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Systematic Biology

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https://read.qxmd.com/read/30753719/fossils-with-feathers-and-philosophy-of-science
#1
Joyce C Havstad, N Adam Smith
The last half century of paleornithological research has transformed the way that biologists perceive the evolutionary history of birds. This transformation has been driven, since 1969, by a series of exciting fossil discoveries combined with intense scientific debate over how best to interpret these discoveries. Ideally, as evidence accrues and results accumulate, interpretive scientific agreement forms. But this has not entirely happened in the debate over avian origins: the accumulation of scientific evidence and analyses has had some effect, but not a conclusive one, in terms of resolving the question of avian origins...
February 11, 2019: Systematic Biology
https://read.qxmd.com/read/30726979/robust-design-for-coalescent-model-inference
#2
Kris V Parag, Oliver G Pybus
The coalescent process describes how changes in the size or structure of a population influence the genealogical patterns of sequences sampled from that population. The estimation of (effective) population size changes from genealogies that are reconstructed from these sampled sequences is an important problem in many biological fields. Often, population size is characterised by a piecewise-constant function, with each piece serving as a population size parameter to be estimated. Estimation quality depends on both the statistical coalescent inference method employed, and on the experimental protocol, which controls variables such as the sampling of sequences through time and space, or the transformation of model parameters...
February 6, 2019: Systematic Biology
https://read.qxmd.com/read/30726954/assessing-combinability-of-phylogenomic-data-using-bayes-factors
#3
Suman Neupane, Karolina Fucíková, Louise A Lewis, Lynn Kuo, Ming-Hui Chen, Paul O Lewis
With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths...
February 6, 2019: Systematic Biology
https://read.qxmd.com/read/30690622/priors-and-posteriors-in-bayesian-timing-of-divergence-analyses-the-age-of-butterflies-revisited
#4
Nicolas Chazot, Niklas Wahlberg, Andr Eacute Victor Lucci Freitas, Charles Mitter, Conrad Labandeira, Jae-Cheon Sohn, Ranjit Kumar Sahoo, Noemy Seraphim, Rienk de Jong, Maria Heikkilä
The need for robust estimates of times of divergence is essential for downstream analyses, yet assessing this robustness is still rare. We generated a time-calibrated genus-level phylogeny of butterflies (Papilionoidea), including 994 taxa, up to 10 gene fragments and an unprecedented set of 12 fossils and 10 host-plant node calibration points. We compared marginal priors and posterior distributions to assess the relative importance of the former on the latter. This approach revealed a strong influence of the set of priors on the root age but for most calibrated nodes posterior distributions shifted from the marginal prior, indicating significant information in the molecular dataset...
January 25, 2019: Systematic Biology
https://read.qxmd.com/read/30668834/marginal-likelihoods-in-phylogenetics-a-review-of-methods-and-applications
#5
Jamie R Oaks, Kerry A Cobb, Vladimir N Minin, Adam D Leaché
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory...
January 22, 2019: Systematic Biology
https://read.qxmd.com/read/30668824/osf-builder-a-new-tool-for-constructing-and-representing-evolutionary-histories-involving-introgression
#6
Guillaume E Scholz, Andrei-Alin Popescu, Martin I Taylor, Vincent Moulton, Katharina T Huber
Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this paper we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short...
January 22, 2019: Systematic Biology
https://read.qxmd.com/read/30668800/integration-of-anatomy-ontologies-and-evo-devo-using-structured-markov-models-suggests-a-new-framework-for-modeling-discrete-phenotypic-traits
#7
Sergei Tarasov
Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes - hierarchical and hidden - which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks underlying trait development...
January 22, 2019: Systematic Biology
https://read.qxmd.com/read/30649562/homoplasy-based-partitioning-outperforms-alternatives-in-bayesian-analysis-of-discrete-morphological-data
#8
Brunno B Rosa, Gabriel A R Melo, Marcos S Barbeitos
Bayesian analysis of morphological data is becoming increasingly popular mainly (but not only) because it allows for time-calibrated phylogenetic inference using relaxed morphological clocks and tip dating whenever fossils are available. As with molecular data, recent studies have shown that modeling among character rate variaton (ACRV) in morphological matrices greatly improves phylogenetic inference. In a likelihood framework this may be accomplished, for instance, by employing a hidden Markov model (HMM) to assign characters to rate categories drawn from a (discretized) Γ distribution and/or by partitioning datasets according to rate heterogeneity and estimating per-partition branch lengths, conditioned on a single topology...
