Current Search: phylogeography (x)
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- Title
- BIOGEOGRAPHY AND DIVERSIFICATION IN THE NEOTROPICS: TESTING MACROEVOLUTIONARY HYPOTHESES USING MOLECULAR PHYLOGENETIC DATA.
- Creator
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Daza Rojas, Juan Manuel, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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Lineage diversification in the Neotropics is an interesting topic in evolutionary biology and one of the least understood. The complexity of the region precludes generalizations regarding the historical and evolutionary processes responsible for the observed high diversity. Here, I use molecular data to infer evolutionary relationships and test hypotheses of current taxonomy, species boundaries, speciation and biogeographic history in several lineages of Neotropical snakes. I comprehensively...
Show moreLineage diversification in the Neotropics is an interesting topic in evolutionary biology and one of the least understood. The complexity of the region precludes generalizations regarding the historical and evolutionary processes responsible for the observed high diversity. Here, I use molecular data to infer evolutionary relationships and test hypotheses of current taxonomy, species boundaries, speciation and biogeographic history in several lineages of Neotropical snakes. I comprehensively sampled a widely distributed Neotropical colubrid snake and Middle American pitvipers and combined my data with published sequences. Within the colubrid genus Leptodeira, mitochondrial and nuclear markers revealed a phylogeograhic structure that disagrees with the taxonomy based only on morphology. Instead, the phylogenetic structure corresponds to specific biogeographic regions within the Neotropics. Molecular evidence combined with explicit divergence time estimates reject the hypothesis that highland pitvipers in Middle America originated during the climatic changes during the Pleistocene. My data, instead, shows that pitviper diversification occurred mainly during the Miocene, a period of active orogenic activity. Using multiple lineages of Neotropical snakes in a single phylogenetic tree, I describe how the closure of the Isthmus of Panama generated several episodes of diversification as opposed to the Motagua-Polochic fault in Guatemala where a single vicariant event may have led to diversification of snakes with different ecological requirements. This finding has implications for future biogeographic studies in the region as explicit temporal information can be readily incorporated in molecular clock analyses. Bridging the gap between the traditional goals of historical biogeography (i.e., area relationships) with robust statistical methods, my research can be applied to multiple levels of the biological hierarchy (i.e., above species level), other regional systems and other sub-disciplines in biology such as medical research, evolutionary ecology, taxonomy and conservation.
Show less - Date Issued
- 2010
- Identifier
- CFE0003101, ucf:48328
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003101
- Title
- Conservation and population biology: genetics, demography and habitat requirements of the Atlantic coast beach mice.
- Creator
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Kalkvik, Haakon, Parkinson, Christopher, Stout, I, Hoffman, Eric, Weishampel, John, Doonan, Terry, University of Central Florida
- Abstract / Description
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The conservation biology field seeks to preserve biodiversity and the processes shaping that variation. Conservation biology is intimately tied to evolutionary research, in order to identify evolutionary distinct lineages that may be in danger of disappearing. Interestingly, patterns and processes of lineage divergence and persistence change with respect to spatial and temporal scale. I seek to evaluate biodiversity, the factors that have shaped this heterogeneity, and how this variability...
Show moreThe conservation biology field seeks to preserve biodiversity and the processes shaping that variation. Conservation biology is intimately tied to evolutionary research, in order to identify evolutionary distinct lineages that may be in danger of disappearing. Interestingly, patterns and processes of lineage divergence and persistence change with respect to spatial and temporal scale. I seek to evaluate biodiversity, the factors that have shaped this heterogeneity, and how this variability persists. To accomplish this I used a phylogeographic approach as well as niche and population modeling on the Peromyscus maniculatus species group found widely distributed in North America. My emphasis was on the southeastern U.S. species P. polionotus and its distinct beach forms. At a continental scale, I found that environmental niches are likely involved in generating and/or maintaining genetic lineages within the P. maniculatus species group. These findings add to a growing number of studies that have identified lineages occupying different environmental spaces. At a regional scale, I supported the hypothesis that barrier islands on the Atlantic coast of Florida were colonized by an ancestral form of P. polionotus by a single colonization, from the central Florida area. Subsequently, at least two distinct lineages diverged (P. p. phasma and P. p. niveiventris). I also found evidence that suggests that the extinct form of beach mouse (P. p. decoloratus) is part of the P. p. phasma lineage. At the population level, I evaluated changes in genetic diversity in historical samples compared to those that experienced recent human encroachment on natural habitat I used tissue preserved in natural history collections to compare with live-trapped specimens, and found that P. p. niveiventris has maintained historical genetic diversity levels. I suggest that the continuation of historical levels of genetic diversity is due to the presence of a single large area of continuous habitat in the central portion of the species' current distribution. Finally, I evaluated the importance of scrub and beach habitat to the population dynamics of beach mice. Beach mice have traditionally have been associated with beach dunes rather than with the scrub habitat found more inland on barrier islands. Using almost three years of capture-recapture data from Cape Canaveral Air Force Station (CCAFS), I created a stochastic matrix model to assess the relative contribution of populations from the two different habitats to a variety of demographic measures. Both field data and model results provided evidence that the population dynamics of beach mice may rely much more on scrub habitat than formerly documented. Overall, my research emphasized a hierarchical approach to evaluate biodiversity and the processes shaping differentiation at different spatial and temporal scales. The methods and findings give insight into speciation at different scales, and can be applied to a wide range of taxa for questions related to evolutionary and conservation biology.
