Multilocus phylogeography and phylogenetics using sequence-based markers

Brito, Patrícia H.; Edwards, Scott V.

doi:10.1007/s10709-008-9293-3

Cited by 310 publications

(249 citation statements)

References 160 publications

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“…In three of these four cases, the molecular markers used to assay the nuclear genome were microsatellites. It is important to note that because of their complex mutational patterns, microsatellites may imply higher gene flow than might otherwise be estimated from other nuclear markers with a simpler mutation mechanisms, such as SNPs (Brito & Edwards 2008). While differences in the biogeographic patterns between microsatellites and mtDNA are not necessarily expected, it would be valuable in the future for some of these cases to be confirmed with additional multi-locus nuclear markers.…”

Section: Box 3 Mitochondrial Structure In the Absence Of Geographic mentioning

confidence: 99%

The biogeography of mitochondrial and nuclear discordance in animals

2012

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Combining nuclear (nuDNA) and mitochondrial DNA (mtDNA) markers has improved the power of molecular data to test phylogenetic and phylogeographic hypotheses and has highlighted the limitations of studies using only mtDNA markers. In fact, in the past decade, many conflicting geographic patterns between mitochondrial and nuclear genetic markers have been identified (i.e. mito-nuclear discordance). Our goals in this synthesis are to: (i) review known cases of mito-nuclear discordance in animal systems, (ii) to summarize the biogeographic patterns in each instance and (iii) to identify common drivers of discordance in various groups. In total, we identified 126 cases in animal systems with strong evidence of discordance between the biogeographic patterns obtained from mitochondrial DNA and those observed in the nuclear genome. In most cases, these patterns are attributed to adaptive introgression of mtDNA, demographic disparities and sex-biased asymmetries, with some studies also implicating hybrid zone movement, human introductions and Wolbachia infection in insects. We also discuss situations where divergent mtDNA clades seem to have arisen in the absence of geographic isolation. For those cases where foreign mtDNA haplotypes are found deep within the range of a second taxon, data suggest that those mtDNA haplotypes are more likely to be at a high frequency and are commonly driven by sex-biased asymmetries and ⁄ or adaptive introgression. In addition, we discuss the problems with inferring the processes causing discordance from biogeographic patterns that are common in many studies. In many cases, authors presented more than one explanation for discordant patterns in a given system, which indicates that likely more data are required. Ideally, to resolve this issue, we see important future work shifting focus from documenting the prevalence of mito-nuclear discordance towards testing hypotheses regarding the drivers of discordance. Indeed, there is great potential for certain cases of mitochondrial introgression to become important natural systems within which to test the effect of different mitochondrial genotypes on whole-animal phenotypes.

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Section: Box 3 Mitochondrial Structure In the Absence Of Geographic mentioning

confidence: 99%

The biogeography of mitochondrial and nuclear discordance in animals

2012

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“…IM simultaneously estimates divergence between two populations and the rate of gene flow between them. Importantly, this coalescent approach incorporates the stochasticity of mutation and genetic drift when calculating parameters, which in turn are associated with populations rather than genes (Brito and Edwards 2008). Thus, the key output of IM, in Bayesian parlance, is credibility intervals for each parameter -the 90% highest posterior densities (HPDs).…”

Section: Paraphyly Between Species and Hypothesis Testingmentioning

confidence: 99%

Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds

Joseph

Omland

2009

Emu - Austral Ornithology

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Abstract.With examples from Australo-Papuan ornithology, we examine the technical and theoretical roots of molecular phylogeography and review its development. We describe the progression from ad hoc interpretation of gene trees in single species phylogeographic studies through to comparative phylogeography and currently advocated model-testing approaches. Mitochondrial DNA (mtDNA) sequences have provided most advances to date, although we demonstrate and advocate the future use of multilocus datasets analysed with coalescent methods. We examine interrelationships among speciation research, historical biogeography, phylogeography and landscape genetics. Mitochondrial paraphyly, in which individuals of one species or population have mtDNA that is more closely related to that of another than to their own, emerges in 44% of Australian studies to date as a common, important result in Australian avian phylogeography. Accordingly, we explore at length its most common causes and its impact on case studies in Australo-Papuan avian phylogeography. The impact of so much paraphyly on avian phylogeography and taxonomy is a major theme of the review. We suggest a full research agenda for avian phylogeography in the AustraloPapuan region that spans diverse topics: the need for more studies of pelagic birds, spatio-temporal links between New Guinea and Australia, island populations, testing of long-established biogeographical hypotheses, and integration of molecular and non-molecular datasets into integrated evolutionary understanding of species and populations. Studying the full continuum of divergences from landscape genetics, to phylogeography, to recently diverged species with evidence of paraphyly, to highly divergent species with many fixed differences will lead to a more complete understanding of the processes and patterns of avian evolution.

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“…This technology has led to the sequencing of large numbers of nearly complete transcriptomes (3), high-resolution genetic mapping (4), population genetic studies (5), and phylogeographic analysis of methicillin-resistant bacteria based on whole-genome sequences (6). For many species, however, such genomic resources are modest or not available, and fine-scale resolution of population dynamics or phylogeographies has been based on mitochondrial or chloroplast DNA, microsatellites, or a combination of these approaches (7). Here, we present a cost-and labor-effective method to resolve the postglacial phylogeography of a nonmodel organism, the North American pitcher plant mosquito, Wyeomyia smithii (Coq.).…”

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confidence: 99%

Resolving postglacial phylogeography using high-throughput sequencing

Emerson

Merz

Catchen

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

405

374

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The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient technique to determine the fine-scale phylogenetic relationships among recently diverged populations in a species. This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii, from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000-19,000 B.P. The RAD tag method can be used to identify detailed patterns of phylogeography in any organism regardless of existing genomic data, and, more broadly, to identify incipient speciation and genome-wide variation in natural populations in general.genomics | restriction site-associated DNA tag | second-generation sequencing | Wyeomyia smithii

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Multilocus phylogeography and phylogenetics using sequence-based markers

Cited by 310 publications

References 160 publications

The biogeography of mitochondrial and nuclear discordance in animals

The biogeography of mitochondrial and nuclear discordance in animals

Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds

Resolving postglacial phylogeography using high-throughput sequencing

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