The Experts below are selected from a list of 5889 Experts worldwide ranked by ideXlab platform
Anne D Yoder - One of the best experts on this subject based on the ideXlab platform.
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integrating statistical genetic and geospatial methods brings new power to phylogeography
Molecular Phylogenetics and Evolution, 2011Co-Authors: Lauren M. Chan, Jason L Brown, Anne D YoderAbstract:The field of phylogeography continues to grow in terms of power and accessibility. Initially uniting population genetics and phylogenetics, it now spans disciplines as diverse as geology, statistics, climatology, ecology, physiology, and bioinformatics to name a few. One major and recent integration driving the field forward is between “statistical phylogeography” and Geographic Information Systems (GIS) (Knowles, 2009). Merging genetic and geospatial data, and their associated methodological toolkits, is helping to bring explicit hypothesis testing to the field of phylogeography. Hypotheses derived from one approach can be reciprocally tested with data derived from the other field and the synthesis of these data can help place demographic events in an historical and spatial context, guide genetic sampling, and point to areas for further investigation. Here, we present three practical examples of empirical analysis that integrate statistical genetic and GIS tools to construct and test phylogeographic hypotheses. Insights into the evolutionary mechanisms underlying recent divergences can benefit from simultaneously considering diverse types of information to iteratively test and reformulate hypotheses. Our goal is to provide the reader with an introduction to the variety of available tools and their potential application to typical questions in phylogeography with the hope that integrative methods will be more broadly and commonly applied to other biological systems and data sets.
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phylogeography s past present and future 10 years after avise 2000
Molecular Phylogenetics and Evolution, 2010Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Jeannine Cavenderbares, Leslie J Rissler, Bryan C Carstens, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
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Phylogeography's past, present, and future
Molecular Phylogenetics and Evolution, 2009Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Leslie J Rissler, Bryan C Carstens, Jeannine Cavender-bares, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
Bryan C Carstens - One of the best experts on this subject based on the ideXlab platform.
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applications of next generation sequencing to phylogeography and phylogenetics
Molecular Phylogenetics and Evolution, 2013Co-Authors: John E Mccormack, Bryan C Carstens, Sarah M Hird, Amanda J Zellmer, Robb T BrumfieldAbstract:This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence data for phylogeography and phylogenetics. However, the focus on non-model organisms, in addition to uncertainty about which sample preparation methods and analyses are appropriate for different research questions and evolutionary timescales, have contributed to a lag in the application of NGS to these fields. Here, we outline some of the major obstacles specific to the application of NGS to phylogeography and phylogenetics, including the focus on non-model organisms, the necessity of obtaining orthologous loci in a costeffective manner, and the predominate use of gene trees in these fields. We describe the most promising methods of sample preparation that address these challenges. Methods that reduce the genome by restriction digest and manual size selection are most appropriate for studies at the intraspecific level, whereas methods that target specific genomic regions (i.e., target enrichment or sequence capture) have wider applicability from the population level to deep-level phylogenomics. Additionally, we give an overview of how to analyze NGS data to arrive at data sets applicable to the standard toolkit of phylogeography and phylogenetics, including initial data processing to alignment and genotype calling (both SNPs and loci involving many SNPs). Even though whole-genome sequencing is likely to become affordable rather soon, because phylogeography and phylogenetics rely on analysis of hundreds of individuals in many cases, methods that reduce the genome to a subset of loci should remain more cost-effective for some time to come.
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phylogeography s past present and future 10 years after avise 2000
Molecular Phylogenetics and Evolution, 2010Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Jeannine Cavenderbares, Leslie J Rissler, Bryan C Carstens, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
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Phylogeography's past, present, and future
Molecular Phylogenetics and Evolution, 2009Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Leslie J Rissler, Bryan C Carstens, Jeannine Cavender-bares, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
Leslie J Rissler - One of the best experts on this subject based on the ideXlab platform.
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Union of phylogeography and landscape genetics
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Leslie J RisslerAbstract:Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the “microgeographic races” of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography.