Show less - Date Issued
- 2012
- Identifier
- CFE0004392, ucf:49372
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004392
- Title
- TAXONOMY VERSUS PHYLOGENY: PHYLOGEOGRAPHY OF MARSH RABBITS WITHOUT HOPPING TO CONCLUSIONS.
- Creator
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Tursi, Rosanna, Hoffman, Eric, University of Central Florida
- Abstract / Description
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Subspecific taxonomic designations solely based on morphological characters can often lead to erroneous assumptions about the evolutionary history of populations. This study sought to investigate evolutionary questions and conservation implications associated with morphological subspecific designations of island populations. To this end, I focused my attention on the Lower Keys of Florida, a unique chain of islands with well-known geologic history and rich in endemic, endangered subspecies. I...
Show moreSubspecific taxonomic designations solely based on morphological characters can often lead to erroneous assumptions about the evolutionary history of populations. This study sought to investigate evolutionary questions and conservation implications associated with morphological subspecific designations of island populations. To this end, I focused my attention on the Lower Keys of Florida, a unique chain of islands with well-known geologic history and rich in endemic, endangered subspecies. I employed genetic analyses to evaluate historical variation and contemporary restriction of gene flow between the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) and its sister mainland taxa. A Bayesian phylogeny using 1063 base pairs of the mitochondrial cytochrome b gene did not recover reciprocal monophyly of the three named subspecies, and a 95% statistical parsimony haplotype network showed haplotypes being shared among subspecies. Furthermore, clustering analyses using 10 microsatellite loci identified a break within the Lower Keys, separating the western Lower Keys from the island of Big Pine Key. Surprisingly, Big Pine Key grouped with mainland populations and exhibits higher genetic diversity than the western Lower Keys islands. These unexpected findings suggest either a stepping-stone colonization pattern or recent gene flow between the mainland and Big Pine Key via natural dispersal or undocumented man-mediated transfers. Although these results suggest that subspecies designations within S. palustris are unwarranted, this study supports the designation western Lower Keys population as a discrete unit of conservation with regard to both DPS and ESU criteria. The importance of using several lines of evidence to uncover the evolutionary history of populations and implications for the conservation of island populations are discussed.
Show less - Date Issued
- 2010
- Identifier
- CFE0003418, ucf:48380
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003418
- Title
- Go with the flow: patterns of connectivity in low dispersal coral reef gobies (Coryphopterus spp.) throughout the western Atlantic.
- Creator
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Volk, Daniel, Hoffman, Eric, Ferreira, Carlos, Cook, Geoffrey, University of Central Florida
- Abstract / Description
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Gene flow is an integral biological process that can mediate speciation. While many consider the ocean to be an open environment, there are many barriers that limit gene flow, particularly in the western Atlantic. I analyzed data from two widespread, coral reef fishes, the bridled goby (Coryphopterus glaucofraenum) and sand-canyon goby (C. venezuelae), throughout their range in the western Atlantic. Using two genetic datasets, mitochondrial DNA (mtDNA) and genomic SNPs, I investigated the...
Show moreGene flow is an integral biological process that can mediate speciation. While many consider the ocean to be an open environment, there are many barriers that limit gene flow, particularly in the western Atlantic. I analyzed data from two widespread, coral reef fishes, the bridled goby (Coryphopterus glaucofraenum) and sand-canyon goby (C. venezuelae), throughout their range in the western Atlantic. Using two genetic datasets, mitochondrial DNA (mtDNA) and genomic SNPs, I investigated the evolutionary history of these species and inferred the location and strength of putative barriers. My results suggest that several unique lineages have genetically diverged from one another in the presence of two major barriers. First, the Amazon River has isolated Brazil from the Caribbean and second, a unique lineage was found at an isolated oceanic island, Atol das Rocas, off the northeast coast of Brazil. Furthermore, minor barriers have caused slight genetic differentiation in each of the Caribbean species off the coast of Venezuela, while on the Brazilian coast, there are up to two barriers that separate three genetically unique areas. The stronger of the two barriers is located at Cabo Frio near an upwelling system and the weaker barrier coincides with the outflow of the S(&)#227;o Francisco River. Overall, this research highlights how barriers impact speciation and genetic structure within these gobies in the western Atlantic and more broadly, deepens our understanding about the role of oceanographic features in the speciation process.
Show less - Date Issued
- 2017
- Identifier
- CFE0006924, ucf:51690
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006924
- Title
- Biogeography and systematics of the Nerodia clarkii/Nerodia fasciata clade in Florida.
