxygen

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

APA (6^th Edition):

Adam, P. (2018). Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean : La vie avant l’oxygène : une approche combinée entre phylogénomique et paléogeochimie pour décrypter la nature et le fonctionnement du microbiota de l’Archéen ancient. (Doctoral Dissertation). Sorbonne Paris Cité. Retrieved from http://www.theses.fr/2018USPCC153

Chicago Manual of Style (16^th Edition):

Adam, Panagiotis. “Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean : La vie avant l’oxygène : une approche combinée entre phylogénomique et paléogeochimie pour décrypter la nature et le fonctionnement du microbiota de l’Archéen ancient.” 2018. Doctoral Dissertation, Sorbonne Paris Cité. Accessed January 25, 2021. http://www.theses.fr/2018USPCC153.

MLA Handbook (7^th Edition):

Adam, Panagiotis. “Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean : La vie avant l’oxygène : une approche combinée entre phylogénomique et paléogeochimie pour décrypter la nature et le fonctionnement du microbiota de l’Archéen ancient.” 2018. Web. 25 Jan 2021.

Vancouver:

Adam P. Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean : La vie avant l’oxygène : une approche combinée entre phylogénomique et paléogeochimie pour décrypter la nature et le fonctionnement du microbiota de l’Archéen ancient. [Internet] [Doctoral dissertation]. Sorbonne Paris Cité; 2018. [cited 2021 Jan 25]. Available from: http://www.theses.fr/2018USPCC153.

Council of Science Editors:

Adam P. Life before oxygen : linking phylogenomics and paleogeochemistry to unravel the nature and function of microbiota in the early Archean : La vie avant l’oxygène : une approche combinée entre phylogénomique et paléogeochimie pour décrypter la nature et le fonctionnement du microbiota de l’Archéen ancient. [Doctoral Dissertation]. Sorbonne Paris Cité; 2018. Available from: http://www.theses.fr/2018USPCC153

25. Gonzalez, Vanessa Liz. Evolution of Bivalvia: Multi-level phylogenetic and phylogenomic reconstructions within Bivalvia (Mollusca) with emphasis on resolving familial relationships within Archiheterodonta (Bivalvia: Heterodonta).

Degree: PhD, Biology, Organismic and Evolutionary, 2013, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169800

► With an estimated 8,000-20,000 species, bivalves represent the second largest living class of molluscs (Bieler et al. 2013). Revived interest in molluscan phylogeny has resulted… (more)

Subjects/Keywords: Biology; Evolution & development; Zoology; Archiheterodonta; Bivalvia; Phylogenomics; Phylogeny; Systematics; Taxonomy

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APA (6^th Edition):

Gonzalez, V. L. (2013). Evolution of Bivalvia: Multi-level phylogenetic and phylogenomic reconstructions within Bivalvia (Mollusca) with emphasis on resolving familial relationships within Archiheterodonta (Bivalvia: Heterodonta). (Doctoral Dissertation). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169800

Chicago Manual of Style (16^th Edition):

Gonzalez, Vanessa Liz. “Evolution of Bivalvia: Multi-level phylogenetic and phylogenomic reconstructions within Bivalvia (Mollusca) with emphasis on resolving familial relationships within Archiheterodonta (Bivalvia: Heterodonta).” 2013. Doctoral Dissertation, Harvard University. Accessed January 25, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169800.

MLA Handbook (7^th Edition):

Gonzalez, Vanessa Liz. “Evolution of Bivalvia: Multi-level phylogenetic and phylogenomic reconstructions within Bivalvia (Mollusca) with emphasis on resolving familial relationships within Archiheterodonta (Bivalvia: Heterodonta).” 2013. Web. 25 Jan 2021.

Vancouver:

Gonzalez VL. Evolution of Bivalvia: Multi-level phylogenetic and phylogenomic reconstructions within Bivalvia (Mollusca) with emphasis on resolving familial relationships within Archiheterodonta (Bivalvia: Heterodonta). [Internet] [Doctoral dissertation]. Harvard University; 2013. [cited 2021 Jan 25]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169800.

