MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Molecular Biology and Evolution, Journal Year: 2016, Volume and Issue: 33(7), P. 1870 - 1874

Published: March 22, 2016

Abstract We present the latest version of Molecular Evolutionary Genetics Analysis (M ega ) software, which contains many sophisticated methods and tools for phylogenomics phylomedicine. In this major upgrade, M has been optimized use on 64-bit computing systems analyzing larger datasets. Researchers can now explore analyze tens thousands sequences in . The new also provides an advanced wizard building timetrees includes a functionality to automatically predict gene duplication events family trees. is made available two interfaces: graphical command line. user interface (GUI) native Microsoft Windows application that be used Mac OS X. line as applications Windows, Linux, They are intended high-throughput scripted analysis. Both versions from www.megasoftware.net free charge.

Language: Английский

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TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

Molecular Biology and Evolution, Journal Year: 2017, Volume and Issue: 34(7), P. 1812 - 1819

Published: March 25, 2017

Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding the temporal patterns divergences over last five decades, number increasing quickly due an exponential growth in available collection molecular sequences from diverse large genes. Our TimeTree resource a public knowledge-base with primary focus make all derived using sequence data scientists, educators, general consistent accessible format. Here, we report major expansion resource, which more than triples (>97,000) assembled (>3,000). Furthermore, scientists can access not only time between two or higher taxa, but also timetree group timeline that traces species' evolution through time. The new visualizations are integrated display events earth environmental history geological time, will lead broader better interplay change biosphere diversity Earth. next generation publicly online at http://www.timetree.org.

Language: Английский

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PIWI-interacting RNAs: small RNAs with big functions

Nature Reviews Genetics, Journal Year: 2018, Volume and Issue: 20(2), P. 89 - 108

Published: Nov. 16, 2018

Language: Английский

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How many species of mammals are there?

Journal of Mammalogy, Journal Year: 2017, Volume and Issue: 99(1), P. 1 - 14

Published: Nov. 15, 2017

Accurate taxonomy is central to the study of biological diversity, as it provides needed evolutionary framework for taxon sampling and interpreting results. While number recognized species in class Mammalia has increased through time, tabulation those increases relied on sporadic release revisionary compendia like Mammal Species World (MSW) series. Here, we present Diversity Database (MDD), a digital, publically accessible, updateable list all mammalian species, now available online: https://mammaldiversity.org. The MDD will continue be updated manuscripts describing new higher taxonomic changes are released. Starting from baseline 3rd edition MSW (MSW3), performed review published since 2004 digitally linked names their original descriptions subsequent articles an interactive, hierarchical database. We found 6,495 currently mammals (96 recently extinct, 6,399 extant), compared 5,416 MSW3 (75 5,341 extant)—an increase 1,079 about 13 years, including 11 newly described having gone extinct last 500 years. tabulate 1,251 recognitions, at least 172 unions, multiple major, higher-level changes, additional 88 genera (1,314 now, 1,226 MSW3) 14 families (167 153). Analyses description time across biogeographic regions show long-term global rate ~25 per year, with Neotropics overall most species-dense region mammals, followed closely by Afrotropics. mammalogical community online database joining digital efforts already established amphibians (AmphibiaWeb, AMNH's Amphibian World), birds (e.g., Avibase, IOC Bird List, HBW Alive), non-avian reptiles (The Reptile Database), fish FishBase, Catalog Fishes). Una taxonomía que precisamente refleje la realidad biológica es fundamental para el estudio de diversidad vida, ya proporciona armazón evolutivo necesario muestreo taxones e interpretación resultados del mismo. Si bien número especies reconocidas en clase ha aumentado con tiempo, tabulación esos aumentos se basado las esporádicas publicaciones compendios revisiones taxonómicas, tales como serie Especies mamíferos mundo (MSW por sus siglas inglés). En este trabajo presentamos Base Datos Diversidad Mamíferos (MDD inglés): una lista todas mamíferos, actualizable y accesible públicamente, disponible dirección URL https://mammaldiversity.org/. El actualizará regularidad medida publiquen artículos describan nuevas o introduzcan cambios diferentes categorías taxonómicas. Con tercera edición (MSW3) punto partida, realizamos revisión profundidad los taxonómicos publicados partir 2004. Los nombres nuevamente descriptas (o ascendidas subespecies) fueron conectadas digitalmente base datos interactiva jerárquica descripciones originales posteriores. indican existen actualmente extintas, vivientes), comparación vivientes): un aumento aproximadamente años, incluyendo consideradas extintas últimos años. Señalamos nuevos reconocimientos especies, al menos uniones varios mayor nivel taxonómico, géneros adicionales reconocidos, comparados familias recién 153 MSW3). análisis témporo-geográficos (en principales regiones mundo) sugieren promedio mundial largo plazo 25 año, siendo Neotrópico región densidad mundo, seguida cerca Afrotrópical. comunidad mastozoólogos conectada actualizable, suma esfuerzos digitales establecidos anfibios aves (p. ej., "no voladores" peces

