Dataset Information

Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.

ABSTRACT: Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data become more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and chromosomal inversion are expected to result in changes in the underlying gene trees along a chromosome, while changes in selective pressure and mutational rates for different genomic regions may lead to shifts in the underlying mutational process. We propose the split score as a general method for quantifying support for a particular phylogenetic relationship within a genomic data set. Because the split score is based on algebraic properties of a matrix of site pattern frequencies, it can be rapidly computed, even for data sets that are large in the number of taxa and/or in the length of the alignment, providing an advantage over other methods (e.g., maximum likelihood) that are often used to assess such support. Using simulation, we explore the properties of the split score, including its dependence on sequence length, branch length, size of a split and its ability to detect true splits in the underlying tree. Using a sliding window analysis, we show that split scores can be used to detect changes in the underlying evolutionary process for genome-scale data from primates, mosquitoes, and viruses in a computationally efficient manner. Computation of the split score has been implemented in the software package SplitSup.

SUBMITTER: Allman ES

PROVIDER: S-EPMC6075200 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.

Allman Elizabeth S ES Kubatko Laura S LS Rhodes John A JA

Systematic biology 20170701 4

Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data become more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and chromosomal inversion are expected to result in changes in the underlying gene trees along a chromosome, while changes in selective pressure and mutational rates for different genomic regions may lead to shifts in the underlying mutational process. We propose the split ...[more]

PMID: 28123114

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Project description:BackgroundHuman mobility is fundamental to understanding global issues in the health and social sciences such as disease spread and displacements from disasters and conflicts. Detailed mobility data across spatial and temporal scales are difficult to collect, however, with movements varying from short, repeated movements to work or school, to rare migratory movements across national borders. While typical sources of mobility data such as travel history surveys and GPS tracker data can inform different typologies of movement, almost no source of readily obtainable data can address all types of movement at once.MethodsHere, we collect Google Location History (GLH) data and examine it as a novel source of information that could link fine scale mobility with rare, long distance and international trips, as it uniquely spans large temporal scales with high spatial granularity. These data are passively collected by Android smartphones, which reach increasingly broad audiences, becoming the most common operating system for accessing the Internet worldwide in 2017. We validate GLH data against GPS tracker data collected from Android users in the United Kingdom to assess the feasibility of using GLH data to inform human movement.ResultsWe find that GLH data span very long temporal periods (over a year on average in our sample), are spatially equivalent to GPS tracker data within 100 m, and capture more international movement than survey data. We also find GLH data avoid compliance concerns seen with GPS trackers and bias in self-reported travel, as GLH is passively collected. We discuss some settings where GLH data could provide novel insights, including infrastructure planning, infectious disease control, and response to catastrophic events, and discuss advantages and disadvantages of using GLH data to inform human mobility patterns.ConclusionsGLH data are a greatly underutilized and novel dataset for understanding human movement. While biases exist in populations with GLH data, Android phones are becoming the first and only device purchased to access the Internet and various web services in many middle and lower income settings, making these data increasingly appropriate for a wide range of scientific questions.

Project description:Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes. While many processes can result in discord between gene trees and species trees, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is considered to be a dominant cause for gene tree heterogeneity. Coalescent-based methods have been developed to estimate species trees, many of which operate by combining estimated gene trees, and so are called "summary methods". Because summary methods are generally fast (and much faster than more complicated coalescent-based methods that co-estimate gene trees and species trees), they have become very popular techniques for estimating species trees from multiple loci. However, recent studies have established that summary methods can have reduced accuracy in the presence of gene tree estimation error, and also that many biological datasets have substantial gene tree estimation error, so that summary methods may not be highly accurate in biologically realistic conditions. Mirarab et al. (Science 2014) presented the "statistical binning" technique to improve gene tree estimation in multi-locus analyses, and showed that it improved the accuracy of MP-EST, one of the most popular coalescent-based summary methods. Statistical binning, which uses a simple heuristic to evaluate "combinability" and then uses the larger sets of genes to re-calculate gene trees, has good empirical performance, but using statistical binning within a phylogenomic pipeline does not have the desirable property of being statistically consistent. We show that weighting the re-calculated gene trees by the bin sizes makes statistical binning statistically consistent under the multispecies coalescent, and maintains the good empirical performance. Thus, "weighted statistical binning" enables highly accurate genome-scale species tree estimation, and is also statistically consistent under the multi-species coalescent model. New data used in this study are available at DOI: http://dx.doi.org/10.6084/m9.figshare.1411146, and the software is available at https://github.com/smirarab/binning.

Dataset Information

Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.

Publications

Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.

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