- Creator
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Territo, Gregory, Parkinson, Christopher, Hoffman, Eric, Fauth, John, University of Central Florida
- Abstract / Description
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Biogeography provides a window into the evolutionary history of populations, and helps explain the diversity and distribution of life through time. Viewed from a systematic perspective, biogeographic studies generate convincing arguments to explain the relationships among organisms and categorize them into useful taxonomies. When taxonomies do not reflect evolutionary histories, inaccurate representations of biodiversity confound future studies and conservation efforts. Two thamnophiine...
Show moreBiogeography provides a window into the evolutionary history of populations, and helps explain the diversity and distribution of life through time. Viewed from a systematic perspective, biogeographic studies generate convincing arguments to explain the relationships among organisms and categorize them into useful taxonomies. When taxonomies do not reflect evolutionary histories, inaccurate representations of biodiversity confound future studies and conservation efforts. Two thamnophiine snakes, Nerodia clarkii and Nerodia fasciata, harbor unique morphological and ecological adaptations that obscured natural groupings, leading to controversial taxonomic delimitations. Additionally, population declines documented in N. clarkii compressicauda and N. clarkii taeniata led managers to list N. clarkii taeniata as threatened in 1977. I generated a baseline for continued biogeographic and systematic study of the Nerodia clarkii/fasciata clade. I used mitochondrial DNA to build a parsimony-based haplotype network, infer the phylogenetic relationships between the two species and their thamnophiine relatives, and estimate the divergence times of major N. clarkii/fasciata clades. With these data, I tested biogeographic and systematic hypotheses about the origin and distribution of diversity in this clade. I used principal components analyses to summarize morphological data and discuss ecological observations in search of characters that may unite genetic or taxonomic units. The analyses revealed a peninsular and a panhandle clade in Florida that appeared to diverge as a result of Pleistocene glacial fluctuations. I found no support genetically, morphologically, or ecologically for the current taxonomy, indicating a need for range-wide research to generate revised nomenclature. My results do not support the protection status of N. clarkii taeniata.
Show less - Date Issued
- 2013
- Identifier
- CFE0004760, ucf:49764
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004760
- Title
- GENETIC AND PHENOTYPIC EVOLUTION IN THE ORNATE CHORUS FROG (PSEUDACRIS ORNATA): TESTING THE RELATIVE ROLES OF NATURAL SELECTION, MIGRATION, AND GENETIC DRIFT.
- Creator
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Degner, Jacob, Hoffman, Eric, University of Central Florida
- Abstract / Description
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Understanding how migration, genetic drift, and natural selection interact to maintain the genetic and phenotypic variation we observe in natural populations is a central goal of population genetics. Amphibians provide excellent model organisms for investigating the interplay between these evolutionary forces because amphibians are generally characterized by limited dispersal abilities, high philopatry, and are obligately associated with the areas around suitable habitats (e.g. breeding ponds...
Show moreUnderstanding how migration, genetic drift, and natural selection interact to maintain the genetic and phenotypic variation we observe in natural populations is a central goal of population genetics. Amphibians provide excellent model organisms for investigating the interplay between these evolutionary forces because amphibians are generally characterized by limited dispersal abilities, high philopatry, and are obligately associated with the areas around suitable habitats (e.g. breeding ponds). Thus, on relatively small geographic scales, the relative effects of all of these evolutionary forces can be studied together. Here, we study the interaction of migration, genetic drift, natural selection, and historical process in the ornate chorus frog (Pseudacris ornata). We report the development and characterization of 10 polymorphic microsatellite genetic markers. Number of alleles per locus ranged from 2 to 21 averaging 9.2 and expected heterozygosities ranged from 0.10 to 0.97 averaging 0.52. However, in an analysis of two populations, three locus-by-population comparisons exhibited significant heterozygote deficiencies and indicated that null alleles may be present some loci. Furthermore, we characterized genetic structure and historical biogeographic patterns in P. ornata using these microsatellite markers along with mitochondrial DNA sequence data. Our data indicate that in these frogs, migration may play a large role in determining population structure as pairwise estimates of FST were relatively small ranging from 0.04 to 0.12 (global FST = 0.083). Additionally, we observed an overall pattern of isolation-by-distance in neutral genetic markers across the species range. Moreover, our data suggest that the Apalachicola River basin does not impede gene flow in P. ornata as it does in many vertebrate taxa. Interestingly, we identified significant genetic structure between populations separated by only 6 km. However, this fine scale genetic structure was only present in the more urbanized of two widespread sampling localities. Finally, in this study, we demonstrated that there was a significant correlation between the frequency of green frogs and latitude. There was a higher frequency of green frogs in southern samples and a lower frequency of green frogs in northern samples. However, when we interpreted this phenotypic cline in light of the overall pattern of isolation-by-distance, it was apparent that the neutral evolutionary forces of genetic drift and migration could explain the cline, and the invocation of natural selection was not necessary.
Show less - Date Issued
- 2007
- Identifier
- CFE0001721, ucf:47319
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001721