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Systematic Biology

Katharina T Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri
Tree reconciliation is the mathematical tool that is used to investigate the coevolution of organisms, such as hosts and parasites. A common approach to tree reconciliation involves specifying a model that assigns costs to certain events, such as cospeciation, and then tries to find a mapping between two specified phylogenetic trees which minimises the total cost of the implied events. For such models, it has been shown that there may be a huge number of optimal solutions, or at least solutions that are close to optimal...
November 10, 2018: Systematic Biology
Daniel J MacGuigan, Thomas J Near
Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes...
November 3, 2018: Systematic Biology
Robert M Zink, Hernán Vázquez-Miranda
Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships...
October 29, 2018: Systematic Biology
Laure Barrabé, Sébastien Lavergne, Giliane Karnadi-Abdelkader, Bryan Drew, Philippe Birnbaum, Gildas Gâteblé
Phylogenies recurrently demonstrate that oceanic island systems have been home to rapid clade diversification and adaptive radiations. The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of such radiations. However, neutral processes may also drive speciation during clade radiations, with ecological divergence occurring following speciation. Here we document an exceptionally rapid and unique radiation of Lamiaceae within the New Caledonian biodiversity hotspot...
October 26, 2018: Systematic Biology
Guillaume Billet, Jérémie Bardin
Accurate modeling of the complexity of morphological evolution is crucial for morphological phylogenetics and for performing tests on a wide variety of evolutionary scenarios. In this context, morphological integration and the problem of correlated categorical characters represent a major challenge. In particular, the magnitude and implications of correlations among serially homologous structures such as teeth have been much debated but were never tested statistically within a broad phylogenetic context. Here, we present a large-scale empirical study analyzing the serial variation of cingular crests on successive molars (M1, M2 and M3) of 274 placental species in a phylogenetic context...
October 26, 2018: Systematic Biology
Jonas Eberle, Erika Bazzato, Silvia Fabrizi, Michele Rossini, Mariastella Colomba, Davide Cillo, Marco Uliana, Ignazio Sparacio, Guido Sabatinelli, Rachel C M Warnock, Giuseppe Carpaneto, Dirk Ahrens
Accurate delimitation of species is crucial for a stable taxonomy, which provides the foundation for the study of evolutionary biology, ecology and essentially all biological disciplines. Several approaches towards impartial and repeatable taxonomic practices are available but all existing methods have potentially unacceptable shortcomings. In particular, problems can arise when the underlying model assumptions are violated, for instance in the presence of reduced gene flow. This is observed in the context of sex-biased dispersal, which is a common but underappreciated feature in many groups of organisms...
October 26, 2018: Systematic Biology
Michael Nute, Ehsan Saleh, Tandy Warnow
The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the most popular protein alignment methods as well as the statistical co-estimation method BAli-Phy on 1192 protein data sets from established benchmarks as well as on 120 simulated data sets...
October 17, 2018: Systematic Biology
Daisy Shepherd, Steffen Klaere
The test for model-to-data fitness is a fundamental principle within the statistical sciences. The purpose of such a test is to assess whether the selected best-fitting model adequately describes the behaviour in the data. Despite their broad application across many areas of statistics, goodness of fit tests for phylogenetic models have received much less attention than model selection methods in the last decade. At present a number of approaches have been suggested. However, these are often flawed, with problems ranging from the presence of systematic error in the models themselves to the difficulties presented by the nature of phylogenetic data...
October 17, 2018: Systematic Biology
D S Caetano, L J Harmon
Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped to the branches of the phylogeny to test for shifts in evolutionary integration while incorporating the uncertainty related to trait evolution and ancestral regimes with joint estimation of all parameters of the model using Bayesian Markov chain Monte Carlo...
October 17, 2018: Systematic Biology
Leonel Herrera-Alsina, Paul van Els, Rampal S Etienne
Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The State-dependent Speciation and Extinction (SSE) framework contains methods to detect the dependence of diversification on these traits. For the analysis of traits with multiple states, MuSSE (Multiple-States dependent Speciation and Extinction) was developed. However, MuSSE and other state-dependent speciation and extinction models have been shown to yield false positives, because they cannot separate differential diversification rates from dependence of diversification on the observed traits...
September 26, 2018: Systematic Biology
Sebastien Roch, Michael Nute, Tandy Warnow
With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when different genomic regions can evolve differently, is a common phenomenon in multi-locus datasets, and reduces the accuracy of standard methods for species tree estimation that do not take this heterogeneity into account. New methods have been developed for species tree estimation that specifically address gene tree heterogeneity, and that have been proven to converge to the true species tree when the number of loci and number of sites per locus both increase (i...