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phylogeography s past present and future 10 years after avise 2000
Molecular Phylogenetics and Evolution, 2010Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Jeannine Cavenderbares, Leslie J Rissler, Bryan C Carstens, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
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Phylogeography's past, present, and future
Molecular Phylogenetics and Evolution, 2009Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Leslie J Rissler, Bryan C Carstens, Jeannine Cavender-bares, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
Michael J Hickerson - One of the best experts on this subject based on the ideXlab platform.
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phylogeography s past present and future 10 years after avise 2000
Molecular Phylogenetics and Evolution, 2010Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Jeannine Cavenderbares, Leslie J Rissler, Bryan C Carstens, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
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Phylogeography's past, present, and future
Molecular Phylogenetics and Evolution, 2009Co-Authors: Michael J Hickerson, P. F. Victoriano, C H Graham, Leslie J Rissler, Bryan C Carstens, Jeannine Cavender-bares, J.b. Johnson, Keith A. Crandall, Anne D YoderAbstract:a b s t r a c t Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and popu- lation genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phyloge- ography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally con- ceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of ''likelihood-free" approximate Bayesian methods should per- mit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the con- current rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evo- lutionary biology.
Scott V Edwards - One of the best experts on this subject based on the ideXlab platform.
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reticulation divergence and the phylogeography phylogenetics continuum
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Scott V Edwards, Sally Potter, Jonathan Jonathan Schmitt, Jason G Bragg, Craig MoritzAbstract:Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
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Reticulation, divergence, and the phylogeography–phylogenetics continuum
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Scott V Edwards, Sally Potter, Jonathan Jonathan Schmitt, Jason G Bragg, Craig MoritzAbstract:Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
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next generation sequencing and the expanding domain of phylogeography
Folia Zoologica, 2015Co-Authors: Scott V Edwards, Allison J Shultz, Shane C CampbellstatonAbstract:Phylogeography is experiencing a revolution brought on by next-generation sequencing methods. A historical survey of the phylogeographic literature suggests that phylogeography typically incorporates new questions, expanding on its classical domain, when new technologies offer novel or increased numbers of molecular markers. A variety of methods for subsampling genomic variation, including restriction site associated DNA sequencing (Rad-seq) and other next generation approaches, are proving exceptionally useful in helping to define major phylogeographic lineages within species as well as details of historical demography. Next-generation methods are also blurring the edges of phylogeography and related fields such as association mapping of loci under selection, and the emerging paradigm is one of simultaneously inferring both population history across geography and genomic targets of selection. However, recent examples, including some from our lab on Anolis lizards and songbirds, suggest that genome subsampling methods, while extremely powerful for the classical goals of phylogeography, may fail to allow phylogeography to fully achieve the goals of this new, expanded domain. Specifically, if genome-wide linkage disequilibrium is low, as is the case in many species with large population sizes, most genome subsampling methods will not sample densely enough to detect selected variants, or variants closely linked to them. We suggest that whole-genome resequencing methods will be essential for allowing phylogeographers to robustly identify loci involved in phenotypic divergence and speciation, while at the same time allowing free choice of molecular markers and further resolution of the demographic history of species.
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multilocus phylogeography and phylogenetics using sequence based markers
Genetica, 2009Co-Authors: Patricia H Brito, Scott V EdwardsAbstract:We review recent trends in phylogeography and phylogenetics and argue that these two fields stand to be reunited by the common yardstick provided by sequence and SNP data and by new multilocus methods for phylogenetic analysis. Whereas the modern incarnation of both fields was spawned by PCR approaches applied to mitochondrial DNA in the late 1980s, the two fields diverged during the 1990s largely due to the adoption by phylogeographers of microsatellites, in contrast to the adoption of nuclear sequence data by phylogeneticists. Sequence-based markers possess a number of advantages over microsatellites, even on the recent time scales that are the purview of phylogeography. Using examples primarily from vertebrates, we trace the maturation of nuclear gene phylogeography and phylogenetics and suggest that the abundant instances of gene tree heterogeneity beckon a new generation of phylogenetic methods that focus on estimating species trees as distinct from gene trees. Whole genomes provide a powerful common yardstick on which both phylogeography and phylogenetics can assume their proper place as ends of a continuum.