Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l
We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and pr...
Source: Systematic Biology - June 12, 2020 Category: Biology Source Type: research
Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity
AbstractOrganismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the g...
Source: Systematic Biology - June 10, 2020 Category: Biology Source Type: research
Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems
AbstractThe common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse “true spiders” (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of m ultiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of tr...
Source: Systematic Biology - June 4, 2020 Category: Biology Source Type: research
Modeling Mito-nuclear Compatibility and Its Role in Species Identification
AbstractMitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation —as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, ...
Source: Systematic Biology - June 4, 2020 Category: Biology Source Type: research
Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets
AbstractThere are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000 –400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabiliz...
Source: Systematic Biology - May 27, 2020 Category: Biology Source Type: research
Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST
AbstractMarkov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective ...
Source: Systematic Biology - May 16, 2020 Category: Biology Source Type: research
Consistency of SVDQuartets and Maximum Likelihood for Coalescent-Based Species Tree Estimation
AbstractNumerous methods for inferring species-level phylogenies under the coalescent model have been proposed within the last 20 years, and debates continue about the relative strengths and weaknesses of these methods. One desirable property of a phylogenetic estimator is that of statistical consistency, which means intuitively that as more data are collected, the probability that the estimated tree has the same topology as the true tree goes to 1. To date, consistency results for species tree inference under the multispecies coalescent (MSC) have been derived only for summary statistics methods, such as ASTRAL and MP-EST...
Source: Systematic Biology - May 16, 2020 Category: Biology Source Type: research
Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics
AbstractThe bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has be...
Source: Systematic Biology - May 16, 2020 Category: Biology Source Type: research
Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space
AbstractHow can we best learn the history of a protein ’s evolution? Ideally, a model of sequence evolution should capture both the process that generates genetic variation and the functional constraints determining which changes are fixed. However, in practical terms the most suitable approach may simply be the one that combines the convenience of ea sily available input data with the ability to return useful parameter estimates. For example, we might be interested in a measure of the strength of selection (typically obtained using a codon model) or an ancestral structure (obtained using structural modeling based on inf...
Source: Systematic Biology - April 30, 2020 Category: Biology Source Type: research
Corrigendum to: Phylogeny Estimation Given Sequence Length Heterogeneity
Vladimir Smirnov and Tandy Warnow (Source: Systematic Biology)
Source: Systematic Biology - April 23, 2020 Category: Biology Source Type: research
The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms
AbstractThe Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept ofSeifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the article also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: “Specie...
Source: Systematic Biology - April 16, 2020 Category: Biology Source Type: research
Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts during the Global Diversification of Viburnum
AbstractPhylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, while incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant cladeViburnum (Adoxaceae) that we currently recognize in our ongoing world...
Source: Systematic Biology - April 8, 2020 Category: Biology Source Type: research
Comparative Phylogenetics of Papilio Butterfly Wing Shape and Size Demonstrates Independent Hindwing and Forewing Evolution
AbstractThe complex forces that shape butterfly wings have long been a subject of experimental and comparative research. Butterflies use their wings for flight, camouflage, mate recognition, warning, and mimicry. However, general patterns and correlations among wing shape and size evolution are still poorly understood. We collected geometric morphometric measurements from over 1400 digitized museum specimens ofPapilio swallowtails and combined them with phylogenetic data to test two hypotheses: 1) forewing shape and size evolve independently of hindwing shape and size and 2) wing size evolves more quickly than wing shape. ...
Source: Systematic Biology - April 7, 2020 Category: Biology Source Type: research
To Hop or Not to Hop? The Answer Is in the Bird Trees
AbstractBirds can use different types of gaits to move on the ground: they either walk, hop, or run. Although velocity can easily explain a preference for running, it remains unclear what drives a bird species to favor hopping over walking. As many hopping birds are relatively small and arboreal, we wanted to test the link between size, arboreality, and hopping ability. First, we carried out ancestral character state reconstructions of size range, hopping ability, and habitat traits on over 1000 species of birds. We found that both hopping ability and arboreality were derived and significantly correlated traits in avian ev...
Source: Systematic Biology - February 24, 2020 Category: Biology Source Type: research
A Multitype Birth –Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates
We present a new multitype birth –death model (MTBD) that can estimate lineage-specific birth and death rates. This corresponds to estimating lineage-dependent speciation and extinction rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees. In contrast with previous m odels, we do not presume to know the trait driving the rate differences, nor do we prohibit the same rates from appearing in different parts of the phylogeny. Using simulated data sets, we show that the MTBD model can reliably infer the presence of multiple evolutionary regimes, their positions ...
Source: Systematic Biology - February 24, 2020 Category: Biology Source Type: research
