Download or read book Speciation Phylogeography and Gene Flow in Giant Salamanders Dicamptodon written by Craig A. Steele and published by . This book was released on 2006 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt: Giant salamanders of the genus Dicamptodon occur in the Pacific Northwest of North America. The variety of geographic distributions and life history traits displayed among this genus provide opportunities to test hypotheses concerning regional biogeography, effects of Pleistocene glaciation, comparative phylogeography, and patterns of gene flow. A genus-level phylogeny was constructed to test competing biogeographic hypotheses concerning the disjunct distribution of the Idaho giant salamander (D. aterrimus ), and a Pleistocene speciation hypothesis for the Cope's giant salamander (D. copei). Results indicate speciation and distribution of D. aterrimus is attributable to the orogeny of the Cascade Mountains rather than recent inland dispersal and that D. copei is distantly related to other coastal species and likely originated much earlier than the Pleistocene. Patterns of intraspecific variation were examined for the widespread Pacific giant salamander (D. tenebrosus) and hypotheses concerning the location and number of Pleistocene refugia were tested. Results indicate that D. tenebrosus was restricted to two Pleistocene refugia, one in the Columbia River valley and another in the Klamath-Siskiyou Mountains, and has recently expanded northward from these refugia into its current distribution. Phylogeographic patterns for D. copei were compared to that of the codistributed Van Dyke's salamander (Plethodon vandykei). Results reveal that sympatric populations displayed identical phylogeographic topologies, suggesting shared evolutionary histories, but topologies were ultimately incongruent due to several highly divergent allopatric populations of D. copei. Comparative patterns of genetic population structure were examined for sympatric populations of D. tenebrosus and D. copei. Results indicate that the metamorphosing species, D. tenebrosus, displayed a lack of population structure while the non-metamorphosing species, D. copei, displayed a larger degree of population structure. These results help explain the phylogeographic patterns presented for each species. The large distribution and post-glacial expansion by D. tenebrosus was facilitated by its high dispersal ability while the low dispersal ability of D. copei lead to a small and fragmented geographic range and greater phylogeographic structure within its range. These results suggest that understanding life history variation on a local scale can lead to a better understanding of the mechanistic underpinnings of species' distributions in general.
Download or read book Impacts of Landscape Features on the Genetic Structure of the California Giant Salamander Dicamptodon Ensatus written by Briana Callahan and published by . This book was released on 2010 with total page 74 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Scale Dependent Genetic Structure of Idaho Giant Salamanders Dicamptodon Aterrimus in Stream Networks written by Lindy Beth Mullen and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Stream network structure constrains population processes of freshwater organisms, with individual, population and community level consequences. This consistent structure provides a framework in which examination of life-history influences on population genetic structure may provide general insight. I examined how stream network structure affects gene flow and genetic structure of the facultatively paedomorphic Idaho Giant salamander, Dicamptodon aterrimus in Idaho and Montana, USA. I used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks and (ii) testing for genetic isolation by distance along stream corridors versus overland pathways. Replicated sampling of streams within catchments within three river basins revealed that stream hierarchical scales had strong effects on gene flow and genetic structure. AMOVA identified significant structure among all hierarchical levels (among streams, among catchments, among basins), and divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in-stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration according to the stream hierarchy model, but divergence among catchments and among basins was due to genetic drift, consistent with the death valley model of population structure (Meffe and Vrijenhoek 1988). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander with contrasting effects at different hierarchical scales.
