Systematic Biology - Editorial Board
(Source: Systematic Biology)
Source: Systematic Biology - August 26, 2017 Category: Biology Source Type: research
Systematic Biology Volume 66, Number 5 September 2017 - Front Cover
(Source: Systematic Biology)
Source: Systematic Biology - August 26, 2017 Category: Biology Source Type: research
Phylogenetic Factor Analysis
AbstractPhylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that generates model residuals or the traits themselves. For high-dimensional traits, inferring all pair-wise correlations within the multivariate diffusion is limiting. To circumvent this problem, we propose phylogenetic factor analysis (PFA) that assumes a small unknown number of independent evolutionary factors arise along the phylogeny and these factors generate clusters of dependent...
Source: Systematic Biology - August 7, 2017 Category: Biology Source Type: research
Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
AbstractProteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time a...
Source: Systematic Biology - August 7, 2017 Category: Biology Source Type: research
Cladogenetic and Anagenetic Models of Chromosome Number Evolution: A Bayesian Model Averaging Approach
AbsstractChromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work byMayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, th...
Source: Systematic Biology - July 26, 2017 Category: Biology Source Type: research
When Homoplasy Is Not Homoplasy: Dissecting Trait Evolution by Contrasting Composite and Reductive Coding
AbstractThe conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs. reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method ...
Source: Systematic Biology - July 13, 2017 Category: Biology Source Type: research
Multivariate Phylogenetic Comparative Methods: Evaluations, Comparisons, and Recommendations
AbstractRecent years have seen increased interest in phylogenetic comparative analyses of multivariate data sets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the data set, but display increasing model misspecification as the number of trait ...
Source: Systematic Biology - July 13, 2017 Category: Biology Source Type: research
Genomic Signature of an Avian Lilliput Effect across the K-Pg Extinction
AbstractSurvivorship following major mass extinctions may be associated with a decrease in body size —a phenomenon called the Lilliput Effect. Body size is a strong predictor of many life history traits (LHTs), and is known to influence demography and intrinsic biological processes. Pronounced changes in organismal size throughout Earth history are therefore likely to be associated with concomita nt genome-wide changes in evolutionary rates. Here, we report pronounced heterogeneity in rates of molecular evolution (varying up to $\sim$20-fold) across a large-scale avian phylogenomic data set and show that nucleotide subst...
Source: Systematic Biology - July 13, 2017 Category: Biology Source Type: research
Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing
AbstractDisentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genusLinaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evalu...
Source: Systematic Biology - July 11, 2017 Category: Biology Source Type: research
Why Concatenation Fails Near the Anomaly Zone
AbstractGenome-scale sequencing has been of great benefit in recovering species trees but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge and has prompted the development of new strategies that can make the best use of available data. One such strategy —the concatenation of gene alignments—can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in ...
Source: Systematic Biology - July 11, 2017 Category: Biology Source Type: research
An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times
AbstractThe explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites that have similar evolutionary characteristics into the same partition and those with different characteristics into differe...
Source: Systematic Biology - July 4, 2017 Category: Biology Source Type: research
Taming the BEAST —A Community Teaching Material Resource for BEAST 2
AbstractPhylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods...
Source: Systematic Biology - June 29, 2017 Category: Biology Source Type: research
Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands
We present an improved time-calibrated molecular phylogeny of Cetartiodactyla, with phylogenetic reconstruction of ancestral ruminant diets and habitats, based on characteristics of extant taxa. Using this timeline, as well as the fossil record of grasslands, we conduct phylogenetic comparative analyses showing that hypsodonty in ruminants evolved as an adaptation to both diet and habitat. Our results demonstrate a slow, perhaps constrained, evolution of hypsodonty toward estimated optimal states, excluding the possibility of immediate adaptation. This augments recent findings that slow adaptation is not uncommon on millio...
Source: Systematic Biology - June 20, 2017 Category: Biology Source Type: research
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
AbstractNoncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not u...
Source: Systematic Biology - June 16, 2017 Category: Biology Source Type: research