Council of Science Editors:

Gonzalez VL. Evolution of Bivalvia: Multi-level phylogenetic and phylogenomic reconstructions within Bivalvia (Mollusca) with emphasis on resolving familial relationships within Archiheterodonta (Bivalvia: Heterodonta). [Doctoral Dissertation]. Harvard University; 2013. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11169800

26. Derkarabetian, Shahan. Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores).

Degree: Evolution, Ecology and Organismal Biology, 2017, University of California – Riverside

URL: http://www.escholarship.org/uc/item/2491j6ff

► My dissertation research utilizes next-generation sequencing (NGS) technology and associated bioinformatics processing to answer systematic and evolutionary questions in Opiliones (harvestmen) at different taxonomic scales,… (more)

▼ My dissertation research utilizes next-generation sequencing (NGS) technology and associated bioinformatics processing to answer systematic and evolutionary questions in Opiliones (harvestmen) at different taxonomic scales, focusing on the Laniatores superfamily Travunioidea and particularly the travunioid genus Sclerobunus. Opiliones are a diverse group of arachnids with over 6500 described species distributed on every continent except Antarctica. Despite relatively high diversity (e.g., more described species than mammals), harvestmen are poorly studied. This dissertation research has three main projects. The first chapter is a higher-level phylogenetics and taxonomic study of the Travunioidea, a clade of ~80 species of harvestmen distributed throughout the Holarctic. Here I utilized ultraconserved elements (UCE) for phylogenomic reconstruction using multiple types of phylogenetic reconstruction methods. Based on results, a new taxonomic classification is proposed for the Travunioidea, including the identification and diagnosis of a new family, and I reassess the phylogenetic utility of morphological characters used to differentiate and diagnose travunioid taxa. The second chapter focuses on species delimitation of the western North American travunioid genus Sclerobunus. I utilized modern integrative taxonomic methods, using both discovery-based and validation-based approaches by combining morphometrics, mitochondrial genetic data, genitalic morphology, and nuclear genetic data derived from newly developed genes based on a comparative transcriptomics approach. This research resulted in a revision of the genus including synonymy of the genus Cyptobunus, elevation of four subspecies, and the description of five new species. The third chapter is a phylogeographic analysis of Sclerobunus robustus, a species distributed throughout the southwestern United States. A hypothesis-based framework was adopted, where stable habitats (i.e., potential refugia) were identified through ecological niche modeling, and hypotheses regarding genetic patterns associated with these refugia were developed. Hypotheses were tested by using genetic data in the form of loci and SNPs derived from double-digest RAD sequencing methods. Two large refugial regions were identified and population genomic analyses supported the presence of both.

Subjects/Keywords: Biology; Systematic biology; integrative taxonomy; Opiliones; phylogenomics; population genomics; species delimitation

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APA (6^th Edition):

Derkarabetian, S. (2017). Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores). (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/2491j6ff

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):

Derkarabetian, Shahan. “Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores).” 2017. Thesis, University of California – Riverside. Accessed January 25, 2021. http://www.escholarship.org/uc/item/2491j6ff.

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

MLA Handbook (7^th Edition):

Derkarabetian, Shahan. “Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores).” 2017. Web. 25 Jan 2021.

Vancouver:

Derkarabetian S. Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores). [Internet] [Thesis]. University of California – Riverside; 2017. [cited 2021 Jan 25]. Available from: http://www.escholarship.org/uc/item/2491j6ff.

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

Council of Science Editors:

Derkarabetian S. Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores). [Thesis]. University of California – Riverside; 2017. Available from: http://www.escholarship.org/uc/item/2491j6ff

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

27. Bardon, Léa. Phylogénomique et histoire évolutive de deux familles de plantes à fleurs tropicales : Phylogenomics and evolutionary histories of two tropical flowering plant families.

Degree: Docteur es, Ecologie, biodiversité et évolution, 2015, Université Toulouse III – Paul Sabatier

URL: http://www.theses.fr/2015TOU30321

►

Les Néotropiques représentent un réservoir exceptionnel de biodiversité mais l'origine de cette diversité ainsi que les patrons de diversification in situ restent peu compris. La… (more)

Subjects/Keywords: Phylogénomique; Biogéographie; Diversification; Chrysobalanaceae; Humiriaceae; Phylogenomics; Biogeography; Diversification; Chrysobalanaceae; Hmiriaceae

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

APA (6^th Edition):

Bardon, L. (2015). Phylogénomique et histoire évolutive de deux familles de plantes à fleurs tropicales : Phylogenomics and evolutionary histories of two tropical flowering plant families. (Doctoral Dissertation). Université Toulouse III – Paul Sabatier. Retrieved from http://www.theses.fr/2015TOU30321

Chicago Manual of Style (16^th Edition):

Bardon, Léa. “Phylogénomique et histoire évolutive de deux familles de plantes à fleurs tropicales : Phylogenomics and evolutionary histories of two tropical flowering plant families.” 2015. Doctoral Dissertation, Université Toulouse III – Paul Sabatier. Accessed January 25, 2021. http://www.theses.fr/2015TOU30321.