Download or read book Phylogeography and Range Limit Evolution in the Cumberland Plateau Salamander Plethodon Kentucki written by Emily F. Watts and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene flow and geography are critically influential factors in shaping the genetic history of a species. Gene flow can have beneficial effects on a population that may allow for new adaptations to occur, such as increasing genetic variation. However, gene flow may also result in negative consequences for populations if their fitness is decreased through the introduction of non-optimized traits or through selection resulting in a reduction of locally adapted individuals. Asymmetrical gene flow can even prevent local adaptation in edge populations when gene flow from central populations adapted to central conditions swamps locally adapted populations. This phenomenon can prevent a species from expanding its range, as it is unable to adapt to local conditions at the range edges. Thus, patterns of gene flow can determine the extent to which gene flow slows or promotes adaptation. Gene flow can also create problems for the inference of species relationships, because it is a source of gene tree-species tree discordance. While speciation is commonly modeled as a finite event, divergence is a process. Even after divergence, hybridization is common, and neglecting to account for it can lead to incorrect species tree inference. Nonetheless, the development of species tree inference methods that account for gene flow remains in its infancy. Even with the addition of more loci from genomic-scale data, gene flow misleads phylogenetic reconstruction. Thus, it is vital to account for gene flow with phylogenetic networks when inferring species relationships. This dissertation examines the role of gene flow in constraining adaptation in the Cumberland Plateau Salamander, Plethodon kentucki, a cryptic species with respect to the sympatric Northern Slimy Salamander, Plethodon glutinosus. After its description in 1983 by Highton and MacGregor using allozyme data, its taxonomic status was unclear, as the authors reported extreme levels of genetic differentiation for a single species with a narrow distribution, and follow-up studies found patterns of genetic variation that were discordant with the allozyme data. In chapter 1, I describe genetic variation within P. kentucki and conclude it is best recognized as a single species with substantial genetic structure within its limited distribution. In chapter 2, I describe the heterogeneity of the landscape within the range of P. kentucki. I also quantify the genetic connectivity across the range of P. kentucki and describe how the two interact to maintain the range of P. kentucki. I also test a novel theory about how different types of range edges impact adaptation at the periphery of a species’ range. This dissertation also examines the role of gene flow in confounding phylogenetic inference using two prominent phylogenetic network methods. In chapter 3, I use computer modeling to examine how these two methods perform under varying degrees of gene flow and population history, as well as how they perform under two different datasets. This dissertation explores the role of gene flow, or lack thereof, in maintaining species boundaries, inhibiting range expansion, and confounding the inference of species relationships.
Download or read book The Biology of Plethodontid Salamanders written by Richard C. Bruce and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume offers a state-of-the-art overview of plethodontid salamanders. Readers will find the best current understanding of many aspects of the evolution, systematics, development, morphology, life history, ecology, and field methodology of these animals.
Download or read book Phylogeography Historical Distribution Migration and Species Boundaries in the Salamander Ensatina Eschscholtzii as Measured with Mitochondrial DNA Sequences written by Duncan Stuart Parks and published by . This book was released on 2000 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Phylogeography of California written by Kristina A. Schierenbeck and published by Univ of California Press. This book was released on 2014-08-26 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogeography of California examines the evolution of a variety of taxaÑancient and recent, native and migratoryÑto elucidate evolutionary events both major and minor that shaped the distribution, radiation, and speciation of the biota of California. The book also interprets evolutionary history in a geological context and reviews new and emerging phylogeographic patterns. Focusing on a region that is defined by physical and political boundaries, Kristina A. Schierenbeck provides a phylogeographic survey of CaliforniaÕs diverse flora and fauna according to their major organismal groups. Life history and ecological characteristics, which play prominent roles in the various outcomes for respective clades, are also considered throughout the work. Supporting scholars and researchers who study evolutionary diversification, the book analyzes research that helps assess one of the major challenges in phylogeographic studies: understanding changes in population structures shaped by geological and geographical processes. California is one of only twenty-five acknowledged biological hotspots worldwide, and the phylogeographic history of the state can be extrapolated to study other regions in western North America. Further consideration is given to implications for conservation, recommendations concerning the biogeographic provinces that roughly define the state of California, and predictions related to climate change.
