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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...
May 18, 2018: Systematic Biology
Jonathan S Mitchell, Rampal S Etienne, Daniel L Rabosky
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification - extinction rates in particular - can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree...
May 18, 2018: Systematic Biology
Tobias Andermann, Alexandre M Fernandes, Urban Olsson, Mats Töpel, Bernard Pfeil, Bengt Oxelman, Alexandre Aleixo, Brant C Faircloth, Alexandre Antonelli
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies...
May 15, 2018: Systematic Biology
Haim Ashkenazy, Itamar Sela, Eli Levy Karin, Giddy Landan, Tal Pupko
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this filtering is often obscured by the resulting loss of phylogenetic signal...
May 15, 2018: Systematic Biology
Richard H Adams, Drew R Schield, Daren C Card, Todd A Castoe
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct computer simulations to explore the effects of violating this assumption in the form of species-specific positive selection when estimating species trees, species delimitations, and coalescent parameters under the model. We simulated datasets under an array of evolutionary scenarios that differ in both speciation parameters (i...
May 11, 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) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis...
April 27, 2018: Systematic Biology
Josef C Uyeda, Rosana Zenil-Ferguson, Matthew W Pennell
As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against - unreplicated evolutionary events...
April 25, 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...
April 25, 2018: Systematic Biology
Odile Maliet, Fanny Gascuel, Amaury Lambert
Phylogenetic diversity (PD) is a measure of the evolutionary legacy of a group of species, which can be used to define conservation priorities. It has been shown that an important loss of species diversity can sometimes lead to a much less important loss of PD, depending on the topology of the species tree and on the distribution of its branch lengths. However, the rate of decrease of PD strongly depends on the relative depths of the nodes in the tree and on the order in which species become extinct. We introduce a new, sampling-consistent, three-parameter model generating random trees with covarying topology, clades relative depths and clades relative extinction risks...
April 16, 2018: Systematic Biology
F Sara Ceccarelli, Nicolás Mongiardino Koch, Eduardo M Soto, Mariana L Barone, Miquel A Arnedo, Martín J Ramírez
While grasslands, one of Earth's major biomes, are known for their close evolutionary ties with ungulate grazers, these habitats are also paramount to the origins and diversification of other animals. Within the primarily South American spider subfamily Amaurobioidinae (Anyphaenidae), several species are found living in the continent's grasslands, with some displaying putative morphological adaptations to dwelling unnoticed in the grass blades. Here, a dated molecular phylogeny provides the backbone for analyses revealing the ecological and morphological processes behind these spiders' grassland adaptations...
April 14, 2018: Systematic Biology
Kyung Min Lee, Sami M Kivelä, Vladislav Ivanov, Axel Hausmann, Lauri Kaila, Niklas Wahlberg, Marko Mutanen
A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, RAD (Restriction site Associated DNA) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for non-model species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa...
April 14, 2018: Systematic Biology
Sonal Singhal, Conrad J Hoskin, Patrick Couper, Sally Potter, Craig Moritz
As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceeded heterogeneously. Here, we address these challenges as we diagnose and describe species in three co-occurring species groups of Australian lizards. By integrating genomic and morphological data with data on hybridization and introgression from contact zones, we explore several approaches - and their relative benefits and weaknesses - for testing the validity of cryptic lineages...
April 4, 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...
March 19, 2018: Systematic Biology
Jamie McCann, Tae-Soo Jang, Jiri Macas, Gerald M Schneeweiss, Nicholas J Matzke, Petr Novák, Tod F Stuessy, José L Villaseñor, Hanna Weiss-Schneeweiss
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid...
March 19, 2018: Systematic Biology
Colby Long, Laura Kubatko
Most current methods for inferring species-level phylogenies under the coa-lescent 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...
March 15, 2018: Systematic Biology
Kaitlin C Maguire, Douglas J Shinneman, Kevin M Potter, Valerie D Hipkins
Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America...
March 14, 2018: Systematic Biology
Frank T Burbrink, Marcelo Gehara
Most phylogenies are typically represented as purely bifurcating. However, as genomic data has 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...
March 9, 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. Here 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...
March 8, 2018: Systematic Biology
Dingqiao Wen, Yun Yu, Jiafan Zhu, Luay Nakhleh
PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g...
March 5, 2018: Systematic Biology
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March 1, 2018: Systematic Biology
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