MLA Handbook (7^th Edition):

Bardon, Léa. “Phylogénomique et histoire évolutive de deux familles de plantes à fleurs tropicales : Phylogenomics and evolutionary histories of two tropical flowering plant families.” 2015. Web. 25 Jan 2021.

Vancouver:

Bardon L. Phylogénomique et histoire évolutive de deux familles de plantes à fleurs tropicales : Phylogenomics and evolutionary histories of two tropical flowering plant families. [Internet] [Doctoral dissertation]. Université Toulouse III – Paul Sabatier; 2015. [cited 2021 Jan 25]. Available from: http://www.theses.fr/2015TOU30321.

Council of Science Editors:

Bardon L. Phylogénomique et histoire évolutive de deux familles de plantes à fleurs tropicales : Phylogenomics and evolutionary histories of two tropical flowering plant families. [Doctoral Dissertation]. Université Toulouse III – Paul Sabatier; 2015. Available from: http://www.theses.fr/2015TOU30321

28. Aouad, Monique. Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis : Étude phylogénomique de l'histoire évolutive des archées et de leur lien avec l'eucaryogenèse.

Degree: Docteur es, Biologie, 2018, Lyon

URL: http://www.theses.fr/2018LYSE1246

► L'explosion des données de séquençage a permis de résoudre la plupart des relations phylogénétiques chez les archées. Néanmoins, de nombreuses questions restent à résoudre à… (more)

▼ L'explosion des données de séquençage a permis de résoudre la plupart des relations phylogénétiques chez les archées. Néanmoins, de nombreuses questions restent à résoudre à l'échelle du domaine des archées et à l'échelle des trois domaines du vivant. Parmi elles, les relations phylogénétiques au sein du cluster II, notamment la position des archées halophiles extrêmes qui ont été placées à différentes positions dans l'arbre en fonction des marqueurs et des modèles de reconstruction utilisés, ainsi que la position de la racine des archées et la position des eucaryotes à la lumière des lignées d'archées nouvellement séquencées. Au cours de ma thèse, j'ai contribué à (i) affiner la phylogénie du domaine des Archaea en se concentrant sur les relations phylogénétiques au sein du cluster II, en particulier les positions des lignées halophiles extrêmes par rapport aux méthanogènes à travers des analyses dédiées à cette partie spécifique de l'arbre, et (ii) établir une phylogénie globale des archées afin de comprendre leur histoire évolutive ancienne et leur lien avec les eucaryotes à travers une analyse phylogénomique en deux étapes à l'échelle des trois domaines du vivant. D'abord, en utilisant des approches de génomique comparée sur 155 génomes complets appartenant aux Halobacteria, Nanohaloarchaea, méthanogènes de classe II, Archaeoglobales et Diaforarchaea, j'ai identifié 258 protéines portant un signal phylogénétique fiable pour étudier les relations de parente au sein du cluster II. En combinant différentes approches limitant l'impact du signal non phylogénétique sur l'inférence phylogénétique (comme la méthode Slow-Fast et le recodage des acides aminés), j'ai montré que les Nanohaloarchaea branchent avec les Methanocellales et les Halobacteria branchent avec les Methanomicrobiales. Ce jeu de données a ensuite été utilisé pour étudier la position d'une troisième lignée halophile extrême, les Methanonatronarchaeia, qui se positionnent entre les Archaeoglobales et les Diaforarchaea. Ces résultats suggèrent que l'adaptation à la salinité extrême serait apparue au moins trois fois de manière indépendante chez les archées et que les similitudes phénotypiques observées chez les Nanohaloarchaea, Halobacteria et Methanonatronarchaeia résulteraient d'une convergence évolutive, éventuellement accompagnée de transferts de gènes horizontaux. Enfin, ces résultats suggèrent que le groupement basal des Nanohaloarchaea avec d'autres lignées des DPANN serait la conséquence d'un artefact de reconstruction. Pour la deuxième partie de ma thèse, j'ai appliqué une stratégie consistant à analyser séparément les trois domaines du vivant considérés deux à deux, en mettant à jour 72 familles protéiques précédemment identifiées par Raymann et ses collègues (2015) pour inclure toutes les nouvelles lignées d'archées séquencées depuis la publication de cette étude comme les Asgard, les DPANN, les Stygia, les Acherontia, etc. Au total, mon échantillonnage taxonomique comprend 435 archées, 18 eucaryotes et 67 bactéries. Les résultats des analyses… Advisors/Committee Members: Brochier-Armanet, Céline (thesis director), Gouy, Manolo (thesis director).

