subject:(nuclear introns)

Brigham Young University

1. Benavides, Edgar. Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal.

Degree: PhD, 2006, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd

► In this collection of papers I have summarized my investigations into the field of evolutionary genetics and more specifically into patterns of biodiversity and… (more)

▼ In this collection of papers I have summarized my investigations into the field of evolutionary genetics and more specifically into patterns of biodiversity and evolutionary processes. The lizards (and frogs) studied here share common features in that they are largely present in unique environments, which are also regions that are biologically understudied. Most of these taxa show high degrees of endemism, interesting natural history characteristics, and each group manifests distinctive adaptations of general evolutionary interest. My work in the genus Telmatobius has been a progressive approach that began in my MS program, and it first focused on alpha taxonomy, morphological variation, and species boundaries. This work led to new studies initiated and completed at BYU involving further taxonomic revision (Formas et al., 2003; Chapter 1), and then revisiting and re-evaluating species boundaries established earlier (with allozyme markers) and this time with population level molecular (mitochondrial DNA) markers (Chapter 2). Our results indicate that the striking differences in size, coloration and general appearance in the various Lake Titicaca morphotypes are not genetically based. Further, there is evidence that these morphotypes have evolved very rapidly after demographic bottlenecks eroded present genetic variability. Telmatobius frogs of Lake Titicaca are listed by the International (IUCN) as critically endangered. We support this classification and further suggest studies to explore open questions like the possibility of adaptation along ecological resource gradients. Lizards of the genus Microlophus are interesting but for different reasons, and studies of this group constitutes the bulk of my dissertation work. The genus includes both Galapagos insular species, and continental taxa distributed in a linear gradient along > 4000 km of the western coast of South America. In studying Microlophus I first tackled the unresolved phylogenetic relationships within the genus (Chapter 3) and then pay attention to phylogeographic aspects of the most speciose lizard radiation in the Galapagos Archipelago (Chapter 4). Chapter 3 is a single manuscript provisionally accepted in the journal Systematic Biology. This paper introduces the lizard genus Microlophus (“lava lizards”) as a study system, and includes a large nuclear data set accompanied by an equally large mitochondrial data set (7877 characters in total). This paper explicitly differentiates among sequence alignments of gene regions that vary in tempo and class of mutational events. We show that this recognition is important and we suggest ways to appropriately deal with the alignment of multi-locus non-coding DNA data sets. A secondary finding in this study is that mtDNA and nDNA topologies are discordant with each other but that both are strongly supported, and that the nuclear topology is concordant with species distribution patterns along coastal South America. We hypothesize that in this particular region of the tree, the nuclear genome recovers a topology…

Subjects/Keywords: nuclear introns; alignment; length mutations; Microlophus; secondary contact; mitochondrial-nuclear conflict; phylogenetics; Galapagos; mtDNA; phylogeography; nested clade analysis; colonization routes; volcanism; lava lizards; Biology

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

APA (6^th Edition):

Benavides, E. (2006). Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal. (Doctoral Dissertation). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd

Chicago Manual of Style (16^th Edition):

Benavides, Edgar. “Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal.” 2006. Doctoral Dissertation, Brigham Young University. Accessed March 05, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd.

MLA Handbook (7^th Edition):

Benavides, Edgar. “Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal.” 2006. Web. 05 Mar 2021.

Vancouver:

Benavides E. Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal. [Internet] [Doctoral dissertation]. Brigham Young University; 2006. [cited 2021 Mar 05]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd.