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2007 with total page 960 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Dividing Link written by Thomas James Devitt and published by . This book was released on 2010 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plethodontid salamanders of the Ensatina eschscholtzii complex have received special attention from evolutionary biologists because they represent one of the very few examples of a ring species, a case where two reproductively isolated forms are connected by a chain of intergrading populations surrounding a central geographic barrier. Ensatina has become a textbook example of speciation, yet there still remain fundamental gaps in our knowledge of this fascinating system. In this study, consisting of three components, I extend previous work on the Ensatina complex in new directions. In Chapter 1, I conducted a fine-scale genetic analysis of a hybrid zone between the geographically terminal forms of the ring using Bayesian methods for hybrid identification and classification in combination with mathematical cline analyses. F1s and pure parentals dominated the sample. Cline widths were concordant and narrow with respect to dispersal, but there is cytonuclear discordance, both in terms of introgression and the geographic position of mitochondrial versus nuclear clines. Nearly all hybrids possess mitochondrial DNA from one parental type (klauberi suggesting isolation is asymmetrical. Selection against hybrids is inferred to be strong (2̃1%), but whether this selection is endogenous (genetically-based) or exogenous (environmentally-based) remains to be tested. In Chapter 2, I investigated the role of late Quaternary climate change on phylogeographic patterns within the Large-blotched Ensatina (Ensatina eschscholtzii klauberi). Intersecting species distribution models constructed under current climatic conditions, as well as two different historical time periods (Last Glacial Maximum, 21 ka and mid-Holocene, 6 ka), predicted stable refugial areas where the species may have persisted throughout climatic fluctuations. Significant phylogeographic structure exists, but geographic structuring of genetic variation by refugia was not supported. Results suggest that populations in putative refugia have not been isolated for very long, or that gene flow may have masked any earlier periods of divergence in allopatry. In Chapter 3, I conducted a multilocus phylogeographic analysis of the entire Ensatina eschscholtzii complex to reexamine previous phylogenetic hypotheses based on mitochondrial DNA alone. A concatenation approach was used in addition to newer methods that model the relationship between the species tree and the gene trees embedded within them. The concatenated tree was similar to previous mitochondrial trees, identifying well-supported coastal and inland clades, and recovering oregonensis and platensis as paraphyletic. The concatenated tree was not well resolved at the base. Basal relationships recovered by the species tree were well resolved, but most relationships were not well supported compared to the concatenated tree. Results are generally consistent with previous efforts based on mtDNA, but provide further resolution to the Ensatina phylogeny, while highlighting the difficult nature of inferring species trees from samples of closely related populations that are experiencing gene flow.
Download or read book Chinese Giant Salamanders written by Susan Schafer and published by Cavendish Square Publishing, LLC. This book was released on 2014-08-01 with total page 50 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chinese Giant Salamanders are the largest amphibians to swim the rivers and crawl on banks. Learn about their history, behavior, lifecycle, and the conservation efforts that are being done to protect these slimy creatures.
Download or read book Feeding Ecology of Larvae of the Pacific Giant Salamander Dicamptodon Tenebrosus and Their Role as Top Predator in a Headwater Stream Benthic Community written by Michael S. Parker (Professor of biology) and published by . This book was released on 1992 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Phylogenetic History Morphological Parallelism and Speciation in a Complex of Appalachian Salamanders genus Desmognathus written by Nathan D. Jackson and published by . This book was released on 2005 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the mechanisms that generate shared morphologies across closely related taxa is important when identifying distinct evolutionary lineages using morphological characters. Desmognathus salamanders are an ideal group for testing hypotheses concerning the correlation between morphological similarity and genetic exchange within and among nominal species due to a pattern of high discordance between the two. Phylogeographic hypotheses are tested for populations of the D. quadramaculatus species complex throughout southern Appalachia by combining phylogenetic and population genetic methods with geographical information. Phylogenetic and phylogeographic inferences are then assessed in conjunction with morphological characteristics that have traditionally diagnosed taxonomic entities to understand the genetic basis of shared morphology in this complex, and to assess species boundaries. A history of fragmentation followed by range expansion is suggested as a recurrent pattern that has shaped the current population structure within this complex. The current taxonomy is found to unite populations that share similar morphologies due to parallel evolution rather than ancestry. We suggest revisions in taxonomy that will better reflect the evolutionary history of these lineages. Appreciation of the hidden genetic variation and homoplasious morphological variation often present in and among salamander species can foster the implementation of more appropriate methods for detecting and recognizing the complex history of these organisms.
