Comparative anatomy and phylogeny of the Forcipulatacea (Echinodermata: Asteroidea): insights from ossicle morphology

A new phylogenetic analysis of the superorder Forcipulatacea is presented. Forcipulatacea is one of the three major groups of sea stars (Asteroidea: Echinodermata), composed of 400 extant species. The sampled taxa are thought to represent the morphological diversity of the group. Twenty-nine forcipulate taxa were sampled belonging to Asteriidae, Stichasteridae, Heliasteridae, Pedicellasteridae, Zoroasteridae and Brisingida. Specimens were dissected with bleach. Detailed description of the skeleton and the anatomy of the ossicles were investigated using scanning electron microscopy. Comparative anatomy allowed the scoring of 115 phylogenetically informative characters. The consensus tree resulting from the analysis recovers Asteriidae, Stichasteridae, Zoroasteridae and Brisingida as monophyletic. All types of morphological features contribute to tree resolution and may be appropriate for taxon diagnosis. The synapomorphies supporting different clades are described and discussed. Brisingida and Zoroasteridae are the best-supported clades. The potentially challenging position of Brisingida in the tree may be explained by homoplastic changes, but also by the presence of numerous non-applicable characters.

Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees

An ideal bacterial phylogenetic tree accurately retraces evolutionary history and accurately incorporates mutational, recombination and other events on the appropriate branches. Current strain-level bacterial phylogenetic analysis based on large numbers of genomes lacks reliability and resolution, and is hard to be replicated, confirmed and reused, because of the highly divergent nature of microbial genomes. We present SNPs and Recombination Events Tree (SaRTree), a pipeline using six “living trees” modules that addresses problems arising from the high numbers and variable quality of bacterial genome sequences. It provides for reuse of the tree and offers a major step toward global standardization of phylogenetic analysis by generating deposit files including all steps involved in phylogenetic inference. The tree itself is a “living tree” that can be extended by addition of more sequences, or the deposit can be used to vary the programs or parameters used, to assess the effect of such changes. This approach will allow phylogeny papers to meet the traditional responsibility of providing data and analysis that can be repeated and critically evaluated by others. We used the Acinetobacter baumannii global clone I to illustrate use of SaRTree to optimize tree resolution. An Escherichia coli tree was built from 351 sequences selected from 11,162 genome sequences, with the others added back onto well-defined branches, to show how this facility can greatly improve the outcomes from genome sequencing. SaRTree is designed for prokaryote strain-level analysis but could be adapted for other usage.

Full Likelihood Inference from the Site Frequency Spectrum based on the Optimal Tree Resolution

We develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated. We assume that the population may have demographically changed and may be non-panmictically structured, as reflected by the branch lengths and the topology of the genealogical tree of the sample, respectively. We also assume that mutations conform to the infinitely-many-sites model. We achieve this by a controlled Markov process that generates ‘particles’ in the hidden space of SFS histories which are always compatible with the observed SFS.To produce the particles, we use Aldous’ Beta-splitting model for a one parameter family of prior distributions over genealogical topologies or shapes (including that of the Kingman coalescent) and allow the branch lengths or epoch times to have a parametric family of priors specified by a model of demography (including exponential growth and bottleneck models). Assuming independence across unlinked loci, we can estimate the likelihood of a population scenario based on a large collection of independent SFS by an importance sampling scheme, using the (unconditional) distribution of the genealogies under this scenario when the latter is available. When it is not available, we instead compute the joint likelihood of the tree balance parameter β assuming that the tree topology follows Aldous’ Beta-splitting model, and of the demographic scenario determining the distribution of the inter-coalescence times or epoch times in the genealogy of a sample, in order to at least distinguish different equivalence classes of population scenarios leading to different tree balances and epoch times. Simulation studies are conducted to demonstrate the capabilities of the approach with publicly available code.

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should therefore examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic datasets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ~2000 exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic datasets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference.

Monophyly of Heterandriini (Teleostei: Poeciliidae) revisited: a critical review of the data

The systematics and taxonomy of poeciliid fishes (guppies and allies) remain poorly understood despite the relative importance of these species as model systems in the biological sciences. This study focuses on testing the monophyly of the nominal poeciliine tribe Heterandriini and the genus Heterandria, through examination of the morphological characters on which the current classification is based. These characters include aspects of body shape (morphometrics), scale and fin-ray counts (meristics), pigmentation, the cephalic laterosensory system, and osteological features of the neurocranium, oral jaws and suspensorium, branchial basket, pectoral girdle, and the gonopodium and its supports. A Maximum Parsimony analysis was conducted of 150 characters coded for 56 poeciliid and outgroup species, including 22 of 45 heterandriin species (from the accounted in Parenti & Rauchenberger, 1989), or seven of nine heterandriin species (from the accounted in Lucinda & Reis, 2005). Multistate characters were analyzed as both unordered and ordered, and iterative a posteriori weighting was used to improve tree resolution. Tree topologies obtained from these analyses support the monophyly of the Middle American species of "Heterandria," which based on available phylogenetic information, are herein reassigned to the genus Pseudoxiphophorus. None of the characters used in previous studies to characterize the nominal taxon Heterandriini are found to be unambiguously diagnostic. Some of these characters are shared with species in other poeciliid tribes, and others are reversed within the Heterandriini. These results support the hypothesis that Pseudoxiphophorus is monophyletic, and that this clade is not the closest relative of H. formosa (the type species) from southeastern North America. Available morphological data are not sufficient to assess the phylogenetic relationships of H. formosa with respect to other members of the Heterandriini. The results further suggest that most tribe-level taxa of the Poeciliinae are not monophyletic, and that further work remains to resolve the evolutionary relationships of this group.

What about intraspecific variation? Reassessment of taxonomic and phylogenetic characters in the genus Synoeca de Saussure (Hymenoptera: Vespidae: Polistinae)

Morphological variation within and between species of the genus Synoeca was studied to test species status and to propose characters that fulfill the principles of communicability, unit delimitation, and conjunction for taxonomic and phylogenetic analyses. Twenty-six morphological characters obtained from the literature were analyzed; 16 of these characters clearly exhibited delimited states but only four of them were unique for each species. The status of every species of the genus was supported by geometric morphometrics of the head (front view, dorsal view and metasomal tergum 1) and by the presence of unique character states for each species. Phylogenetic analyses included nest and genitalia characters. Character reassessment provided a less resolved tree to that previously published. Including polymorphic characters did not improve tree resolution or clade support, while applying the conjunction test offered a more resolved and better supported tree. The study revealed the importance of analyzing variation in taxonomic and phylogenetic studies within and between species. A new key to species and a phylogenetic hypothesis are offered.