January 11, 2019: Systematic Biology
https://read.qxmd.com/read/30605547/convergent-evolution-of-the-army-ant-syndrome-and-congruence-in-big-data-phylogenetics-each-important-word-in-the-title-should-begin-with-a-capital-letter
#9
Marek L Borowiec
Army ants are a charismatic group of organisms characterized by a suite of morphological and behavioral adaptations that includes obligate collective foraging, frequent colony relocation, and highly specialized wingless queens. This "army ant syndrome" underlies the ecological success of army ants and its evolution has been the subject of considerable debate. It has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question in a phylogenetic framework I generated data from 2,166 loci and a comprehensive taxon sampling representing all 27 genera and 155 or approximately 22% of doryline species...
January 3, 2019: Systematic Biology
https://read.qxmd.com/read/30597118/strengthening-the-interaction-of-the-virology-community-with-the-international-committee-on-taxonomy-of-viruses-ictv-by-linking-virus-names-and-their-abbreviations-to-virus-species
#10
Charles H Calisher, Thomas Briese, J Rodney Brister, Rémi N Charrel, Ralf Dürrwald, Hideki Ebihara, Charles F Fulhorst, George Fú Gao, Martin H Groschup, Andrew D Haddow, Timothy H Hyndman, Sandra Junglen, Boris Klempa, Jonas Klingström, Andrew M Kropinski, Mart Krupovic, A Desiree LaBeaud, Piet Maes, Norbert Nowotny, Márcio Roberto Teixeira Nunes, Susan L Payne, Sheli R Radoshitzky, Dennis Rubbenstroth, Sead Sabanadzovic, Takahide Sasaya, Mark D Stenglein, Arvind Varsani, Victoria Wahl, Scott C Weaver, Francisco Murilo Zerbini, Nikos Vasilakis, Jens H Kuhn
The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (orders to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world and therefore have limited use for ICTV-devised taxa...
December 31, 2018: Systematic Biology
https://read.qxmd.com/read/30597116/a-general-method-for-simultaneously-accounting-for-phylogenetic-and-species-sampling-uncertainty-via-rubin-s-rules-in-comparative-analysis
#11
Shinichi Nakagawa, Pierre de Villemereuil
Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species' trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this assumption is most likely incorrect. So far, Markov chain Monte Carlo, MCMC-based Bayesian methods have mainly been deployed to account for such 'phylogenetic uncertainty' in PCMs. Here, we propose an approach with which phylogenetic uncertainty is incorporated in a simple, readily implementable and reliable manner...
December 31, 2018: Systematic Biology
https://read.qxmd.com/read/30597106/phylotocol-promoting-transparency-and-overcoming-bias-in-phylogenetics
#12
Melissa B DeBiasse, Joseph F Ryan
The integrity of science requires that the process be based on sound experimental design and objective methodology. Strategies that increase reproducibility and transparency in science protect this integrity by reducing conscious and unconscious biases. Given the large number of analysis options and the constant development of new methodologies in phylogenetics, this field is one that would particularly benefit from more transparent research design. Here, we introduce phylotocol (fī·lō·´tə·kôl), an a priori protocol-driven approach in which all analyses are planned and documented at the start of a project...
December 31, 2018: Systematic Biology
https://read.qxmd.com/read/30535172/an-algorithm-for-morphological-phylogenetic-analysis-with-inapplicable-data
#13
Martin D Brazeau, Thomas Guillerme, Martin R Smith
Morphological data play a key role in the inference of biological relationships and evolutionary history, and are essential for the interpretation of the fossil record. The hierarchical interdependence of many morphological characters, however, complicates phylogenetic analysis. In particular, many characters only apply to a subset of terminal taxa. The widely used "reductive coding" approach treats taxa in which a character is inapplicable as though data on the character's state is simply missing (unknown)...
December 11, 2018: Systematic Biology
https://read.qxmd.com/read/30535394/a-universal-probe-set-for-targeted-sequencing-of-353-nuclear-genes-from-any-flowering-plant-designed-using-k-medoids-clustering
#14
Matthew G Johnson, Lisa Pokorny, Steven Dodsworth, Laura R Botigué, Robyn S Cowan, Alison Devault, Wolf L Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T Kim, James H Leebens-Mack, Ilia J Leitch, Olivier Maurin, Douglas E Soltis, Pamela S Soltis, Gane Ka-Shu Wong, William J Baker, Norman J Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants)...