Download or read book Landscape Genetic Analysis and Population Structure of Three Sympatric Amphibians in a Managed Redwood Forest of Northwestern California written by Cindy Castaneda and published by . This book was released on 2015 with total page 50 pages. Available in PDF, EPUB and Kindle. Book excerpt: Timber harvesting of coast redwood (Sequoia sempervirens) in California has altered habitat that is important to population connectivity of amphibian species. I employed a landscape genetic analysis to reveal landscape features of the redwood forest that influence population genetic structure among populations of coastal giant salamanders (D. tenebrosus), tailed frogs (A. truei), and southern torrent salamanders (R. variegatus). SAMOVA analysis indicated twelve ( K = 12) genetically differentiated populations of tailed frogs where clustering of populations for most watersheds was observed. Low subdivision (K = 2) of coastal giant salamander populations was depicted by SAMOVA and suggested a general north to south clustering. A single haplotype was identified in southern torrent salamanders; hence, no groups were differentiated. Gene flow in tailed frogs was significantly associated with forest structure; however, no landscape features were correlated with gene flow in coastal giant salamanders and southern torrent salamanders. A pattern of isolation by distance was found only in tailed frogs. Results indicate low dispersal in tailed frogs limited by habitat and broad terrestrial movement in coastal giant salamanders that is not spatially restricted.
Download or read book Ecology and Genetics of Lungless Salamanders Family Plethodontidae in the Gulf Coastal Plain written by Jennifer Yasmin Lamb and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: During the last half century, lungless salamanders (Family Plethodontidae) have been the subject of numerous studies in the fields of ecology and genetics. While most works have focused on the species-rich Eastern Highlands region, there has been a recent shift towards plethodontid assemblages within the Coastal Plain. The research presented herein applies hierarchical occupancy models and both mitochondrial and nuclear genes to address questions pertinent to the biology and conservation of plethodontids within the Gulf Coastal Plain. The results of a multi-species Bayesian single-season occupancy model indicated that two environmental gradients, upstream drainage area and stream drying, influenced the probability of occurrence for multiple species of stream-breeding plethodontids. Further, species varied in their responses to these gradients. A second model was used to ask whether asymmetric interactions also influenced occurrence for three species of brook salamanders (Genus Eurycea). More specifically, the model tested whether the southern two-lined salamander (E. cirrigera) might act as the dominant predator and or competitor to either the three-lined (E. guttolineata) or dwarf (E. quadridigitata) salamanders. The results of this second model suggested that environmental gradients likely work in tandem with negative interactions to shape the distribution of E. guttolienata within the Gulf Coastal Plain. Like hierarchical occupancy models, genetic tools are also shedding light on complex relationships among and within species of lungless salamanders. This research investigated phylogeographic patterns within a wide-ranging species of plethodontid, the spotted dusky salamander (Desmognathus conanti). Sequence data revealed that there were geographically discrete, deeply divergent mitochondrial lineages within D. conanti which may be the result of isolation brought about by fluctuating sea levels during the late Miocene through the Pleistocene. Data from six rapidly mutating microsatellite markers indicated that there had been recent gene flow across some of these lineages in the southern Gulf Coastal Plain. However, these data also suggest that a northern lineage may have remained distinct. The relationships described and occurrence probabilities estimated by the aforementioned models, in combination with conclusions from analyses of genetic data, improve our ability to conserve regional plethodontid biodiversity within this unique physiographic province.
