Announcements
(Source: Systematic Biology)
Source: Systematic Biology - June 23, 2022 Category: Biology Source Type: research
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support
AbstractGenomic data have only sometimes brought resolution to the tree of life. Large phylogenomic studies can reach conflicting conclusions about important relationships, with mutually exclusive hypotheses receiving strong support. Reconciling such differences requires a detailed understanding of how phylogenetic signal varies among data sets. Two complementary strategies for better understanding phylogenomic conflicts are to examine support on a locus-by-locus basis and use support values that capture a larger range of variation in phylogenetic information, such as likelihood ratios. Likelihood ratios can be calculated ...
Source: Systematic Biology - March 22, 2022 Category: Biology Source Type: research
On the Need for New Measures of Phylogenomic Support
AbstractThe scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount of information with which to draw inferences about evolutionary history. However, standard approaches to assessing confidence in those inferences (e.g., nonparametric bootstrap proportions [BP] and Bayesian posterior probabilities [PPs]) are still deeply influenced by statistical procedures and frameworks that were developed when information was much more limited. These approaches largely quantify uncertainty caused by limited amounts of data, which is often vanishingly small wi...
Source: Systematic Biology - February 17, 2022 Category: Biology Source Type: research
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent
AbstractAs genomic sequence data become increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent (MSC) methods address these issues. This is achieved by constraining a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 —a software package for e...
Source: Systematic Biology - February 17, 2022 Category: Biology Source Type: research
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex)
AbstractMany phylogeographic studies on species with large ranges have found genetic –geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomi...
Source: Systematic Biology - November 23, 2021 Category: Biology Source Type: research
Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution
AbstractAlthough phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We uneq...
Source: Systematic Biology - November 23, 2021 Category: Biology Source Type: research
A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution
AbstractAn evolutionary process is reflected in the sequence of changes of any trait (e.g., morphological or molecular) through time. Yet, a better understanding of evolution would be procured by characterizing correlated evolution, or when two or more evolutionary processes interact. Previously developed parametric methods often require significant computing time as they rely on the estimation of many parameters. Here, we propose a minimal likelihood framework modeling the joint evolution of two traits on a known phylogenetic tree. The type and strength of correlated evolution are characterized by a few parameters tuning ...
Source: Systematic Biology - November 18, 2021 Category: Biology Source Type: research
Different Evolutionary Pathways Lead to Incomplete Convergence of Elongate Body Shapes in Carnivoran Mammals
AbstractAlthough convergence is often recognized as a ubiquitous feature across the Tree of Life, whether the underlying traits also exhibit similar evolutionary pathways towards convergent forms puzzles biologists. In carnivoran mammals, “elongate,” “slender,” and “long” are often used to describe and even to categorize mustelids (martens, polecats, and weasels), herpestids (mongooses), viverrids (civets and genets), and other carnivorans together. But just how similar these carnivorans are and whether there is convergen ce in the morphological component that contribute to elongation has never been assessed. H...
Source: Systematic Biology - November 15, 2021 Category: Biology Source Type: research
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs
In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate poten tial evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference—a region of a tree that possesses short branches and no “support” for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspec...
Source: Systematic Biology - November 13, 2021 Category: Biology Source Type: research
How to Render Species Comparable Taxonomic Units Through Deep Time: A Case Study on Intraspecific Osteological Variability in Extant and Extinct Lacertid Lizards
AbstractGenerally, the species is considered to be the only naturally occurring taxon. However, species recognized and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species because the only available data for species delimitation in fossils are derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, and intergeneric osteological variability in extant species of lac...
Source: Systematic Biology - November 6, 2021 Category: Biology Source Type: research
On Information Rank Deficiency in Phenotypic Covariance Matrices
This article investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in a model system. Lastly, we propose methods to treat for this information rank deficiency. Our first goal is to establish how the rank of a typical geometric morphometric covariance matrix relates to the information entropy of its eigenvalue spectrum. This requires clear definiti...
Source: Systematic Biology - November 4, 2021 Category: Biology Source Type: research
Relative Time Constraints Improve Molecular Dating
AbstractDating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. For example, horizontal gene transfer events and ancient coevolutionary interactions such as (endo)symbioses occur between contemporaneous species and thus can imply temporal relationships between two nodes in a phylogeny. Temporal constraints from these alternative sources can be particularly helpful when the geological r...
Source: Systematic Biology - October 20, 2021 Category: Biology Source Type: research
Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails
We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinaesubfam. nov. is designated for the clade comprisingTectus, Cittarium, andRochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models versus concatenated partitioned analyses and...
Source: Systematic Biology - October 18, 2021 Category: Biology Source Type: research
Announcements
(Source: Systematic Biology)
Source: Systematic Biology - October 13, 2021 Category: Biology Source Type: research
Phylogenetic Signal and Bias in Paleontology
AbstractAn unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data sets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological data sets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morp...
Source: Systematic Biology - September 1, 2021 Category: Biology Source Type: research
