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

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MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

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

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

In animals, PIWI-interacting RNAs (piRNAs) of 21–35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis. PIWI-interacting RNAs (piRNAs) have numerous crucial biological roles, particularly transposon silencing in the germ line. In this Review, the authors describe our latest understanding of piRNA biogenesis and functions across diverse species, highlighting how, despite the universal importance of transposon control, different species have evolved intriguingly distinct mechanistic routes to achieve this.

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PIWI-interacting RNAs: small RNAs with big functions

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

How many species of mammals are there

Discoveries over the past two decades demonstrate that regions distributed throughout the association cortex, often called the default network, are suppressed during tasks that demand external attention and are active during remembering, envisioning the future and making social inferences. This Review describes progress in understanding the organization and function of networks embedded within these association regions. Detailed high-resolution analyses of single individuals suggest that the default network is not a single network, as historically described, but instead comprises multiple interwoven networks. The multiple networks share a common organizational motif (also evident in marmoset and macaque anatomical circuits) that might support a general class of processing function dependent on internally constructed rather than externally constrained representations, with each separate interwoven network specialized for a distinct processing domain. Direct neuronal recordings in humans and monkeys reveal evidence for competitive relationships between the internally and externally oriented networks. Findings from rodent studies suggest that the thalamus might be essential to controlling which networks are engaged through specialized thalamic reticular neurons, including antagonistic subpopulations. These association networks (and presumably thalamocortical circuits) are expanded in humans and might be particularly vulnerable to dysregulation implicated in mental illness. The brain’s default network is thought to comprise a set of regions in the association cortex. Randy Buckner and Lauren DiNicola review findings from humans, monkeys and rodents indicating that multiple subnetworks make up the default network and explore the implications of these observations.

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

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

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Tree of Life Reveals Clock-Like Speciation and Diversification

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, approximately two million years, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

Tree of life reveals clock-like speciation and diversification

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

/pdf/timetree-5-an-expanded-resource-for-species-divergence-times-fcg7l5sf.pdf

TimeTree 5: An Expanded Resource for Species Divergence Times

As the cost of DNA sequencing drops, we are moving beyond one genome per species to one genome per individual to improve prevention, diagnosis, and treatment of disease by using personal genotypes. Computational methods are frequently applied to predict impairment of gene function by nonsynonymous mutations in individual genomes and single nucleotide polymorphisms (nSNPs) in populations. These computational tools are, however, known to fail 15%-40% of the time. We find that accurate discrimination between benign and deleterious mutations is strongly influenced by the long-term (among species) history of positions that harbor those mutations. Successful prediction of known disease-associated mutations (DAMs) is much higher for evolutionarily conserved positions and for original-mutant amino acid pairs that are rarely seen among species. Prediction accuracies for nSNPs show opposite patterns, forecasting impediments to building diagnostic tools aiming to simultaneously reduce both false-positive and false-negative errors. The relative allele frequencies of mutations diagnosed as benign and damaging are predicted by positional evolutionary rates. These allele frequencies are modulated by the relative preponderance of the mutant allele in the set of amino acids found at homologous sites in other species (evolutionarily permissible alleles [EPAs]). The nSNPs found in EPAs are biochemically less severe than those missing from EPAs across all allele frequency categories. Therefore, it is important to consider position evolutionary rates and EPAs when interpreting the consequences and population frequencies of human mutations. The impending sequencing of thousands of human and many more vertebrate genomes will lead to more accurate classifiers needed in real-world applications.

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Michael Suleski

Papers

Tree of Life Reveals Clock-Like Speciation and Diversification

Tree of life reveals clock-like speciation and diversification

TimeTree 5: An Expanded Resource for Species Divergence Times

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations