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Systematic Biology

Daniel Edler, Thaís Guedes, Alexander Zizka, Martin Rosvall, Alexandre Antonelli
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps...
October 1, 2016: Systematic Biology
Kevin M Kocot, Torsten H Struck, Julia Merkel, Damien S Waits, Christiane Todt, Pamela M Brannock, David A Weese, Johanna T Cannon, Leonid L Moroz, Bernhard Lieb, Kenneth M Halanych
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error...
September 23, 2016: Systematic Biology
Charles S P Foster, Hervé Sauquet, Marlien van der Merwe, Hannah McPherson, Maurizio Rossetto, Simon Y W Ho
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyse a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale...
September 20, 2016: Systematic Biology
Ryan A Folk, Jennifer R Mandel, John V Freudenstein
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages - clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp) and mitochondrial (~470,000 bp) data...
September 16, 2016: Systematic Biology
Nathan V Whelan, Kenneth M Halanych
As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny rather than rigorous testing with known trees via simulation...
September 14, 2016: Systematic Biology
Marcin Bogusz, Simon Whelan
Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbor joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods...
September 14, 2016: Systematic Biology
Alexandre Antonelli, Hannes Hettling, Fabien L Condamine, Karin Vos, R Henrik Nilsson, Michael J Sanderson, Hervé Sauquet, Ruud Scharn, Daniele Silvestro, Mats Töpel, Christine D Bacon, Bengt Oxelman, Rutger A Vos
Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction...
September 10, 2016: Systematic Biology
Raimundo Real, A Márcia Barbosa, Joseph W Bull
Species distributions are typically represented by records of their observed occurrence at a given spatial and temporal scale. Such records are inevitably incomplete and contingent on the spatial-temporal circumstances under which the observations were made. Moreover, organisms may respond differently to similar environmental conditions at different places or moments, so their distribution is, in principle, not completely predictable. We argue that this uncertainty exists, and warrants considering species distributions as analogous to coherent quantum objects, whose distributions are better described by a wavefunction rather than by a set of locations...
September 10, 2016: Systematic Biology
Celine Scornavacca, Nicolas Galtier
The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among genes, and the related issue of whether to account for ILS in species tree reconstruction, are matters of intense controversy. Here, focusing on full-genome data in placental mammals, we empirically test two assumptions underlying current usage of tree-building methods that account for ILS. We show that in this dataset (i) distinct exons from a common gene do not share a common genealogy, and (ii) ILS is only a minor determinant of the existing phylogenetic conflict...
September 7, 2016: Systematic Biology
James S Albert, Donald R Schoolmaster, Victor Tagliacollo, Scott M Duke-Sylvester
Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands...
September 1, 2016: Systematic Biology
K Kobert, A Stamatakis, T Flouri
The phylogenetic likelihood function is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values...
August 29, 2016: Systematic Biology
T C Hsieh, Anne Chao
Measures of phylogenetic diversity are basic tools in many studies of systematic biology. Faith's PD (sum of branch lengths of a phylogenetic tree connecting all focal species) is the most widely used phylogenetic measure. Like species richness, Faith's PD based on sampling data is highly dependent on sample size and sample completeness. The sample-size- and sample-coverage-based integration of rarefaction and extrapolation of Faith's PD was recently developed to make fair comparison across multiple assemblages...
August 26, 2016: Systematic Biology
Michael Matschiner, Zuzana Musilová, Julia M I Barth, Zuzana Starostová, Walter Salzburger, Mike Steel, Remco Bouckaert
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates...
August 25, 2016: Systematic Biology
Alexandra Gavryushkina, Tracy A Heath, Daniel T Ksepka, Tanja Stadler, David Welch, Alexei J Drummond
The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework...
August 24, 2016: Systematic Biology
Britta S Meyer, Michael Matschiner, Walter Salzburger
Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation...
August 18, 2016: Systematic Biology
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No abstract text is available yet for this article.
August 18, 2016: Systematic Biology
R Alexander Pyron
Here, I combine previously underutilized models and priors to perform more biologically-realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backwards transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for 'asymmetric...
August 11, 2016: Systematic Biology
N Magain, J Miadlikowska, B Goffinet, E Sérusiaux, F Lutzoni
Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here, we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred from five nuclear loci and the rbcLX region, respectively...
August 6, 2016: Systematic Biology
Paula Tataru, Maria Simonsen, Thomas Bataillon, Asger Hobolth
The Wright-Fisher model provides an elegant mathematical framework for understanding allele frequency data. In particular, the model can be used to infer the demographic history of species and identify loci under selection. A crucial quantity for inference under the Wright-Fisher model is the distribution of allele frequencies (DAF). Despite the apparent simplicity of the model, the calculation of the DAF is challenging. We review and discuss strategies for approximating the DAF, and how these are used in methods that perform inference from allele frequency data...
August 2, 2016: Systematic Biology
Mats Töpel, Alexander Zizka, Maria Fernanda Calió, Ruud Scharn, Daniele Silvestro, Alexandre Antonelli
Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units...
August 2, 2016: Systematic Biology
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