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The brain’s default network: updated anatomy, physiology and evolving insights

Nature reviews. Neuroscience, Journal Year: 2019, Volume and Issue: 20(10), P. 593 - 608

Published: Sept. 6, 2019

Language: Английский

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Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(12), P. e3000494 - e3000494

Published: Dec. 4, 2019

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility comparative biologists. To establish a robust timescale all approximately 6,000 living mammals, we developed credible sets capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach tree building applies newly assembled 31-gene supermatrix two levels Bayesian inference: (1) backbone relationships ages among major lineages, using fossil node or tip dating, (2) species-level "patch" with nonoverlapping in-groups each correspond one representative lineage the backbone. Species unsampled DNA either excluded ("DNA-only" trees) imputed within taxonomic constraints branch lengths drawn from local birth–death models ("completed" trees). Joining patches backbones results extant Mammalia branches estimated under same modeling framework, thereby facilitating rate comparisons lineages as disparate marsupials placentals. We compare our previous estimates mammal-wide phylogeny times, finding broadly concordant studies, recent (tip-level) rates speciation more accurately study than "supertree" approaches, which unresolved nodes led branch-length artifacts. Credible mammalian history now available download at http://vertlife.org/phylosubsets, enabling investigations long-standing questions biology.

Language: Английский

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Earth BioGenome Project: Sequencing life for the future of life

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(17), P. 4325 - 4333

Published: April 23, 2018

Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific social challenges new millennium. These require fundamental knowledge organization, evolution, functions, interactions millions planet’s organisms. Herein, we present a perspective on Earth BioGenome Project (EBP), moonshot for biology that aims to sequence, catalog, characterize genomes all eukaryotic over period 10 years. The outcomes EBP will inform broad range major issues facing humanity, such as impact climate change biodiversity, conservation endangered species ecosystems, preservation enhancement ecosystem services. We describe hurdles project faces, including data-sharing policies ensure permanent, freely available resource future discovery while respecting access benefit sharing guidelines Nagoya Protocol. also organizational in executing an ambitious project, structure proposed achieve project’s goals. far-reaching potential benefits creating open digital repository genomic information life can be realized only by coordinated international effort.

Language: Английский

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TimeTree 5: An Expanded Resource for Species Divergence Times

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(8)

Published: Aug. 1, 2022

Abstract We present the fifth edition of TimeTree Life resource (TToL5), a product timetree life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible all. Using TToL5 web portal, users can retrieve studies divergence times between species, timeline species’ evolution beginning with origin life, for given group at desired taxonomic rank. contains time information on 137,306 41% more than previous edition. The interface is now Americans Disabilities Act-compliant mobile-friendly, result comprehensive source code refactoring. also offers programmatic access species timelines through an application programming interface, which timetree.temple.edu/api. publicly available timetree.org.

Language: Английский

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The evolutionary history of vertebrate RNA viruses

Nature, Journal Year: 2018, Volume and Issue: 556(7700), P. 197 - 202

Published: March 29, 2018

Language: Английский

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The biology of color

Science, Journal Year: 2017, Volume and Issue: 357(6350)

Published: Aug. 3, 2017

In living color Animals live in a colorful world, but we rarely stop to think about how this is produced and perceived, or it evolved. Cuthill et al. review used for social signals between individual animals affects interactions with parasites, predators, the physical environment. New approaches are elucidating aspects of animal coloration, from requirements complex cognition perception mechanisms evolutionary dynamics surrounding its development diversification. Science , issue p. eaan0221

Language: Английский

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