December 10, 2018: Systematic Biology
https://read.qxmd.com/read/30521050/rad-seq-data-reveal-a-cryptic-viburnum-species-on-the-north-american-coastal-plain
#15
Elizabeth L Spriggs, Deren A R Eaton, Patrick W Sweeney, Caroline Schlutius, Erika J Edwards, Michael J Donoghue
Species are the starting point for most studies of ecology and evolution, but the proper circumscription of species can be extremely difficult in morphologically variable lineages, and there are still few convincing examples of molecularly-informed species delimitation in plants. We focus here on the Viburnum nudum complex, a highly variable clade that is widely distributed in eastern North America. Taxonomic treatments have mostly divided this complex into northern (V. nudum var. cassinoides) and southern (V...
December 6, 2018: Systematic Biology
https://read.qxmd.com/read/30521024/resolving-deep-nodes-in-an-ancient-radiation-of-neotropical-fishes-in-the-presence-of-conflicting-signals-from-incomplete-lineage-sorting
#16
Fernando Alda, Victor A Tagliacollo, Maxwell J Bernt, Brandon T Waltz, William B Ludt, Brant C Faircloth, Michael E Alfaro, James S Albert, Prosanta Chakrabarty
Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements...
December 6, 2018: Systematic Biology
https://read.qxmd.com/read/30517732/golden-orbweavers-ignore-biological-rules-phylogenomic-and-comparative-analyses-unravel-a-complex-evolution-of-sexual-size-dimorphism
#17
Matjaž Kuntner, Chris A Hamilton, Ren-Chung Cheng, Matjaž Gregoric, Nik Lupše, Tjaša Lokovšek, Emily Moriarty Lemmon, Alan R Lemmon, Ingi Agnarsson, Jonathan A Coddington, Jason E Bond
Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope's Rule (phyletic size increase), Rensch's Rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length ≥ 2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid)...
December 4, 2018: Systematic Biology
https://read.qxmd.com/read/30481358/reconstructing-the-evolution-of-giant-extinct-kangaroos-comparing-the-utility-of-dna-morphology-and-total-evidence
#18
Manuela Cascini, Kieren J Mitchell, Alan Cooper, Matthew J Phillips
Combined "total evidence" analysis of molecular and morphological data offers the opportunity to objectively merge fossils into the tree of life, and challenges the primacy of solely DNA based phylogenetic and dating inference, even among modern taxa. To investigate the relative utility of DNA, morphology, and total evidence for evolutionary inference, we sequenced the first near-complete mitochondrial genomes from extinct Australian megafauna: a 40-50 thousand year old giant short-faced kangaroo (Simosthenurus occidentalis) and giant wallaby (Protemnodon anak)...
November 27, 2018: Systematic Biology
https://read.qxmd.com/read/30481343/phylogenies-and-diversification-rates-variance-cannot-be-ignored
#19
Daniel L Rabosky
A recent pair of articles published in the journal Evolution presented a test for assessing the validity of hierarchical macroevolutionary models. The premise of the test is to compare numerical point estimates of parameters from two levels of analysis; if the estimates differ, the hierarchical model is purportedly flawed. The articles in question (Meyer and Wiens 2017; Meyer et al. 2018) apply their proposed test to BAMM, a scientific software program that uses a Bayesian mixture model to estimate rates of evolution from phylogenetic trees...
November 27, 2018: Systematic Biology
https://read.qxmd.com/read/30476308/stochastic-character-mapping-of-state-dependent-diversification-reveals-the-tempo-of-evolutionary-decline-in-self-compatible-onagraceae-lineages
#20
William A Freyman, Sebastian Höhna
A major goal of evolutionary biology is to identify key evolutionary transitions that correspond with shifts in speciation and extinction rates. Stochastic character mapping has become the primary method used to infer the timing, nature, and number of character state transitions along the branches of a phylogeny. The method is widely employed for standard substitution models of character evolution. However, current approaches cannot be used for models that specifically test the association of character state transitions with shifts in diversification rates such as state-dependent speciation and extinction (SSE) models...
November 26, 2018: Systematic Biology
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