In the Light of Evolution Volume X: Comparative Phylogeography (2017) / Chapter Skim
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9 Reticulation, Divergence, and the PhylogeographyPhylogenetics Continuum - Scott V. Edwards, Sally Potter, C. Jonathan Schmitt, Jason G. Bragg, and Craig Moritz
9 Reticulation, Divergence, and the PhylogeographyPhylogenetics Continuum - Scott V. Edwards, Sally Potter, C. Jonathan Schmitt, Jason G. Bragg, and Craig Moritz
Pages 171-190
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From page 171... ...
To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic bar rier 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.
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From page 172... ...
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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. Aside from variation induced by the coalescent process within and across species, we are only beginning to understand how such gene tree heterogeneity arises (Fontaine et al., 2015; Nater et al., 2015)
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Reticulation in the form of recombination causes gene trees to depart from a strictly bifurcating pattern, hence posing challenges for some methods of reconstructing evolutionary history (Lanier and Knowles, 2012)
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These gene trees represent independent coalescent histories and highlight various sources of gene tree discordance. Blue, green, and yellow gene trees highlight variation due to differing mutation rates and stochastic coalescent histories (including ILS)
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From page 176... ...
KEY PROCESSES OF DIVERGENCE AND RETICULATION IN NATURE Comparative Phylogeography Across the Australian Monsoonal Tropics In essence, comparative phylogeography is about establishing commonalities of spatial patterns of genetic and gene tree diversity across codistributed species (Bermingham and Moritz, 1998; Avise, 2000)
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(C) Distribution of rooted triplets shows that gene trees exhibiting deeper divergence times across the CB than the KTEB are the most frequent in all taxa except the shaded-litter rainbow skink.
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From page 178... ...
Relative to birds and mammals, these taxa exhibit phylogeographic structure at a finer spatial scale, often with cryptic species and greater phylogenetic depth among regions, possibly reflecting a combination of lower dispersal and higher localized persistence through cycles of harsh climate. Deep structure across the CB, and often also the KTEB, is observed across phylogenetically and ecologically diverse reptiles, including species complexes of agamid lizards (Melville et al., 2011)
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From page 179... ...
, we found diverse gene tree distributions across the region, with gene trees exhibiting deeper divergence times across the CB than the KTEB being the most frequent (Fig. 9.3 and Table S3)
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From page 180... ...
Reticulation Driven by Ecology and Introgression Our comparative phylogeographic analysis for northern Australia highlights the complex mix of divergence and reticulation and diverse spatial and temporal scales of phylogeographic structure that can emerge. Much of this heterogeneity appears to relate to differences among species in their capacity to persist or disperse across the landscape as climates oscillated over the Quaternary.
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From page 181... ...
In the context of comparative phylogeography, insights into reticulation processes can be gleaned by comparing outcomes for taxa with varying ecologies and lineage divergence times across a common geographic and paleoenvironmental setting. Suture zones can be useful for this purpose, where multiple taxa have co-occurring contact zones (Dasmahapatra et al., 2010)
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From page 182... ...
. A key factor emerging from these studies and earlier scans of intraspecific diversity is the strong effect of recombination rate variation on the spatial patterning of genomic diversity, mediated most strongly by hitchhiking (Charlesworth et al., 1993)
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From page 183... ...
Conversely, in the genomic era, comparative phylogeographers will not just have to master details of environmental history, species' ecology, and the plethora of methods for NGS and demographic inference but will also have to comprehend effects of selection and recombination rate variation across the genome. This challenge is exciting and will serve to strengthen further the link between population genomics and phylogenetics.
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From page 184... ...
Such selection is not necessarily a problem; after all, much of the animal mitochondrial genome, despite its high variability, is under purifying selection. However, purifying selection will likely reduce variation and bias the site-frequency spectrum toward low-frequency variants in a manner similar to, but less extreme than, selective sweeps, making gene trees compressed toward the tips (Nielsen, 2005)
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From page 185... ...
Ultimately, phylogeographers should embrace a diversity of marker types even within individual studies, not only to allow the phylogeographic history of different marker types to illuminate each other but also to study genomic diversity and history in an unbiased way that facilitates the discovery of genomic loci underlying adaptation. Insight into Processes of Reticulation from Gene Tree Outliers Gene tree outliers, like Fst outliers, may be important indicators of nonneutral or locus-specific processes in the genome.
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From page 186... ...
Many computational methods targeted at the phylogeography– phylogenetics continuum necessarily ignore some kinds of reticulation. Key examples include models to estimate species trees from multiple unlinked loci using the multispecies coalescent (MSC)
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. Sequentially Markovian coalescent models have obvious applications in traditional species tree methods and may alleviate lingering concerns about recombination.
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From page 188... ...
now use linked or unlinked SNP data to estimate phylogenetic trees without explicitly estimating constituent gene trees. It remains to be seen whether the limited genealogical information in SNPs is compensated for by the large number of SNPs that can be collected in typical phylogenomic datasets.
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From page 189... ...
for access to tissues and data of rock-wallabies; Ke Bi and Sonal Singhal for assistance with Carlia data collection and preparation of Fig. 9.4; Brant Faircloth, John McCormack, and Robb Brumfield for assistance in acquisition of online datasets; and John Wakeley, Rudy Yoshida, and Alan Lemmon for helpful discussion.
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