Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

Cutter, Asher D.

doi:10.1016/j.ympev.2013.06.006

Cited by 67 publications

(77 citation statements)

References 157 publications

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“…3, 4). Theory predicts that the low polymorphism chromosome centers should exhibit reduced heterogeneity in the timing of divergence among populations, owing to more complete lineage sorting (Charlesworth 1998;Cutter 2013;Pease and Hahn 2013). Indeed, interpopulation divergence of the chromosome center versus arm PSMC profiles is consistent with this expectation (Fig.…”

Section: Low Recombination Regions Show Drastic Skews In Polymorphismsupporting

confidence: 59%

“…and a per-site mutation rate each generation of μ = 2.7 × 10 −9 (Denver et al 2009). This yields T = 35.0 million generations (Mgen) ago; lower π anc or μ would result in more ancient T. Divergence in low recombination center regions of chromosomes might better reflect the time since the cessation of gene flow between species, owing to reduced ancestral polymorphism (Cutter 2013;Cruickshank and Hahn 2014), so we also computed T given d S-center = 0.186 and assuming π anc-center = 0 to yield T = 34.8 Mgen ago; higher π anc or μ would result in more recent T. These estimates of neutral divergence excluded 958 loci with d S > 0.8 and ENC < 45 to mitigate against any remaining false ortholog assignments and genes with strong selection on codon usage. For divergence time estimation of the Kerala strains to other strains of C. briggsae, we used this same approach using silent-site D xy instead of d S , with values of D xy-center = 0.0113 and π anc-center = 0.00041 to yield T = 2.02 Mgen ago.…”

Section: Ortholog Identification and Divergence Time Calculationmentioning

confidence: 99%

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Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

et al. 2015

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The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.

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Section: Low Recombination Regions Show Drastic Skews In Polymorphismsupporting

confidence: 59%

Section: Ortholog Identification and Divergence Time Calculationmentioning

confidence: 99%

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

et al. 2015

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“…Finally, reticulation is becoming increasingly conspicuous at the level of diverging species and adaptive radiations (25,35,(41)(42)(43)(44), and is causing biologists to consider "ephemeral species," with frequent lineage mergers, not only among sister taxa but between lineages with any geographic co-occurrence (45). The goal, however imperfect it is now realized, is to develop and apply models that integrate phylogeography, demography, and genome evolution in ways that will allow more nuanced interpretation of myriad interacting evolutionary processes from patterns of genomic diversity (46). Acknowledging and modeling reticulation at various levels in the hierarchy of life will be an important part of reaching this goal.…”

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confidence: 99%

Reticulation, divergence, and the phylogeography–phylogenetics continuum

Edwards

Potter

Schmitt

et al. 2016

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

140

105

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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.monsoon tropics | introgression | comparative phylogeography | species trees | coalescent theory

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“…A large body of recent work has been devoted to the issue of incongruence between the species tree (the true speciation history) and the gene trees evolving within (Anderson et al 2012;Cutter 2013). The traditional approach of concatenating the total genetic evidence into a supermatrix to obtain a global estimate of the predominant phylogenetic signal and hidden support (Gatesy and Baker 2005), without consideration for the heterogeneity of individual partitions, has been to some extent superseded by multispecies coalescent (MSC) techniques (reviewed in: Edwards 2009; Knowles and Kubatko 2010;Anderson et al 2012;Cutter 2013;Leaché et al 2014).…”

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confidence: 99%

“…The traditional approach of concatenating the total genetic evidence into a supermatrix to obtain a global estimate of the predominant phylogenetic signal and hidden support (Gatesy and Baker 2005), without consideration for the heterogeneity of individual partitions, has been to some extent superseded by multispecies coalescent (MSC) techniques (reviewed in: Edwards 2009; Knowles and Kubatko 2010;Anderson et al 2012;Cutter 2013;Leaché et al 2014). The majority of the new MSC algorithms are intended to model at least some of the sources of heterogeneity between different markers, most frequently focusing on the problem of ILS (e.g.…”

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confidence: 99%

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Kozak

Wahlberg

Neild

et al. 2014

Preprint

129

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Abstract.-Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach failed to reflect the underlying variation in the history of individual loci. However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Neotropics over the past 23 myr, or changes caused by diversity-dependent effects on the rate of diversification. We find that the rate of diversification has increased on the branch leading to the presently most species-rich genus Heliconius, but the change occurred gradually and cannot be unequivocally attributed to a specific environmental driver. Our study provides comprehensive comparison of philosophically distinct species tree reconstruction methods and provides insights into the diversification of an important insect radiation in the most biodiverse region of the planet.

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Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

Cited by 67 publications

References 157 publications

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

Reticulation, divergence, and the phylogeography–phylogenetics continuum

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

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