Life Sciences Commons^™

Phylogeography Of An Estuarian Calanoid Copepod; Acartia Tonsa In The Texas Gulf Of Mexico, Nicole J. Figueroa

Theses and Dissertations

The calanoid copepod, Acartia tonsa is one of the most abundant and well-studied estuarian species. However, the idea that this cosmopolitan species has unrestricted dispersal and high gene flow has been challenged. In this study, a more holistic picture of the phylogeography of A. tonsa was developed using the mitochondrial gene cytochrome oxidase one (mtCOI). Multiple new lineages were found in the Texas Gulf of Mexico that are basal to Northeastern Atlantic lineages. Connectivity was also observed between Brazil and the Texas Gulf of Mexico. The revised phylogeny shows a clear pattern of cryptic speciation as the species made a …

Climate-Driven Habitat Shifts In South America: Biogeography, Historical Demography, And Population Genomics Of Anole Lizards, Ivan Prates

Dissertations, Theses, and Capstone Projects

Shifts in the geographic distribution of habitats over time can promote dispersal and vicariance, thereby influencing large-scale biogeographic patterns and ecological processes. The establishment of corridors of suitable habitat across previously disjunct yet ecologically similar regions has been widely linked to climate change over time. Such climate-mediated habitat changes may have played a key role in the assembly of tropical biotas, including those of Amazonia and the coastal Atlantic Forest in South America, two of the most diverse ecosystems on Earth. The history of biogeographic associations between tropical rainforest habitats in response to former climatic shifts, as well as their …

Phylogeography And Population Dynamics Of North American Wolverines (Gulo Gulo Luscus) In Alaska And Western Canada, Dianna Krejsa

Biology ETDs

The circumboreal wolverine (Gulo gulo sp.) is ideal for studying responses to environmental perturbation in the North due to a history of persistence in glacial refugia and subsequent glacial recolonization. Wolverines are also excellent indicators of human influence on the environment due to their close association with remote areas and cold, snowy climes. Through the use of genetic tools (i.e., nuclear microsatellite loci and mitochondrial sequences), I examined population structure of wolverines in Alaska and western Canada to identify signatures of glacial refugia, bottlenecks, and distinctive populations, sex-biased dispersal, gene flow, and source and sink population dynamics. I identified genetic …

Geographic Strain Differentiation Of Schistosoma Japonicum In The Philippines Using Microsatellite Markers, Kharleezelle J. Moendeg

Biology Faculty Publications

Background

Microsatellites have been found to be useful in determining genetic diversities of various medically-important parasites which can be used as basis for an effective disease management and control program. In Asia and Africa, the identification of different geographical strains of Schistosoma japonicum, S. haematobium and S. mansoni as determined through microsatellites could pave the way for a better understanding of the transmission epidemiology of the parasite. Thus, the present study aims to apply microsatellite markers in analyzing the populations of S. japonicum from different endemic areas in the Philippines for possible strain differentiation.

Methodology/ Principal …

An Efficient Pipeline For Assaying Whole-Genome Plastid Variation For Population Genetics And Phylogeography, Brendan F. Kohrn

Dissertations and Theses

Tracking seed dispersal using traditional, direct measurement approaches is difficult and generally underestimates dispersal distances. Variation in chloroplast haplotypes (cpDNA) offers a way to trace past seed dispersal and to make inferences about factors contributing to present patterns of dispersal. Although cpDNA generally has low levels of intraspecific variation, this can be overcome by assaying the whole chloroplast genome. Whole-genome sequencing is more expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among SNPs are lost in pooled samples and treating SNP frequencies as independent estimates of variation provides biased estimates of genetic distance. I have developed …

The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter

Electronic Theses, Projects, and Dissertations

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency …

Molecular Evolution And Phylogeography Of Mitochondrial Dna Cytochrome B Gene In Southern California Santa Ana Speckled Dace (Rhinichthys Osculus), Pia Marie Vanmeter

Electronic Theses, Projects, and Dissertations

In this study, I sequenced the mitochondrial cytochrome b gene to elucidate the extent and pattern of genetic variations among and within populations of Rhinichthys osculus (Santa Ana Speckled Dace) found in the different watersheds in Southern California, Central California Coast and Eastern California Desert. I described and analyzed the structural characteristics and pattern of base sequence substitutions in the cytochrome b gene to understand the molecular evolution of the gene. The Phylogenetic analyses showed that the Southern California Santa Ana Speckled dace is a distinct population from the Central California Coast dace population and Eastern California Desert dace population, …

A Longitudinal Cline Characterizes The Genetic Structure Of Human Populations In The Tibetan Plateau, Choongwon Jeong, Benjamin M. Peter, Buddha Basnyat, Maniraj Neupane, Geoff Childs, Sienna Craig, John Novembre, Anna Di Rienzo

Dartmouth Scholarship

Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their de- mography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with world- wide genetic variation data. We found a clear signal of genetic stratification across the east- west axis within Tibetan samples. Samples from more eastern locations …