Council of Science Editors:

Benavides E. Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal. [Doctoral Dissertation]. Brigham Young University; 2006. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd

2. Lian, Qian. Characterization and putative functional role of a stable intron from the T cell receptor gene.

Degree: PhD, 1993, Oregon Health Sciences University

URL: doi:10.6083/M457198G ; http://digitalcommons.ohsu.edu/etd/2847

Subjects/Keywords: Gene Rearrangement, T-Lymphocyte; Introns; RNA Splicing; RNA, Nuclear

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

APA (6^th Edition):

Lian, Q. (1993). Characterization and putative functional role of a stable intron from the T cell receptor gene. (Doctoral Dissertation). Oregon Health Sciences University. Retrieved from doi:10.6083/M457198G ; http://digitalcommons.ohsu.edu/etd/2847

Chicago Manual of Style (16^th Edition):

Lian, Qian. “Characterization and putative functional role of a stable intron from the T cell receptor gene.” 1993. Doctoral Dissertation, Oregon Health Sciences University. Accessed March 05, 2021. doi:10.6083/M457198G ; http://digitalcommons.ohsu.edu/etd/2847.

MLA Handbook (7^th Edition):

Lian, Qian. “Characterization and putative functional role of a stable intron from the T cell receptor gene.” 1993. Web. 05 Mar 2021.

Vancouver:

Lian Q. Characterization and putative functional role of a stable intron from the T cell receptor gene. [Internet] [Doctoral dissertation]. Oregon Health Sciences University; 1993. [cited 2021 Mar 05]. Available from: doi:10.6083/M457198G ; http://digitalcommons.ohsu.edu/etd/2847.

Council of Science Editors:

Lian Q. Characterization and putative functional role of a stable intron from the T cell receptor gene. [Doctoral Dissertation]. Oregon Health Sciences University; 1993. Available from: doi:10.6083/M457198G ; http://digitalcommons.ohsu.edu/etd/2847

University of Florida

3. Hector, Ronald Earl, 1972-. Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein.

Degree: 2000, University of Florida

URL: https://ufdc.ufl.edu/AA00038398

Subjects/Keywords: Heterogeneous nuclear ribonucleoproteins; In vitro fertilization; Introns; Messenger RNA; Nucleotides; Polyadenylation; RNA; Small nucleolar RNA; Splicing; Yeasts; Department of Molecular Genetics and Microbiology thesis Ph.D ( mesh ); Gene Expression Regulation ( mesh ); Genetic Techniques ( mesh ); Nuclear Proteins ( mesh ); RNA Precursors ( mesh ); RNA, Messenger ( mesh ); RNA-Binding Proteins ( mesh ); Research ( mesh ); City of Gainesville ( local )

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

APA (6^th Edition):

Hector, Ronald Earl, 1. (2000). Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00038398

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):

Hector, Ronald Earl, 1972-. “Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein.” 2000. Thesis, University of Florida. Accessed March 05, 2021. https://ufdc.ufl.edu/AA00038398.

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

MLA Handbook (7^th Edition):

Hector, Ronald Earl, 1972-. “Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein.” 2000. Web. 05 Mar 2021.

Vancouver:

Hector, Ronald Earl 1. Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein. [Internet] [Thesis]. University of Florida; 2000. [cited 2021 Mar 05]. Available from: https://ufdc.ufl.edu/AA00038398.

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

Council of Science Editors:

Hector, Ronald Earl 1. Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein. [Thesis]. University of Florida; 2000. Available from: https://ufdc.ufl.edu/AA00038398

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

University of New Orleans

4. Vogel, Laura Sanders. The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies.

Degree: PhD, Biological Sciences, 2007, University of New Orleans

URL: https://scholarworks.uno.edu/td/579

► Two of the most pervasive threats to species biodiversity are invasive species and habitat loss and degradation. Invasive species are often relatively insensitive to disturbance… (more)

