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Systematic Biology

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https://www.readbyqxmd.com/read/29029306/an-assessment-of-phylogenetic-tools-for-analyzing-the-interplay-between-interspecific-interactions-and-phenotypic-evolution
#1
J P Drury, G F Grether, T Garland, H Morlon
Much ecological and evolutionary theory predicts that interspecific interactions often drive phenotypic diversification and that species phenotypes in turn influence species interactions. Several phylogenetic comparative methods have been developed to assess the importance of such processes in nature; however, the statistical properties of these methods have gone largely untested. Focusing mainly on scenarios of competition between closely-related species, we assess the performance of available comparative approaches for analyzing the interplay between interspecific interactions and species phenotypes...
October 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029295/probabilistic-distances-between-trees
#2
Maryam Garba, Tom M W Nye, Richard J Boys
Most existing measures of distance between phylogenetic trees are based on the geometry or topology of the trees. Instead, we consider distance measures which are based on the underlying probability distributions on genetic sequence data induced by trees. Monte Carlo schemes are necessary to calculate these distances approximately, and we describe efficient sampling procedures. Key features of the distances are the ability to include substitution model parameters and to handle trees with different taxon sets in a principled way...
October 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029339/targeted-enrichment-of-large-gene-families-for-phylogenetic-inference-phylogeny-and-molecular-evolution-of-photosynthesis-genes-in-the-portullugo-clade-caryophyllales
#3
Abigail J Moore, Jurriaan M de Vos, Lillian P Hancock, Eric Goolsby, Erika J Edwards
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis...
September 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029264/a-general-model-for-estimating-macroevolutionary-landscapes
#4
Florian C Boucher, Vincent Démery, Elena Conti, Luke J Harmon, Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029231/analysis-of-phylogenomic-tree-space-resolves-relationships-among-marsupial-families
#5
David A Duchêne, Jason G Bragg, Sebastián Duchêne, Linda E Neaves, Sally Potter, Craig Moritz, Rebecca N Johnson, Simon Y W Ho, Mark D B Eldridge
A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029338/to-include-or-not-to-include-the-impact-of-gene-filtering-on-species-tree-estimation-methods
#6
Erin K Molloy, Tandy Warnow
With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that co-estimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci...
September 15, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945874/erratum
#7
(no author information available yet)
No abstract text is available yet for this article.
September 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945912/the-past-sure-is-tense-on-interpreting-phylogenetic-divergence-time-estimates
#8
Joseph W Brown, Stephen A Smith
Divergence time estimation-the calibration of a phylogeny to geological time-is an integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more...
September 7, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945903/impact-of-model-violations-on-the-inference-of-species-boundaries-under-the-multispecies
#9
Anthony J Barley, Jeremy M Brown, Robert C Thomson
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence, and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process...
September 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945906/use-of-continuous-traits-can-improve-morphological-phylogenetics
#10
Caroline Parins-Fukuchi
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters...
September 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945876/issues-and-perspectives-in-species-delimitation-using-phenotypic-data-atlantean-evolution-in-darwin-s-finches
#11
Carlos Daniel Cadena, Felipe Zapata, Iván Jiménez
Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species...
September 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945862/conflicting-evolutionary-histories-of-the-mitochondrial-and-nuclear-genomes-in-new-world-myotis-bats
#12
Roy N Platt Ii, Brant C Faircloth, Kevin A M Sullivan, Troy J Kieran, Travis C Glenn, Michael W Vandewege, Thomas E Lee, Robert J Baker, Richard D Stevens, David A Ray
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3,648 ultraconserved elements (UCEs)...
August 26, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28950376/phylogenetic-factor-analysis
#13
Max R Tolkoff, Michael E Alfaro, Guy Baele, Philippe Lemey, Marc A Suchard
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that generates model residuals or the traits themselves. For high-dimensional traits, inferring all pair-wise correlations within the multivariate diffusion is limiting. To circumvent this problem, we propose phylogenetic factor analysis (PFA) that assumes a small unknown number of independent evolutionary factors arise along the phylogeny and these factors generate clusters of dependent traits...
August 7, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28950365/modeling-site-heterogeneity-with-posterior-mean-site-frequency-profiles-accelerates-accurate-phylogenomic-estimation
#14
Huai-Chun Wang, Bui Quang Minh, Edward Susko, Andrew J Roger
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses...
August 7, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28945917/cladogenetic-and-anagenetic-models-of-chromosome-number-evolution-a-bayesian-model-averaging-approach
#15
William A Freyman, Sebastian Höhna
Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution...
July 26, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28595363/more-on-the-best-evolutionary-rate-for-phylogenetic-analysis
#16
Seraina Klopfstein, Tim Massingham, Nick Goldman
The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability...
September 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28369655/why-do-phylogenomic-data-sets-yield-conflicting-trees-data-type-influences-the-avian-tree-of-life-more-than-taxon-sampling
#17
Sushma Reddy, Rebecca T Kimball, Akanksha Pandey, Peter A Hosner, Michael J Braun, Shannon J Hackett, Kin-Lan Han, John Harshman, Christopher J Huddleston, Sarah Kingston, Ben D Marks, Kathleen J Miglia, William S Moore, Frederick H Sheldon, Christopher C Witt, Tamaki Yuri, Edward L Braun
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts...
September 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334310/different-from-trees-more-than-metaphors-branching-silhouettes-corals-cacti-and-the-oaks
#18
János Podani
There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may actually carry quite different information...
September 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334227/a-phylogenetic-biogeographic-and-taxonomic-study-of-all-extant-species-of-anolis-squamata-iguanidae
#19
Steven Poe, Adrián Nieto-Montes de Oca, Omar Torres-Carvajal, Kevin De Queiroz, Julián A Velasco, Brad Truett, Levi N Gray, Mason J Ryan, Gunther Köhler, Fernando Ayala-Varela, Ian Latella
Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles...
September 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334079/how-do-cold-adapted-plants-respond-to-climatic-cycles-interglacial-expansion-explains-current-distribution-and-genomic-diversity-in-primula-farinosa-l
#20
Spyros Theodoridis, Christophe Randin, Peter Szövényi, Florian C Boucher, Theofania S Patsiou, Elena Conti
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model...
September 1, 2017: Systematic Biology
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