September 21, 2018: Systematic Biology
Bryan S McLean, Kayce C Bell, Julie M Allen, Kristofer M Helgen, Joseph A Cook
Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a dataset of > 3,950 ultraconserved element (UCE) loci from a classic mammalian radiation, ground-dwelling squirrels of the tribe Marmotini (Sciuridae: Xerinae), to assess sensitivity of phylogenetic estimates to varying per-locus information content across 4 different inference methods (RAxML, ASTRAL, NJst, SVDquartets)...
September 18, 2018: Systematic Biology
Fan Song, Hu Li, Guo-Hua Liu, Wei Wang, Peter James, Douglas D Colwell, Anette Tran, Siyu Gong, Wanzhi Cai, Renfu Shao
Organelle genome fragmentation has been found in a wide range of eukaryotic lineages; however, its use in phylogenetic reconstruction has not been demonstrated. We explored the use of mitochondrial (mt) genome fragmentation in resolving the controversial suborder-level phylogeny of parasitic lice (order Phthiraptera). There are ∼5,000 species of parasitic lice in four suborders (Amblycera, Ischnocera, Rhynchophthirina and Anoplura), which infest mammals and birds. The phylogenetic relationships among these suborders are unresolved despite decades of studies...
September 17, 2018: Systematic Biology
Anthony R Ives
Many researchers want to report an R2 to measure the variance explained by a model. When the model includes correlation among data, such as phylogenetic models and mixed models, defining an R2 faces two conceptual problems. (i) It is unclear how to measure the variance explained by predictor (independent) variables when the model contains covariances. (ii) Researchers may want the R2 to include the variance explained by the covariances by asking questions such as "How much of the data is explained by phylogeny?" Here, I investigate three R2s for phylogenetic and mixed models...
September 17, 2018: Systematic Biology
Luciano Varela, P Sebastián Tambusso, H Gregory McDonald, Richard A Fariña
Sloths, like other xenarthrans, are an extremely interesting group of mammals that, after a long history of evolution and diversification in South America, became established on islands in the Caribbean and later reached North America during the Great American Biotic Interchange. In all three regions, they were part of the impressive Pleistocene megafauna. Most taxa became extinct and only two small, distantly related tree-dwelling genera survived. Here we incorporate several recently described genera of sloths into an assembled morphological data supermatrix and apply Bayesian inference, using phylogenetic and morphological clock methods, to 64 sloth genera...
September 15, 2018: Systematic Biology
Eli Levy Karin, Haim Ashkenazy, Jotun Hein, Tal Pupko
Classic alignment algorithms utilize scoring functions which maximize similarity or minimize edit distances. These scoring functions account for both insertion-deletion (indel) and substitution events. In contrast, alignments based on stochastic models aim to explicitly describe the evolutionary dynamics of sequences by inferring relevant probabilistic parameters from input sequences. Despite advances in stochastic modeling during the last two decades, scoring-based methods are still dominant, partially due to slow running times of probabilistic approaches...
September 15, 2018: Systematic Biology
Jamie R Oaks
A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data...
September 15, 2018: Systematic Biology
Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis
Next Generation Sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the Evolutionary Placement Algorithm (EPA) included in RAxML, or pplacer, are being increasingly used for this purpose...
August 27, 2018: Systematic Biology
Charles Pouchon, Angel Fernández, Jafet M Nassar, Frédéric Boyer, Serge Aubert, Sébastien Lavergne, Jesús Mavárez
The subtribe Espeletiinae (Asteraceae), endemic to the high-elevations in the Northern Andes, exhibits an exceptional diversity of species, growth-forms, and reproductive strategies. This complex of 140 species includes large trees, dichotomous trees, shrubs and the extraordinary giant caulescent rosettes, considered as a classic example of adaptation in tropical high-elevation ecosystems. The subtribe has also long been recognized as a prominent case of adaptive radiation, but the understanding of its evolution has been hampered by a lack of phylogenetic resolution...
November 1, 2018: Systematic Biology
Lisa N Barrow, Alan R Lemmon, Emily Moriarty Lemmon
Comparative phylogeography provides the necessary framework to examine the factors influencing population divergence, persistence, and change over time. Avise (2000) outlined four aspects of concordance that result when data exhibit significant phylogeographic signal: concordance among sites within a locus, among multiple loci within a species, among multiple species within a region, and between genetic patterns and established biogeographic provinces. To fully address each aspect of concordance, we combined target capture of a set of orthologous loci with targeted geographic sampling of multiple species, thus removing any variability introduced by using different genetic markers and heterogeneous sampling distributions...
November 1, 2018: Systematic Biology
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