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Systematic Biology

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https://www.readbyqxmd.com/read/29186593/complex-models-of-sequence-evolution-require-accurate-estimators-as-exemplified-with-the-invariable-site-plus-gamma-model
#1
Lam-Tung Nguyen, Arndt von Haeseler, Bui Quang Minh
The invariable site plus Γ model is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the invariable site plus continuous Γ model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the invariable site plus discrete Γ model, whose identifiability is likely but unproven. How well the parameters of the invariable site plus discrete Γ model are estimated is still disputed...
November 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29186587/effective-online-bayesian-phylogenetics-via-sequential-monte-carlo-with-guided-proposals
#2
Mathieu Fourment, Brian C Claywell, Vu Dinh, Connor McCoy, Frederick A Matsen Iv, Aaron E Darling
Modern infectious disease outbreak surveillance produces continuous streams of sequence data which require phylogenetic analysis as data arrives. Current software packages for Bayesian phylogenetic inference are unable to quickly incorporate new sequences as they become available, making them less useful for dynamically unfolding evolutionary stories. This limitation can be addressed by applying a class of Bayesian statistical inference algorithms called sequential Monte Carlo (SMC) to conduct online inference, wherein new data can be continuously incorporated to update the estimate of the posterior probability distribution...
November 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29186553/corrigendum-to-probabilistic-distances-between-trees
#3
(no author information available yet)
No abstract text is available yet for this article.
November 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29165679/a-two-state-model-of-tree-evolution-and-its-applications-to-alu-retrotransposition
#4
Niema Moshiri, Siavash Mirarab
Models of tree evolution have mostly focused on capturing the cladogenesis processes behind speciation. Processes that derive the evolution of genomic elements, such as repeats, are not necessarily captured by these existing models. In this paper, we design a model of tree evolution that we call the dual-birth model, and we show how it can be useful in studying the evolution of short Alu repeats found in the human genome in abundance. The dual-birth model extends the traditional birth- only model to have two rates of propagation, one for active nodes that propagate often, and another for inactive nodes, that with a lower rate, activate and start propagating...
November 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29106675/the-efficacy-of-consensus-tree-methods-for-summarising-phylogenetic-relationships-from-a-posterior-sample-of-trees-estimated-from-morphological-data
#5
Joseph E O'Reilly, Philip C J Donoghue
Consensus trees are required to summarise trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are co-estimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method...
November 2, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29088474/reconstructing-ecological-niche-evolution-when-niches-are-incompletely-characterized
#6
Erin E Saupe, Narayani Barve, Hannah L Owens, Jacob C Cooper, Peter A Hosner, A Townsend Peterson
Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models...
October 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29088409/co-estimating-reticulate-phylogenies-and-gene-trees-from-multi-locus-sequence-data
#7
Dingqiao Wen, Luay Nakhleh
The multispecies network coalescent (MSNC) is a stochastic process that captures how gene trees grow within the branches of a phylogenetic network. Coupling the MSNC with a stochastic mutational process that operates along the branches of the gene trees gives rise to a generative model of how multiple loci from within and across species evolve in the presence of both incomplete lineage sorting (ILS) and reticulation (e.g., hybridization). We report on a Bayesian method for sampling the parameters of this generative model, including the species phylogeny, gene trees, divergence times, and population sizes, from DNA sequences of multiple independent loci...
October 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29069434/estimating-age-dependent-extinction-contrasting-evidence-from-fossils-and-phylogenies
#8
Oskar Hagen, Tobias Andermann, Tiago B Quental, Alexandre Antonelli, Daniele Silvestro
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction" which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level...
October 23, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029306/an-assessment-of-phylogenetic-tools-for-analyzing-the-interplay-between-interspecific-interactions-and-phenotypic-evolution
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
(no author information available yet)
No abstract text is available yet for this article.
November 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28637293/conserved-nonexonic-elements-a-novel-class-of-marker-for-phylogenomics
#16
Scott V Edwards, Alison Cloutier, Allan J Baker
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species...
November 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28595366/conserving-phylogenetic-diversity-can-be-a-poor-strategy-for-conserving-functional-diversity
#17
Florent Mazel, Arne O Mooers, Giulio Valentino Dalla Riva, Matthew W Pennell
For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policy makers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity [FD]), which may be valuable for a number of reasons. The claim that PD-maximized ("maxPD") sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits...
November 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28431159/likelihood-of-tree-topologies-with-fossils-and-diversification-rate-estimation
#18
Gilles Didier, Marine Fau, Michel Laurin
Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils)...
November 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28431105/extinction-vs-rapid-radiation-the-juxtaposed-evolutionary-histories-of-coelotine-spiders-support-the-eocene-oligocene-orogenesis-of-the-tibetan-plateau
#19
Zhe Zhao, Shuqiang Li
Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region...
November 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28419377/gene-tree-reconciliation-with-mul-trees-to-resolve-polyploidy-events
#20
W C Thomas Gregg, S Hussain Ather, Matthew W Hahn
Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids-autopolyploids and allopolyploids-differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses...
November 1, 2017: Systematic Biology
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