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1 Running Head: PHYLOGENOMICS OF A RAPID RADIATION Title: The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
"... D ow nloaded from 2 Abstract.—Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogeno ..."
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D ow nloaded from 2 Abstract.—Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (<10 loci) datasets. We sequenced hundreds of ultraconserved elements (UCEs) and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be
Manuscript type: Article Recommended MBE section: Methods Evaluating the use of ABBA-BABA statistics to locate introgressed loci
, 2014
"... This is an Open Access article distributed under the terms of the Creative Commons Attribution License ..."
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This is an Open Access article distributed under the terms of the Creative Commons Attribution License
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"... lo are s, IA nite sity, Gossypium loid tro ffer ran ies, is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here. e genu id gen 5) and eage. ..."
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lo are s, IA nite sity, Gossypium loid tro ffer ran ies, is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here. e genu id gen 5) and eage.
Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs
"... Abstract.—Genetic introgression ispervasive innatureandmay lead to large-scalephenotypic assimilationand/oradmixture of populations, but there is limited knowledge on whether large phenotypic changes are typically accompanied by high levels of introgression throughout the genome. Using bioacoustic, ..."
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Abstract.—Genetic introgression ispervasive innatureandmay lead to large-scalephenotypic assimilationand/oradmixture of populations, but there is limited knowledge on whether large phenotypic changes are typically accompanied by high levels of introgression throughout the genome. Using bioacoustic, biometric, and spectrophotometric data from a flycatcher (Tyrannidae) system in the Neotropical genus Zimmerius, we document a mosaic pattern of phenotypic admixture in which a population of Zimmerius viridiflavus in northern Peru (henceforth “mosaic”) is vocally and biometrically similar to conspecifics to the south but shares plumage characteristics with a different species (Zimmerius chrysops) to the north. To clarify the origins of the mosaic population, we used the RAD-seq approach to generate a data set of 37,361 genome-wide single nucleotide polymorphisms (SNPs). A range of population-genetic diagnostics shows that the genome of the mosaic population is largely indistinguishable from southern Z. viridiflavus and distinct from northern Z. chrysops, and the application of parsimony and species tree methods to the genome-wide SNP data set confirms the close affinity of the
A rticle Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
"... Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson’s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestra ..."
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Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson’s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f ̂ d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f ̂ d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f ̂ d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.
DOI:10.1093/sysbio/syv039 Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh.
, 2015
"... Abstract.—Genome sequence data contain abundant information about genealogical history, but methods for extracting and interpreting this information are not yet fully developed. We analyzed genome sequences for multiple accessions of the selfing plant,Arabidopsis thaliana, with the goal of better un ..."
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Abstract.—Genome sequence data contain abundant information about genealogical history, but methods for extracting and interpreting this information are not yet fully developed. We analyzed genome sequences for multiple accessions of the selfing plant,Arabidopsis thaliana, with the goal of better understanding its genealogical history. As expected from accessions of the samespecies,we foundmuchdiscordancebetweennucleargene trees.Nonetheless,we inferred theoptimalpopulation tree under the assumption that all discordance is due to incomplete lineage sorting. To cope with the size of the data (many genes and many taxa), our pipeline is based on parallel computing and divides the problem into four-taxon trees. However, just because a population tree can be estimated does not mean that the assumptions of the multispecies coalescent model hold. Therefore, we implemented a new, nonparametric test to evaluate whether a population tree adequately explains the observed quartet frequencies (the frequencies of gene trees with each resolution of each four-taxon set). This test also considers other models: panmixia and a partially resolved population tree, that is, a tree in which some nodes are collapsed into local panmixia. We found that a partially resolved population tree provides the best fit to the data, providing evidence for tree-like structure within A. thaliana, qualitatively similar to what might be expected between different, closely related
RH: EXPLORING TREE-LIKE PATTERNS USING GENOME SEQUENCES Exploring
"... tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. ..."
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tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh.
