Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales
AbstractPhylogenetic reconstruction based on morphometric data is hampered by homoplasies. For example, many similarities in cranial form between primate taxa more strongly reflect ecological similarities rather than phylogenetic relatedness. However, the way in which the different cranial bones constitute cranial form is, if at all, of less functional relevance and thus largely hidden from selection. We propose that these “constructional details” are better indicators of phylogenetic history than any large-scale shape feature or raw form variable. Within a geometric morphometric context, we show how to analyze the rel...
Source: Systematic Biology - December 18, 2020 Category: Biology Source Type: research
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(Source: Systematic Biology)
Source: Systematic Biology - December 16, 2020 Category: Biology Source Type: research
Uncertainty in Divergence Time Estimation
AbstractUnderstanding and representing uncertainty is crucial in academic research because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogeni...
Source: Systematic Biology - December 12, 2020 Category: Biology Source Type: research
Mapping Africa ’s Biodiversity: More of the Same Is Just Not Good Enough
AbstractSpecies distribution data are fundamental to the understanding of biodiversity patterns and processes. Yet, such data are strongly affected by sampling biases, mostly related to site accessibility. The understanding of these biases is therefore crucial in systematics, biogeography, and conservation. Here we present a novel approach for quantifying sampling effort and its impact on biodiversity knowledge, focusing on Africa. In contrast to previous studies assessing sampling completeness (percentage of species recorded in relation to predicted), we investigate whether the lack of knowledge of a site attracts scienti...
Source: Systematic Biology - December 11, 2020 Category: Biology Source Type: research
The Legacy of Recurrent Introgression during the Radiation of Hares
AbstractHybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification ofLepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1 –4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a c...
Source: Systematic Biology - December 2, 2020 Category: Biology Source Type: research
A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution
AbstractDetecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein-coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a prespecified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolv...
Source: Systematic Biology - November 30, 2020 Category: Biology Source Type: research
The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes
In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild speciesErythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient dom...
Source: Systematic Biology - November 13, 2020 Category: Biology Source Type: research
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution
AbstractIncomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T), and loss (L). These processes are usually modeled independently, but in reality, ILS can affect gene copy number polymorphism, that is, interfere with DTL. This has been previously recognized, but not treated in a satisfactory way, mainly because DTL events are naturally modeled forward-in-time, while ILS is naturally modeled backward-in-time with the coalescent. Here, we consider the joint action of ILS and DTL on the gene t...
Source: Systematic Biology - November 10, 2020 Category: Biology Source Type: research
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales
AbstractThe genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering ...
Source: Systematic Biology - November 10, 2020 Category: Biology Source Type: research
Book Review: A Mathematical Primer of Molecular Phylogenetics, by Xuhua Xia
InA Mathematical Primer of Molecular Phylogenetics, Professor Xuhua Xia provides an introduction to many of the methods commonly used in analyzing molecular sequence data in order to infer a phylogenetic tree. The topics covered in the book follow the progression from data preparation to model definition and model selection to inference of the phylogeny using the chosen model. In describing the methods used at each stage in the process, Professor Xia has gone to considerable effort to provide examples that are based on empirical data, as well as worked details for the analyses performed on these data. These aspects of the ...
Source: Systematic Biology - November 10, 2020 Category: Biology Source Type: research
Do Meristic Characters Used in Phylogenetic Analysis Evolve in an Ordered Manner?
AbstractThe use of ordered characters in phylogenetic analysis has been inconsistent throughout the history of phylogenetic inference. It has become more widespread in recent years, and some have advocated that all characters representing continuous or meristic traits should be ordered as a matter of course. Here, using the example of dental evolution, we examine two factors that may impact on whether meristic characters actually evolve in an ordered manner: the regulatory hierarchy governing the development of teeth that allows large sections of the entire tooth row to be suppressed in a single transition and regionalizat...
Source: Systematic Biology - October 26, 2020 Category: Biology Source Type: research
A Cautionary Note on the Use of Genotype Callers in Phylogenomics
AbstractNext-generation-sequencing genotype callers are commonly used in studies to call variants from newly sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulati...
Source: Systematic Biology - October 21, 2020 Category: Biology Source Type: research
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos
AbstractRapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We fi...
Source: Systematic Biology - October 15, 2020 Category: Biology Source Type: research
Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)
AbstractTaxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set compri...
Source: Systematic Biology - October 15, 2020 Category: Biology Source Type: research
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets
AbstractThe insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and nonparasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and nonparasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2370 orthologous genes. All phylogenomic analyses, includi...
Source: Systematic Biology - September 26, 2020 Category: Biology Source Type: research
