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https://www.readbyqxmd.com/read/28645204/when-homoplasy-is-not-homoplasy-dissecting-trait-evolution-by-contrasting-composite-and-reductive-coding
#1
Alejandro Torres-Montúfar, Thomas Borsch, Helga Ochoterena
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs reductive). Up to now, there is no common agreement to either code characters as complex or simple...
June 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28637223/millions-of-years-behind-slow-adaptation-of-ruminants-to-grasslands
#2
Olja Toljagic, Kjetil L Voje, Michael Matschiner, Lee Hsiang Liow, Thomas F Hansen
The Late-Cretaceous appearance of grasses, followed by the Cenozoic advancement of grasslands as dominant biomes, has contributed to the evolution of a range of specialized herbivores adapted to new diets, as well as to increasingly open and arid habitats. Many mammals including ruminants, the most diversified ungulate suborder, evolved high-crowned (hypsodont) teeth as an adaptation to tooth-wearing diets and habitats. The impact of different causes of tooth wear is still a matter of debate, and the temporal pattern of hypsodonty evolution in relation to the evolution of grasslands remains unclear...
June 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28637293/conserved-non-exonic-elements-a-novel-class-of-marker-for-phylogenomics
#3
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 non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species...
June 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28633306/multivariate-phylogenetic-comparative-methods-evaluations-comparisons-and-recommendations
#4
Dean C Adams, Michael L Collyer
Recent years have seen increased interest in phylogenetic comparative analyses of multivariate datasets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the dataset, but display increasing model misspecification as the number of trait dimensions increases...
June 13, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28595366/conserving-phylogenetic-diversity-can-be-a-poor-strategy-for-conserving-functional-diversity
#5
Florent Mazel, Arne 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 policymakers 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...
June 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28595363/more-on-the-best-evolutionary-rate-for-phylogenetic-analysis
#6
Seraina Klopfstein, Tim Massingham, Nick Goldman
The accumulation of genome-scale molecular datasets for non-model 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...
June 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28482055/combined-analysis-of-extant-rhynchonellida-brachiopoda-using-morphological-and-molecular-data
#7
David W Bapst, Holly A Schreiber, Sandra J Carlson
Independent molecular and morphological phylogenetic analyses have often produced discordant results for certain groups which, for fossil-rich groups, raises the possibility that morphological data might mislead in those groups for which we depend upon morphology the most. Rhynchonellide brachiopods, with more than 500 extinct genera but only 19 extant genera represented today, provide an opportunity to explore the factors that produce contentious phylogenetic signal across datasets, as previous phylogenetic hypotheses generated from molecular sequence data bear little agreement with those constructed using morphological characters...
May 8, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28472519/resolving-relationships-among-the-megadiverse-butterflies-and-moths-with-a-novel-pipeline-for-anchored-phylogenomics
#8
Jesse W Breinholt, Chandra Earl, Alan R Lemmon, Emily Moriarty Lemmon, Lei Xiao, Akito Y Kawahara
The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28472459/resolving-rapid-radiations-within-angiosperm-families-using-anchored-phylogenomics
#9
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford, Emily Moriarty Lemmon, Alan R Lemmon
Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28472434/lineage-diversity-and-size-disparity-in-musteloidea-testing-patterns-of-adaptive-radiation-using-molecular-and-fossil-based-methods
#10
Chris J Law, Graham J Slater, Rita S Mehta
Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28472435/a-metric-on-phylogenetic-tree-shapes
#11
C Colijn, G Plazzotta
The shapes of evolutionary trees are influenced by the nature of the evolutionary process,but comparisons of trees fromdifferent processes are hindered by the challenge of completely describing tree shape. We present a full characterisation of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterisation to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes...
May 2, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28460129/corrigendum
#12
(no author information available yet)
No abstract text is available yet for this article.
April 27, 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
#13
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...
April 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28431159/likelihood-of-tree-topologies-with-fossils-and-diversification-rate-estimation
#14
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)...
April 18, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28419377/gene-tree-reconciliation-with-mul-trees-to-resolve-polyploidy-events
#15
Gregg W C Thomas, 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...
April 13, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28039387/accounting-for-uncertainty-in-gene-tree-estimation-summary-coalescent-species-tree-inference-in-a-challenging-radiation-of-australian-lizards
#16
Mozes P K Blom, Jason G Bragg, Sally Potter, Craig Moritz
Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference...
May 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28003532/uncovering-higher-taxon-diversification-dynamics-from-clade-age-and-species-richness-data
#17
Luna L Sánchez-Reyes, Hélène Morlon, Susana Magallón
The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time-dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age), and taxonomic delimitation can affect estimates of the age-richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations...
May 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/27821704/speciation-with-gene-flow-in-north-american-myotis-bats
#18
Ariadna E Morales, Nathan D Jackson, Tanya A Dewey, Brian C O'Meara, Bryan C Carstens
Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification...
May 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/27798407/construction-of-a-species-level-tree-of-life-for-the-insects-and-utility-in-taxonomic-profiling
#19
Douglas Chesters
Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta)...
May 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/27798405/possibility-and-challenges-of-conversion-of-current-virus-species-names-to-linnaean-binomials
#20
Thomas S Postler, Anna N Clawson, Gaya K Amarasinghe, Christopher F Basler, Sbina Bavari, Mária Benko, Kim R Blasdell, Thomas Briese, Michael J Buchmeier, Alexander Bukreyev, Charles H Calisher, Kartik Chandran, Rémi Charrel, Christopher S Clegg, Peter L Collins, De La Torre Juan Carlos, Joseph L Derisi, Ralf G Dietzgen, Olga Dolnik, Ralf Dürrwald, John M Dye, Andrew J Easton, Sébastian Emonet, Pierre Formenty, Ron A M Fouchier, Elodie Ghedin, Jean-Paul Gonzalez, Balázs Harrach, Roger Hewson, Masayuki Horie, Dàohóng Jiang, Gary Kobinger, Hideki Kondo, Andrew M Kropinski, Mart Krupovic, Gael Kurath, Robert A Lamb, Eric M Leroy, Igor S Lukashevich, Andrea Maisner, Arcady R Mushegian, Sergey V Netesov, Norbert Nowotny, Jean L Patterson, Susan L Payne, Janusz T PaWeska, Clarence J Peters, Sheli R Radoshitzky, Bertus K Rima, Victor Romanowski, Dennis Rubbenstroth, Sead Sabanadzovic, Hélène Sanfaçon, Maria S Salvato, Martin Schwemmle, Sophie J Smither, Mark D Stenglein, David M Stone, Ayato Takada, Robert B Tesh, Keizo Tomonaga, Noël Tordo, Jonathan S Towner, Nikos Vasilakis, Viktor E Volchkov, Victoria Wahl-Jensen, Peter J Walker, Lin-Fa Wang, Arvind Varsani, Anna E Whitfield, F Murilo Zerbini, Jens H Kuhn
Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns...
May 1, 2017: Systematic Biology
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