Phylogeographic Estimation and Simulation of Global Diffusive Dispersal
AbstractThe analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example, for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2D plane; however, the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because spherical Brownian motion (SBM) differs from planar Brownian motion. No statistical method exists for estimating SBM diffusion coefficients from a given timetree and tip coordinates, and no method exists for simulating SBM alon...
Source: Systematic Biology - July 29, 2020 Category: Biology Source Type: research
Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees
AbstractIt is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here, we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-kno...
Source: Systematic Biology - July 28, 2020 Category: Biology Source Type: research
Corrigendum to: “Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae”
Rong Zhang, Yin-Huan Wang, Jian-Jun Jin, Gregory W Stull, Anne Bruneau, Domingos Cardoso, Luciano Paganucci De Queiroz, Michael J Moore, Shu-Dong Zhang, Si-Yun Chen, Jian Wang, De-Zhu Li, Ting-Shuang Yi (Source: Systematic Biology)
Source: Systematic Biology - July 26, 2020 Category: Biology Source Type: research
Phylogeny Estimation Given Sequence Length Heterogeneity
AbstractPhylogeny estimation is a major step in many biological studies, and has many well known challenges. With the dropping cost of sequencing technologies, biologists now have increasingly large datasets available for use in phylogeny estimation. Here we address the challenge of estimating a tree given large datasets with a combination of full-length sequences and fragmentary sequences, which can arise due to a variety of reasons, including sample collection, sequencing technologies, and analytical pipelines. We compare two basic approaches: (1) computing an alignment on the full dataset and then computing a maximum li...
Source: Systematic Biology - July 21, 2020 Category: Biology Source Type: research
Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit
AbstractThe incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees...
Source: Systematic Biology - July 21, 2020 Category: Biology Source Type: research
Relaxed Random Walks at Scale
AbstractRelaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny and more accurately model overdispersed biological data. Increased taxonomic sampling challenges inference under RRWs as the number of unknown parameters grows with the number of taxa. To solve this problem, we present a scalable method to efficiently fit RRWs and infer this branch-specific variation in a Bayesian framework. We develop a Hamiltonian Monte Carlo (HMC) sampler to approximate the high-dimensional, correlated posterior that ex...
Source: Systematic Biology - July 20, 2020 Category: Biology Source Type: research
On the Effect of Asymmetrical Trait Inheritance on Models of Trait Evolution
AbstractCurrent phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a “jump” of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymm...
Source: Systematic Biology - July 18, 2020 Category: Biology Source Type: research
The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment
AbstractSequence alignment is essential for phylogenetic and molecular evolution inference, as well as in many other areas of bioinformatics and evolutionary biology. Inaccurate alignments can lead to severe biases in most downstream statistical analyses. Statistical alignment based on probabilistic models of sequence evolution addresses these issues by replacing heuristic score functions with evolutionary model-based probabilities. However, score-based aligners and fixed-alignment phylogenetic approaches are still more prevalent than methods based on evolutionary indel models, mostly due to computational convenience. Here...
Source: Systematic Biology - July 12, 2020 Category: Biology Source Type: research
Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent
AbstractMouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we investigate mouse lemur diversity in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for two pairs of sister lineages that include three named species...
Source: Systematic Biology - July 8, 2020 Category: Biology Source Type: research
Bayesian Inference of Species Trees using Diffusion Models
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of data sets containing hundreds or thousands of individuals. The method, which we callSnapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements, and accuracy recovering known model parameters. A reanalysis of soybea...
Source: Systematic Biology - July 6, 2020 Category: Biology Source Type: research
Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach
AbstractThe branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth –death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversif ication rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phyloge...
Source: Systematic Biology - July 3, 2020 Category: Biology Source Type: research
Defining Species When There is Gene Flow
AbstractWhatever one ’s definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the mul tispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a geneti c seque...
Source: Systematic Biology - July 3, 2020 Category: Biology Source Type: research
Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal
AbstractPhylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from ...
Source: Systematic Biology - July 3, 2020 Category: Biology Source Type: research
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
AbstractMolecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree –s...
Source: Systematic Biology - June 30, 2020 Category: Biology Source Type: research
On the Selection and Analysis of Clades in Comparative Evolutionary Studies
AbstractResearchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternat...
Source: Systematic Biology - June 14, 2020 Category: Biology Source Type: research
