Probabilistic Distances Between Trees
AbstractMost existing measures of distance between phylogenetic trees are based on the geometry or topology of the trees. Instead, we consider distance measures which are based on the underlying probability distributions on genetic sequence data induced by trees. Monte Carlo schemes are necessary to calculate these distances approximately, and we describe efficient sampling procedures. Key features of the distances are the ability to include substitution model parameters and to handle trees with different taxon sets in a principled way. We demonstrate some of the properties of these new distance measures and compare them t...
Source: Systematic Biology - October 4, 2017 Category: Biology Source Type: research
Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)
AbstractHybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here, we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new s...
Source: Systematic Biology - September 25, 2017 Category: Biology Source Type: research
Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families
AbstractA fundamental challenge in resolving evolutionary relationships across the tree of life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees. We find two distinc...
Source: Systematic Biology - September 22, 2017 Category: Biology Source Type: research
A General Model for Estimating Macroevolutionary Landscapes
AbstractThe evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein –Uhlenbeck process, plus some of their extensions. Here, we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscap...
Source: Systematic Biology - September 22, 2017 Category: Biology Source Type: research
To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
AbstractWith the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that coestimate the gene trees and the species tree, summary methods that compute the ...
Source: Systematic Biology - September 15, 2017 Category: Biology Source Type: research
Erratum
Toljagic O., Voje K.L., Matschiner M., Liow L.H., Hansen T.F. 2017. Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands. Sys. Biol.Doi: 10.1093/sysbio/syx059. (Source: Systematic Biology)
Source: Systematic Biology - September 8, 2017 Category: Biology Source Type: research
The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates
AbstractDivergence time estimation —the calibration of a phylogeny to geological time—is an integral first step in modeling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of y...
Source: Systematic Biology - September 7, 2017 Category: Biology Source Type: research
Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent
AbstractThe use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek...
Source: Systematic Biology - September 4, 2017 Category: Biology Source Type: research
Use of Continuous Traits Can Improve Morphological Phylogenetics
This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference. (Source: Systematic Biology)
Source: Systematic Biology - September 1, 2017 Category: Biology Source Type: research
Issues and Perspectives in Species Delimitation using Phenotypic Data: Atlantean Evolution in Darwin ’s Finches
AbstractProgress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches em...
Source: Systematic Biology - September 1, 2017 Category: Biology Source Type: research
Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats
AbstractThe rapid diversification ofMyotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships withinMyotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships withinMyotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representativeMyotis, primarily from the New World, in conjunction with targeted sequencing o...
Source: Systematic Biology - August 26, 2017 Category: Biology Source Type: research
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Source: Systematic Biology - August 26, 2017 Category: Biology Source Type: research
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Source: Systematic Biology - August 26, 2017 Category: Biology Source Type: research
Systematic Biology Volume 66, Number 5 September 2017 - Back Cover
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Source: Systematic Biology - August 26, 2017 Category: Biology Source Type: research