A Phylogenetic And Environmental Analysis Of Brazilian Placosoma Lizards, Kai A. Farje-Van Vlack

Dissertations and Theses

Placosoma is a genus comprised of the Brazilian spectacled lizards P. champsonotus, P. cipoense, P. cordylinum, P. glabellum, and P. limaverdorum. While P. champsonotus, P. cordylinum, and P. glabellum occupy the southern coast of Brazil, P. cipoense is found in the montane grasslands north of that range, and P. limaverdorum was recently discovered in forest isolates that persist within the semi-arid Caatinga. This study elucidates the ecological and evolutionary relationships among these morphologically similar lizards. Using mitochondrial and nuclear gene sequences, genus-wide phylogenies were inferred through Bayesian inference and a species tree approach, …

Historical Refuges And Recolonization Routes In The Southern Appalachian Mountains, Inferred Through Phylogeographic Analysis Of The Spotted Wintergreen (Chimaphila Maculata), John Daniel Banusiewicz

Electronic Theses and Dissertations

Phylogeography has recently benefited from incorporation of coalescent modeling to test competing scenarios of population history of a species. Ecological niche modeling has also been useful in inferring areas of likely suitable habitat during past climate conditions. Several studies have examined the population history of biota in the Southern Appalachian Mountains and how they responded to climate change associated with the end of the Last Glacial Maximum (~18,000 years ago), though few studies have focused on understory plants. This study redressed that knowledge gap thorough examination of the phylogeographic history of the understory plant Chimaphila maculata, which is native to …

Mitochondrial Genetic Diversity And Structuring Of Northernwhite-Breasted Hedgehogs From The Central Balkans, Mihajla Djan, Milomir Stefanovic, Nevena Velickovic, Nada Cosic, Dusko Cirovic

Turkish Journal of Zoology

Even though the phylogeography of hedgehogs has been well studied, information on the genetic variability of the northern white-breasted hedgehog Erinaceus roumanicus from the Balkans is lacking, since the previous studies were based on very limited sampling across the Balkans. The aim of this study is to estimate the genetic diversity and population structuring of E. roumanicus from the Central Balkans and to complement an already proposed phylogeographic scenario of this species. Tissue samples of 108 road-killed northern white-breasted hedgehogs were collected across the Central Balkan countries of Serbia, Montenegro, Bosnia and Herzegovina, and Macedonia. A partial fragment of the …

High Genetic Distinctiveness Of Wild And Farm Fox (Vulpes Vulpes L.)Populations In Poland: Evidence From Mitochondrial Dna Analysis, Beata Horecka, Kornel Kasperek, Grazyna Jezewska-Witkowska, Brygida Slaska, Iwona Rozempolska-Rucinska, Magdalena Gryzinska, Andrzej Jakubczak

Turkish Journal of Zoology

In Poland, the number of wild red foxes (Vulpes vulpes L.) and the size of the fur-farming industry are growing. There is concern that the gene pool of the wild foxes is being infiltrated by that of the farm animals. We analyzed three groups-Polish farm foxes and wild-living animals from Poland and North America-to investigate the gene flow or introgression between farm and wild red foxes. We took into account the breeding history of the species and the evolutionary relationships between fox populations on different continents. We compared the haplotypes based on the concatenated nucleotide sequences of MT-CO1 (mitochondrially encoded …

Mitochondrial Evidence Indicates A Shallow Phylogeographic Structurefor Jaculus Blanfordi (Murray, 1884) Populations (Rodentia: Dipodidae), Ekaterina Melnikova, Morteza Naderi

Turkish Journal of Zoology

Our study was performed on the phylogeographic structure of Blanford's jerboa (Jaculus blanfordi (Murray, 1884)) collected from nine localities in Iran, Turkmenistan, and Uzbekistan and was based on mitochondrial evidence indicating a slight phylogeographic divergence among the populations. We aimed to amplify two frequently used mitochondrial markers, cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) fragments, from 33 specimens obtained from the abovementioned countries. Our phylogeographic analyses uncovered two distinct groups, thus supporting the presence of two subspecies: J. b. blanfordi in Iran and J. b. turcmenicus in northern Turkmenistan and Uzbekistan. Finally, we discuss the intraspecies …

Evolutionary History Of A Large-Genome Salamander Across Five Disjunct Regions Of The Southeastern United States, Catherine Elizabeth Newman

LSU Doctoral Dissertations

The southeastern United States has a dynamic geologic history. Mountain range uplift, sea level fluctuations, and river basin evolution have shaped species geographic distributions in the region. My dissertation objectively identifies amphibian species with highly fragmented distributions in the Southeast (Chapter 2) and examines the phylogeographic history of one of those species, Plethodon serratus. This salamander species has a widely disjunct range across five regions: the Appalachians, the Ozarks, the Ouachitas, and two allopatric sites in Louisiana. Analyses of mitochondrial and nuclear loci (Chapter 3) showed that P. serratus is comprised of multiple genetic lineages, and the five regions are …