Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals
In this study, we investigate the utility of nonreversible models to root empirical phylogenies and introduce a new bootstrap measure, therootstrap, which provides information on the statistical support for any given root position. [Bootstrap; nonreversible models; phylogenetic inference; root estimation.] (Source: Systematic Biology)
Source: Systematic Biology - August 13, 2021 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - August 11, 2021 Category: Biology Source Type: research
Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets
This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for...
Source: Systematic Biology - July 7, 2021 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - June 16, 2021 Category: Biology Source Type: research
Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils
AbstractThe tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here, we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular data to build a robust species-level phylogeny for c.130 Theaceae species, resolving most impor...
Source: Systematic Biology - June 9, 2021 Category: Biology Source Type: research
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life
AbstractThe Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phyloge...
Source: Systematic Biology - May 10, 2021 Category: Biology Source Type: research
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)
AbstractThe use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a ...
Source: Systematic Biology - May 6, 2021 Category: Biology Source Type: research
Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences
AbstractThe charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes —the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challengin g. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recen...
Source: Systematic Biology - April 23, 2021 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - April 15, 2021 Category: Biology Source Type: research
Species Tree Estimation from Gene Trees by Minimizing Deep Coalescence and Maximizing Quartet Consistency: A Comparative Study and the Presence of Pseudo Species Tree Terraces
In this study, we have extended and adapted the concept of phylogenetic terraces to species tree estimation by “summarizing” a set of gene trees, where multiple species trees with distinct topologies may have exactly the same optimality score (i.e.,quartet score,extra lineage score, etc.). We particularly investigated the presence and impacts of equally optimal trees in species tree estimation from multilocus data using summary methods by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria:maximize quartet consistency (MQC) andminimize deep coalescence (MDC). Methods based on MQ...
Source: Systematic Biology - April 12, 2021 Category: Biology Source Type: research
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses
AbstractSix-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding appr...
Source: Systematic Biology - April 10, 2021 Category: Biology Source Type: research
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)
AbstractSigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main groups of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to...
Source: Systematic Biology - March 31, 2021 Category: Biology Source Type: research
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow
AbstractPhylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae,Phylloscopus, leaf warblers) using onede novo genome assembly and 78 resequenced genomes. On the basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demogr...
Source: Systematic Biology - March 31, 2021 Category: Biology Source Type: research
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification
AbstractPhylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive assessment of the key variables that underpin analyses in this field —including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling. We show that in unrealistically simplistic cases (where substitution rates and speciation rates are constant, ...
Source: Systematic Biology - March 24, 2021 Category: Biology Source Type: research
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity
AbstractPhylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group th...
Source: Systematic Biology - March 24, 2021 Category: Biology Source Type: research