Download or read book Western Plethodon Salamanders as a Model System in Phylogeography written by Tara Anne Pelletier and published by . This book was released on 2015 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plethodon salamanders are fully terrestrial, lungless salamanders found in forested areas throughout North America. My dissertation focuses on five of these salamander species located in the Pacific Northwest (PNW). The PNW has a complex geologic history including events such as volcanism and repeated glaciations. This complexity makes studying biodiversity patterns informative as to what evolutionary processes shape current population and species structure. The five species that are the focus of my dissertation are used to learn about Plethodon salamanders in general, but because these salamanders are at different stages of divergence within and among species, they can further be used to explore methods in phylogeography, which help us better understand the process of evolution. First, I explore demographic model selection using genetic data in P. idahoensis (Chapter 2). The best demographic model for this species is one with population divergence, expansion, and migration. Furthermore, the evaluation of Approximate Bayesian computation techniques highlights the complexities of this method for model selection in phylogeography.
Download or read book Population Genomics and Conservation of Texas Cave and Spring Salamanders Plethodontidae Eurycea written by Andrew Brian Corbin and published by . This book was released on 2020 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding species boundaries and gene flow among the cave and spring salamanders of the central Texas region (genus Eurycea) has been a challenge for many decades. Although previous research has greatly increased our understanding of these salamanders, there are still many unanswered questions involving the number of species in the group and the degree to which populations are connected. The plummeting cost of DNA sequencing has transformed the field of biology, including the field of population genetics. Before the recent advent of high-throughput sequencing, population genetic studies in Eurycea were limited to only a few genetic markers. Here, we leverage next-generation sequencing tot est hypotheses of species boundaries, examine patterns of gene flow, and measure genetic diversity using thousands of genome-wide markers. I find multiple instances of hybridization between distantly related species, and evidence for an undescribed species of an extreme blind cave salamander. I also work with San Antonio Zoo, San Antonio, TX, to build a captive research population of the Texas blind salamander(E. rathbuni) and investigate patterns of diversity and generate preliminary estimates of effective population size for the species.
Download or read book Phylogeographic and Phylogenetic Exploration of Plethodon Plethodontidae Caudata Salamanders in the Pacific Northwest written by and published by . This book was released on 2009 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic studies of amphibians often reveal substantial population structure due to either historical demographics from changing climate and geographic features over varying timeframes. Eight species of terrestrial salamanders (Family: Plethodontidae, Genus: Plethodon) reside in forests of the Pacific Northwest (PNW). Plethodon vehiculum is the most widespread and abundant terrestrial salamander in the PNW yet evolutionary studies are lacking. Using mitochondrial DNA (mtDNA) sequence data (D-loop and cytb) questions regarding the phylogeography of P. vehiculum and phylogenetics of western Plethodons are explored. Two major clades were defined in P. vehiculum, a southern clade in the Klamath-Siskiyou region and a northern clade ranging from northern Oregon to British Columbia using parsimony and maximum likelihood trees and a haplotype network. High divergence levels between the north and south clades are observed warranting further investigation into the southern clade's unique evolutionary trajectory. The northern populations were not highly differentiated with high levels of haplotype sharing, not common in other terrestrial salamander species. A large recent range expansion or high habitat connectivity for these salamanders is suggested. The Columbia River did not act as barrier to dispersal in this species, however, Vancouver Island and the population of Washington's Olympic Peninsula revealed unique haplotypes only to those areas, due to the presence of geographic barriers to dispersal and/or multiple glacial refugia. The D-loop and cytb provided evidence for recent range expansion in the northern clade. This was the first study to incorporate all western Plethodon salamanders in a phylogenetic study. Parsimony and maximum likelihood methods offered strong support for recognized relationships among western Plethodons, however relationships between the major groups remain unhighly supported. Lack of genetic diversity in the mtDNA cytb gene in P. vehiculum is highly inconsistent with other Plethodon salamanders and highlights the importance of understanding mtDNA evolution in ectotherms. Divergence measures were used to estimate divergence times among species, dating all speciation before the Pleistocene glaciations. The southern OR clade of P. vehiculum was dated to have been separated from the northern clade at the start of the Pleistocene. The deep phylogeographic break here justifies the possibility of reclassification of the southern clade.