Subjects/Keywords: Phylogénomique; Évolution; Archées; Eucaryogenèse; Phylogenomics; Evolution; Archaea; Eukaryogenesis; 570

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

APA (6^th Edition):

Aouad, M. (2018). Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis : Étude phylogénomique de l'histoire évolutive des archées et de leur lien avec l'eucaryogenèse. (Doctoral Dissertation). Lyon. Retrieved from http://www.theses.fr/2018LYSE1246

Chicago Manual of Style (16^th Edition):

Aouad, Monique. “Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis : Étude phylogénomique de l'histoire évolutive des archées et de leur lien avec l'eucaryogenèse.” 2018. Doctoral Dissertation, Lyon. Accessed January 25, 2021. http://www.theses.fr/2018LYSE1246.

MLA Handbook (7^th Edition):

Aouad, Monique. “Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis : Étude phylogénomique de l'histoire évolutive des archées et de leur lien avec l'eucaryogenèse.” 2018. Web. 25 Jan 2021.

Vancouver:

Aouad M. Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis : Étude phylogénomique de l'histoire évolutive des archées et de leur lien avec l'eucaryogenèse. [Internet] [Doctoral dissertation]. Lyon; 2018. [cited 2021 Jan 25]. Available from: http://www.theses.fr/2018LYSE1246.

Council of Science Editors:

Aouad M. Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis : Étude phylogénomique de l'histoire évolutive des archées et de leur lien avec l'eucaryogenèse. [Doctoral Dissertation]. Lyon; 2018. Available from: http://www.theses.fr/2018LYSE1246

University of Vermont

29. Romano, Joseph D. Exploring Complex Disease Gene Relationships Using Simultaneous Analysis.

Degree: Microbiology and Molecular Genetics, 2014, University of Vermont

URL: https://scholarworks.uvm.edu/hcoltheses/35

► The characterization of complex diseases remains a great challenge for biomedical researchers due to the myriad interactions of genetic and environmental factors. Adaptation of… (more)

Subjects/Keywords: Translational Bioinformatics; Comparative Genomics; Computational Biology; Bioinformatics; Alzheimer Disease; Phylogenomics

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

APA (6^th Edition):

Romano, J. D. (2014). Exploring Complex Disease Gene Relationships Using Simultaneous Analysis. (Thesis). University of Vermont. Retrieved from https://scholarworks.uvm.edu/hcoltheses/35

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):

Romano, Joseph D. “Exploring Complex Disease Gene Relationships Using Simultaneous Analysis.” 2014. Thesis, University of Vermont. Accessed January 25, 2021. https://scholarworks.uvm.edu/hcoltheses/35.

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

MLA Handbook (7^th Edition):

Romano, Joseph D. “Exploring Complex Disease Gene Relationships Using Simultaneous Analysis.” 2014. Web. 25 Jan 2021.

Vancouver:

Romano JD. Exploring Complex Disease Gene Relationships Using Simultaneous Analysis. [Internet] [Thesis]. University of Vermont; 2014. [cited 2021 Jan 25]. Available from: https://scholarworks.uvm.edu/hcoltheses/35.

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

Council of Science Editors:

Romano JD. Exploring Complex Disease Gene Relationships Using Simultaneous Analysis. [Thesis]. University of Vermont; 2014. Available from: https://scholarworks.uvm.edu/hcoltheses/35

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

Australian National University

30. 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 January 25, 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. 25 Jan 2021.

Vancouver:

Blom M. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . [Internet] [Thesis]. Australian National University; 2016. [cited 2021 Jan 25]. 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

Open Access Theses and Dissertations