Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations
AbstractEvolutionary inferences require reliable phylogenies. Morphological data have traditionally been analyzed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here, we investigate phylogenetic methods using two novel simulation models —one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simult...
Source: Systematic Biology - February 19, 2020 Category: Biology Source Type: research
Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification
AbstractNew techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical da...
Source: Systematic Biology - February 17, 2020 Category: Biology Source Type: research
Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
AbstractThe Viviparidae, commonly known as River Snails, is a dominant group of freshwater snails with a nearly worldwide distribution that reaches its highest taxonomic and morphological diversity in Southeast Asia. The rich fossil record is indicative of a probable Middle Jurassic origin on the Laurasian supercontinent where the group started to diversify during the Cretaceous. However, it remains uncertain when and how the biodiversity hotspot in Southeast Asia was formed. Here, we used a comprehensive genetic data set containing both mitochondrial and nuclear markers and comprising species representing 24 out of 28 gen...
Source: Systematic Biology - February 15, 2020 Category: Biology Source Type: research
Reliable Phylogenetic Regressions for Multivariate Comparative Data: Illustration with the MANOVA and Application to the Effect of Diet on Mandible Morphology in Phyllostomid Bats
AbstractUnderstanding what shapes species phenotypes over macroevolutionary timescales from comparative data often requires studying the relationship between phenotypes and putative explanatory factors or testing for differences in phenotypes across species groups. In phyllostomid bats for example, is mandible morphology associated to diet preferences? Performing such analyses depends upon reliable phylogenetic regression techniques and associated tests (e.g., phylogenetic Generalized Least Squares, pGLS, and phylogenetic analyses of variance and covariance, pANOVA, pANCOVA). While these tools are well established for univ...
Source: Systematic Biology - February 15, 2020 Category: Biology Source Type: research
Identification of Hidden Population Structure in Time-Scaled Phylogenies
AbstractPopulation structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealized genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiolo...
Source: Systematic Biology - February 12, 2020 Category: Biology Source Type: research
Tropical Niche Conservatism Explains the Eocene Migration from India to Southeast Asia in Ochyroceratid Spiders
AbstractBiological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed sp...
Source: Systematic Biology - February 3, 2020 Category: Biology Source Type: research
Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish
AbstractThe Midas cichlids of theAmphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic n...
Source: Systematic Biology - February 3, 2020 Category: Biology Source Type: research
Morphometric Variation at Different Spatial Scales: Coordination and Compensation in the Emergence of Organismal Form
We present biometric strategies and R scripts for identifying patterns of coordination and compensation in the size a nd shape of composite anatomical structures. In an application to human cranial variation, we found that coordinated variation and positive correlations are prevalent for the size of cranial components, whereas their shape was dominated by compensatory variation, leading to strong canalization of cr anial shape at larger scales. We propose that mechanically induced bone formation and remodeling are key mechanisms underlying compensatory variation in cranial shape. Such epigenetic coordination and compensati...
Source: Systematic Biology - February 3, 2020 Category: Biology Source Type: research
Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference
AbstractSampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as “convergence”) and in estimating the correct proportions of the different types of them (known as “mixing”). Here, we introduce a new class of moves, w...
Source: Systematic Biology - January 27, 2020 Category: Biology Source Type: research
Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable
This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny...
Source: Systematic Biology - January 27, 2020 Category: Biology Source Type: research
The Impact of Cross-Species Gene Flow on Species Tree Estimation
AbstractRecent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or a...
Source: Systematic Biology - January 24, 2020 Category: Biology Source Type: research
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Source: Systematic Biology - October 21, 2019 Category: Biology Source Type: research
Corrigendum to: “Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations”
Paul Bastide, Claudia Sol ís-Lemus, Ricardo Kriebel, K. William Sparks, and Cécile Ané (Source: Systematic Biology)
Source: Systematic Biology - August 23, 2019 Category: Biology Source Type: research
Announcements
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Source: Systematic Biology - August 20, 2019 Category: Biology Source Type: research
Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models
AbstractStochastic birth –death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this article, we first provide intuitive reasons for these known tr ansformational symmetries. We then show that these transformational symmetries (encoded in algebraic identities) are preserved even when individuals at the present are sampled with some probability. However, these extended symmetries require the death rate parameter to sometimes take a negative valu e. ...
Source: Systematic Biology - May 28, 2019 Category: Biology Source Type: research
