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Systematic Biology

Bryan S McLean, Kayce C Bell, Julie M Allen, Kristofer M Helgen, Joseph A Cook
Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a dataset of > 3,950 ultraconserved element (UCE) loci from a classic mammalian radiation, ground-dwelling squirrels of the tribe Marmotini (Sciuridae: Xerinae), to assess sensitivity of phylogenetic estimates to varying per-locus information content across 4 different inference methods (RAxML, ASTRAL, NJst, SVDquartets)...
September 18, 2018: Systematic Biology
Fan Song, Hu Li, Guo-Hua Liu, Wei Wang, Peter James, Douglas D Colwell, Anette Tran, Siyu Gong, Wanzhi Cai, Renfu Shao
Organelle genome fragmentation has been found in a wide range of eukaryotic lineages; however, its use in phylogenetic reconstruction has not been demonstrated. We explored the use of mitochondrial (mt) genome fragmentation in resolving the controversial suborder-level phylogeny of parasitic lice (order Phthiraptera). There are ∼5,000 species of parasitic lice in four suborders (Amblycera, Ischnocera, Rhynchophthirina and Anoplura), which infest mammals and birds. The phylogenetic relationships among these suborders are unresolved despite decades of studies...
September 17, 2018: Systematic Biology
Anthony R Ives
Many researchers want to report an R2 to measure the variance explained by a model. When the model includes correlation among data, such as phylogenetic models and mixed models, defining an R2 faces two conceptual problems. (i) It is unclear how to measure the variance explained by predictor (independent) variables when the model contains covariances. (ii) Researchers may want the R2 to include the variance explained by the covariances by asking questions such as "How much of the data is explained by phylogeny?" Here, I investigate three R2s for phylogenetic and mixed models...
September 17, 2018: Systematic Biology
Luciano Varela, P Sebastián Tambusso, H Gregory McDonald, Richard A Fariña
Sloths, like other xenarthrans, are an extremely interesting group of mammals that, after a long history of evolution and diversification in South America, became established on islands in the Caribbean and later reached North America during the Great American Biotic Interchange. In all three regions, they were part of the impressive Pleistocene megafauna. Most taxa became extinct and only two small, distantly related tree-dwelling genera survived. Here we incorporate several recently described genera of sloths into an assembled morphological data supermatrix and apply Bayesian inference, using phylogenetic and morphological clock methods, to 64 sloth genera...
September 15, 2018: Systematic Biology
Eli Levy Karin, Haim Ashkenazy, Jotun Hein, Tal Pupko
Classic alignment algorithms utilize scoring functions which maximize similarity or minimize edit distances. These scoring functions account for both insertion-deletion (indel) and substitution events. In contrast, alignments based on stochastic models aim to explicitly describe the evolutionary dynamics of sequences by inferring relevant probabilistic parameters from input sequences. Despite advances in stochastic modeling during the last two decades, scoring-based methods are still dominant, partially due to slow running times of probabilistic approaches...
September 15, 2018: Systematic Biology
Jamie R Oaks
A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data...
September 15, 2018: Systematic Biology
Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis
Next Generation Sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the Evolutionary Placement Algorithm (EPA) included in RAxML, or pplacer, are being increasingly used for this purpose...
August 27, 2018: Systematic Biology
Adam D Leaché, Tianqi Zhu, Bruce Rannala, Ziheng Yang
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of gene trees and sequence data, which explains why no method can use such data to distinguish between population splits and speciation...
July 5, 2018: Systematic Biology
Patricio Maturana R, Brendon J Brewer, Steffen Klaere, Remco R Bouckaert
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, even for simple models, incurs high computational cost. Another interesting challenge relates to the estimation of the posterior distribution...
June 29, 2018: Systematic Biology
Joseph F Walker, Joseph W Brown, Stephen A Smith
Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Herein, we examined two data sets where supermatrix and coalescent-based species trees conflict. We identified two highly influential "outlier" genes in each data set. When removed from each data set, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate data set have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant data set did not exhibit any obvious systematic error, and therefore, may be the result of some biological process yet to be determined...
September 1, 2018: Systematic Biology
James H Degnan
Simultaneously modeling hybridization and the multispecies coalescent is becoming increasingly common, and inference of species networks in this context is now implemented in several software packages. This article addresses some of the conceptual issues and decisions to be made in this modeling, including whether or not to use branch lengths and issues with model identifiability. This article is based on a talk given at a Spotlight Session at Evolution 2017 meeting in Portland, Oregon. This session included several talks about modeling hybridization and gene flow in the presence of incomplete lineage sorting...
September 1, 2018: Systematic Biology
Jonathan D Mitchell, Jeremy G Sumner, Barbara R Holland
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the $3$-taxon case in some detail, we illustrate that phylogeneticists have been "spoiled" in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like...
September 1, 2018: Systematic Biology
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more...
September 1, 2018: Systematic Biology
Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, K William Sparks, Cécile Ané
The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks...
September 1, 2018: Systematic Biology
Colby Long, Laura Kubatko
Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. Several studies have examined the impact of gene flow (e.g., Eckert and Carstens 2008; Chung and Ané 2011; Leaché et al. 2014; Solís-Lemus et al. 2016) and of ancestral population structure (DeGeorgio and Rosenberg 2016) on the performance of species-level phylogenetic inference, and analytic results have been proven for network models of gene flow (e.g., Solís-Lemus et al...
September 1, 2018: Systematic Biology
Paul D Blischak, Julia Chifman, Andrea D Wolfe, Laura S Kubatko
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees...
September 1, 2018: Systematic Biology
Frank T Burbrink, Marcelo Gehara
Most phylogenies are typically represented as purely bifurcating. However, as genomic data have become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns...
September 1, 2018: Systematic Biology
Liang Li, Liang Lü, Steven A Nadler, David I Gibson, Lu-Ping Zhang, Hui-Xia Chen, Wen-Ting Zhao, Yan-Ning Guo
Ascaridoids are among the commonest groups of zooparasitic nematodes (roundworms) and occur in the alimentary canal of all major vertebrate groups, including humans. They have an extremely high diversity and are of major socio-economic importance. However, their evolutionary history remains poorly known. Herein, we performed a comprehensive phylogenetic analysis of the Ascaridoidea. Our results divided the Ascaridoidea into six monophyletic major clades, i.e., the Heterocheilidae, Acanthocheilidae, Anisakidae, Ascarididae, Toxocaridae, and Raphidascarididae, among which the Heterocheilidae, rather than the Acanthocheilidae, represents the sister clade to the remaining ascaridoids...
September 1, 2018: Systematic Biology
Frédéric Legendre, Fabien L Condamine
Eusociality, Darwin's special difficulty, has been widely investigated but remains a topic of great debate in organismal biology. Eusocial species challenge existing theories, and the impact of highly integrated societies on diversification dynamics is controversial with opposing assertions and hypotheses in the literature. Here, using phylogenetic approaches in termites-the first group that has evolved eusociality-we assessed the fundamental prediction that eusocial lineages have higher diversification rates than non-eusocial clades...
September 1, 2018: Systematic Biology
Emilie J Richards, Jeremy M Brown, Anthony J Barley, Rebecca A Chong, Robert C Thomson
The use of large genomic data sets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological vs. methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance...
September 1, 2018: Systematic Biology
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