Long Branch Attraction Biases in Phylogenetics
AbstractLong branch attraction (LBA) is a prevalent form of bias in phylogenetic estimation but the reasons for it are only partially understood. We argue here that it is largely due to differences in the sizes of the model spaces corresponding to different trees. Trees with long branches together allow much more flexible internal branch length parameter estimation. Consequently, although each tree has the same number of parameters, trees with long branches together have larger effective model spaces. The problem of LBA becomes particularly pronounced with partitioned data. Formulation of tree estimation as model selection...
Source: Systematic Biology - February 2, 2021 Category: Biology Source Type: research
Adaptive Tree Proposals for Bayesian Phylogenetic Inference
AbstractBayesian inference of phylogeny with Markov chain Monte Carlo plays a key role in the study of evolution. Yet, this method still suffers from a practical challenge identified more than two decades ago: designing tree topology proposals that efficiently sample tree spaces. In this article, I introduce the concept of adaptive tree proposals for unrooted topologies, that is, tree proposals adapting to the posterior distribution as it is estimated. I use this concept to elaborate two adaptive variants of existing proposals and an adaptive proposal based on a novel design philosophy in which the structure of the proposa...
Source: Systematic Biology - January 30, 2021 Category: Biology Source Type: research
A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth ’s Largest Lizards
AbstractHybridization between species occurs more frequently in vertebrates than traditionally thought, but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprise $>$300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We ...
Source: Systematic Biology - January 29, 2021 Category: Biology Source Type: research
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses
AbstractPhylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approa...
Source: Systematic Biology - January 28, 2021 Category: Biology Source Type: research
Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)
AbstractAnthozoan cnidarians (corals and sea anemones) include some of the world ’s most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, anal yses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolu...
Source: Systematic Biology - January 28, 2021 Category: Biology Source Type: research
The Comparative Method is Not Macroevolution: Across-Species Evidence for Within-Species Process
AbstractIt is common for studies that employ the comparative method for the study of adaptation, that is, documentation of potentially adaptive across-species patterns of trait –environment or trait–trait correlation, to be designated as “macroevolutionary.” Authors are justified in using “macroevolution” in this way by appeal to definitions such as “evolution above the species level.” I argue that regarding the comparative method as “macroevolutionary” is harmful because it hides in serious ways the true causal content of hypotheses tested with the comparative method. The comparative method is a means ...
Source: Systematic Biology - January 7, 2021 Category: Biology Source Type: research
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)
AbstractEvidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in theTamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (...
Source: Systematic Biology - January 7, 2021 Category: Biology Source Type: research
Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data
AbstractInterspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale data sets has revolutionized hybridization studies to shift from the observation of the presence or absence of hybrids to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. In addition to methods that i...
Source: Systematic Biology - January 6, 2021 Category: Biology Source Type: research
The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)
AbstractGonyleptoidea, largely restricted to the Neotropics, constitutes the most diverse superfamily of Opiliones and includes the largest and flashiest representatives of this arachnid order. However, the relationships among its main lineages (families and subfamilies) and the timing of their origin are not sufficiently understood to explain how this tropical clade has been able to colonize the temperate zone. Here, we used transcriptomics and divergence time dating to investigate the phylogeny of Gonyleptoidea. Our results support the monophyly of Gonyleptoidea and all of its families with more than one species represen...
Source: Systematic Biology - January 5, 2021 Category: Biology Source Type: research
A Multifunction Trade-Off has Contrasting Effects on the Evolution of Form and Function
AbstractTrade-offs caused by the use of an anatomical apparatus for more than one function are thought to be an important constraint on evolution. However, whether multifunctionality suppresses diversification of biomechanical systems is challenged by recent literature showing that traits more closely tied to trade-offs evolve more rapidly. We contrast the evolutionary dynamics of feeding mechanics and morphology between fishes that exclusively capture prey with suction and multifunctional species that augment this mechanism with biting behaviors to remove attached benthic prey. Diversification of feeding kinematic traits ...
Source: Systematic Biology - January 5, 2021 Category: Biology Source Type: research
The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics
AbstractThe phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic data sets whether or not the inferred trees and clades are correct. Here, we study the asymptotic behavior of bootstrap support for the ML tree in large data sets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are...
Source: Systematic Biology - December 30, 2020 Category: Biology Source Type: research
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
AbstractThe phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 speci...
Source: Systematic Biology - December 26, 2020 Category: Biology Source Type: research
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees
AbstractSummarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-...
Source: Systematic Biology - December 26, 2020 Category: Biology Source Type: research
Genomics Reveals Widespread Ecological Speciation in Flightless Insects
AbstractRecent genomic analyses have highlighted parallel divergence in response to ecological gradients, but the extent to which altitude can underpin such repeated speciation remains unclear. Wing reduction and flight loss have apparently evolved repeatedly in montane insect assemblages and have been suggested as important drivers of hexapod diversification. We test this hypothesis using genomic analyses of a widespread wing-polymorphic stonefly species complex in New Zealand. We identified over 50,000 polymorphic genetic markers generated across almost 200Zelandoperla fenestrata stonefly specimens using a newly generate...
Source: Systematic Biology - December 21, 2020 Category: Biology Source Type: research
Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)
AbstractReliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstruc...
Source: Systematic Biology - December 21, 2020 Category: Biology Source Type: research
