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- Title
- USING LANDSCAPE GENETICS TO ASSESS POPULATION CONNECTIVITY IN A HABITAT GENERALIST.
- Creator
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Hether, Tyler, Hoffman, Eric, University of Central Florida
- Abstract / Description
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Understanding the nature of genetic variation in natural populations is an underlying theme of population genetics. In recent years population genetics has benefited from the incorporation of landscape and environmental data into pre-existing models of isolation by distance (IBD) to elucidate features influencing spatial genetic variation. Many of these landscape genetics studies have focused on populations separated by discrete barriers (e.g., mountain ridges) or species with specific...
Show moreUnderstanding the nature of genetic variation in natural populations is an underlying theme of population genetics. In recent years population genetics has benefited from the incorporation of landscape and environmental data into pre-existing models of isolation by distance (IBD) to elucidate features influencing spatial genetic variation. Many of these landscape genetics studies have focused on populations separated by discrete barriers (e.g., mountain ridges) or species with specific habitat requirements (i.e., habitat specialists). One difficulty in using a landscape genetics approach for taxa with less stringent habitat requirements (i.e., generalists) is the lack of obvious barriers to gene flow and preference for specific habitats. My study attempts to fill this information gap to understand mechanisms underlying population subdivision in generalists, using the squirrel treefrog (Hyla squirella) and a system for classifying 'terrestrial ecological systems' (i.e. habitat types). I evaluate this dataset with microsatellite markers and a recently introduced method based on ensemble learning (Random Forest) to identify whether spatial distance, habitat types, or both have influenced genetic connectivity among 20 H. squirella populations. Next, I hierarchically subset the populations included in the analysis based on (1) genetic assignment tests and (2) Mantel correlograms to determine the relative role of spatial distance in shaping landscape genetic patterns. Assignment tests show evidence of two genetic clusters that separate populations in Florida's panhandle (Western cluster) from those in peninsular Florida and southern Georgia (Eastern cluster). Mantel correlograms suggest a patch size of approximately 150 km. Landscape genetic analyses at all three spatial scales yielded improved model fit relative to isolation by distance when including habitat types. A hierarchical effect was identified whereby the importance of spatial distance (km) was the strongest predictor of patterns of genetic differentiation above the scale of the genetic patch. Below the genetic patch, spatial distance was still an explanatory variable but was only approximately 30% as relevant as mesic flatwoods or upland oak hammocks. Thus, it appears that habitat types largely influence patterns of population genetic connectivity at local scales but the signal of IBD becomes the dominant driver of regional connectivity. My results highlight some habitats as highly relevant to increased genetic connectivity at all spatial scales (e.g., upland oak hammocks) while others show no association (e.g., silviculture) or scale specific associations (e.g., pastures only at global scales). Given these results it appears that treating habitat as a binary metric (suitable/non-suitable) may be overly simplistic for generalist species in which gene flow probably occurs in a spectrum of habitat suitability. The overall pattern of spatial genetic and landscape genetic structure identified here provides insight into the evolutionary history and patterns of population connectivity for H. squirella and improves our understanding of the role of matrix composition for habitat generalists.
Show less - Date Issued
- 2010
- Identifier
- CFE0003204, ucf:48580
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003204
- 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
- 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