▼ Two of the most pervasive threats to species biodiversity are invasive species and habitat loss and degradation. Invasive species are often relatively insensitive to disturbance and many expand their range into disturbed and fragmented habitats. This dissertation uses an interdisciplinary approach to investigate how anthropogenic habitat disturbance is precipitating a range expansion in an invasive toad species, Bufo nebulifer, which is driving a decline in its native congener, B. fowleri. I employed a remote sensing and GIS study using historical data to compare changes in the two species distributions and habitat changes, a molecular genetic study to identify interspecific hybrids and their potential effects on the parental species, and an experimental ecology study to look at the effects of competition and predation on the two species. The results of the landscape level analyses of species' distributional changes in different disturbance levels showed that both species' distributions have changed significantly. The distributions of the two species are inversely affected by habitat disturbance; the distribution of B. fowleri in highly degraded habitat has contracted while the expansion of B. nebulifer increased substantially. The molecular genetic study successfully demonstrated the use of nuclear and mitochondrial markers to identify cryptic hybrids and their maternal lineage. Three hybrids were detected using nuclear introns and a morphologically cryptic hybrid was identified using mitochondrial DNA as the progeny of a cross that was previously thought to be inviable. Although relatively few hybrids were currently found, the identification of a cryptic hybrid implies that the rate of historical hybridization may have been drastically underestimated. Ecological studies showed that competition with B. nebulifer tadpoles had a negative effect on both body size measures and survival to metamorphosis for B. fowleri tadpoles. The addition of predators to experiment did not favor the survival of B. fowleri over B. nebulifer. Bufo fowleri's inability to compete with its invasive congener could be a driving mechanism for the decline of B. fowleri and the expansion of B. nebulifer. The methods discussed in this dissertation offer promising and practical new approaches for evaluating and managing changes in the distribution of species of conservation concern. Advisors/Committee Members: Johnson, Steven, Kandl, Karen, Clancy, Mary.

Subjects/Keywords: Bufo fowleri; Bufo nebulifer; invasive species; hybrids; ranges; nuclear DNA; introns; SNPs; mtDNA; remote sensing; GIS; museum data; competition; predation; disturbance

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

APA (6^th Edition):

Vogel, L. S. (2007). The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies. (Doctoral Dissertation). University of New Orleans. Retrieved from https://scholarworks.uno.edu/td/579

Chicago Manual of Style (16^th Edition):

Vogel, Laura Sanders. “The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies.” 2007. Doctoral Dissertation, University of New Orleans. Accessed March 05, 2021. https://scholarworks.uno.edu/td/579.

MLA Handbook (7^th Edition):

Vogel, Laura Sanders. “The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies.” 2007. Web. 05 Mar 2021.

Vancouver:

Vogel LS. The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies. [Internet] [Doctoral dissertation]. University of New Orleans; 2007. [cited 2021 Mar 05]. Available from: https://scholarworks.uno.edu/td/579.

Council of Science Editors:

Vogel LS. The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies. [Doctoral Dissertation]. University of New Orleans; 2007. Available from: https://scholarworks.uno.edu/td/579

5. Schwenke, Piper. History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger).

Degree: 2013, University of Washington

URL: http://hdl.handle.net/1773/21967

► Natural hybridization is common in closely related species especially where they invade novel habitat. The patterns of introgressive hybridization are often asymmetrical and are attributed… (more)

Subjects/Keywords: coalescence; introgression; mitochondria; nuclear introns; phylogenetics; sequence; Fisheries and aquatic sciences; Molecular biology; Fisheries

…to compare gene trees from mitochondrial and several independent nuclear genetic loci (… …to evolve to species monophyly faster than diploid biparentally inherited nuclear loci… …x28;Palumbi 2001). Monophyly at nuclear loci genealogies and shared polymorphisms at… …more susceptible to introgressive hybridization than nuclear loci (Rieseberg and Soltis… …sequence data and diploid nuclear data for each species group and locus were phased into…

10 more images…

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

APA (6^th Edition):

Schwenke, P. (2013). History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger). (Thesis). University of Washington. Retrieved from http://hdl.handle.net/1773/21967

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):

Schwenke, Piper. “History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger).” 2013. Thesis, University of Washington. Accessed March 05, 2021. http://hdl.handle.net/1773/21967.

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

MLA Handbook (7^th Edition):

Schwenke, Piper. “History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger).” 2013. Web. 05 Mar 2021.

Vancouver:

Schwenke P. History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger). [Internet] [Thesis]. University of Washington; 2013. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1773/21967.

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

Council of Science Editors:

Schwenke P. History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger). [Thesis]. University of Washington; 2013. Available from: http://hdl.handle.net/1773/21967

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

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