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  • Phylogenomics, Origin and Diversification of Anthozoans (Phylum Cnidaria).

    abstract::Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally use...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa103

    authors: McFadden CS,Quattrini AM,Brugler MR,Cowman PF,Dueñas LF,Kitahara MV,Paz-García DA,Reimer JD,Rodríguez E

    更新日期:2021-01-28 00:00:00

  • Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias).

    abstract::Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuc...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa085

    authors: Sarver BAJ,Herrera ND,Sneddon D,Hunter SS,Settles ML,Kronenberg Z,Demboski JR,Good JM,Sullivan J

    更新日期:2021-01-07 00:00:00

  • The comparative method is not macroevolution: across-species evidence for within-species process.

    abstract::It is common for studies that employ the comparative method for the study of adaptation, i.e. documentation of potentially adaptive across-species patterns of trait-environment or trait-trait correlation, to be designated as "macroevolutionary." Authors are justified in using "macroevolution" in this way by appeal to ...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa086

    authors: Olson ME

    更新日期:2021-01-07 00:00:00

  • Modeling Phylogenetic Biome Shifts on a Planet with a Past.

    abstract::The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa045

    authors: Landis M,Edwards EJ,Donoghue MJ

    更新日期:2021-01-01 00:00:00

  • Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets.

    abstract::The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morp...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa075

    authors: de Moya RS,Yoshizawa K,Walden KKO,Sweet AD,Dietrich CH,Johnson KP

    更新日期:2020-09-26 00:00:00

  • Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist.

    abstract::Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predic...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa071

    authors: Funk ER,Spellman GM,Winker K,Withrow JJ,Ruegg KC,Zavaleta E,Taylor SA

    更新日期:2020-09-17 00:00:00

  • A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data.

    abstract::Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approa...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa069

    authors: Koch NM,Thompson JR

    更新日期:2020-09-03 00:00:00

  • Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable.

    abstract::In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa003

    authors: Varón-González C,Whelan S,Klingenberg CP

    更新日期:2020-09-01 00:00:00

  • Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference.

    abstract::Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topolog...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa002

    authors: Zhang C,Huelsenbeck JP,Ronquist F

    更新日期:2020-09-01 00:00:00

  • Identification of Hidden Population Structure in Time-Scaled Phylogenies.

    abstract::Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission pat...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa009

    authors: Volz EM,Carsten W,Grad YH,Frost SDW,Dennis AM,Didelot X

    更新日期:2020-09-01 00:00:00

  • Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy.

    abstract::The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of th...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa065

    authors: Kolmann MA,Hughes LC,Hernandez LP,Arcila D,Betancur-R R,Sabaj MH,López-Fernández H,Ortí G

    更新日期:2020-08-12 00:00:00

  • Phylogeographic estimation and simulation of global diffusive dispersal.

    abstract::The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of the...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa061

    authors: Louca S

    更新日期:2020-07-29 00:00:00

  • Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective.

    abstract::Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflic...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa054

    authors: Singhal S,Colston TJ,Grundler MR,Smith SA,Costa GC,Colli GR,Moritz C,Pyron RA,Rabosky DL

    更新日期:2020-07-18 00:00:00

  • Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent.

    abstract::Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur c...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa053

    authors: Poelstra J,Salmona J,Tiley GP,Schüßler D,Blanco MB,Andriambeloson JB,Bouchez O,Campbell CR,Etter PD,Hohenlohe PA,Hunnicutt KE,Iribar A,Johnson EA,Kappeler PM,Larsen PA,Manzi S,Ralison JM,Randrianambinina B,Rasoloariso

    更新日期:2020-07-08 00:00:00

  • Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.

    abstract::Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete tax...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syaa013

    authors: Zhang R,Wang YH,Jin JJ,Stull GW,Bruneau A,Cardoso D,De Queiroz LP,Moore MJ,Zhang SD,Chen SY,Wang J,Li DZ,Yi TS

    更新日期:2020-07-01 00:00:00

  • Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data.

    abstract::Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). Howe...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syz056

    authors: Blair C,Ané C

    更新日期:2020-05-01 00:00:00

  • Monophyly, Taxon Sampling, and the Nature of Ranks in the Classification of Orb-Weaving Spiders (Araneae: Araneoidea).

    abstract::We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the fami...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syz043

    authors: Kallal RJ,Dimitrov D,Arnedo MA,Giribet G,Hormiga G

    更新日期:2020-03-01 00:00:00

  • Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution.

    abstract::Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recent...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syz030

    authors: Allio R,Scornavacca C,Nabholz B,Clamens AL,Sperling FA,Condamine FL

    更新日期:2020-01-01 00:00:00

  • Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models.

    abstract::Stochastic birth-death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this article, we first provide intuitive reasons for these known transfo...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syz039

    authors: Stadler T,Steel M

    更新日期:2019-09-01 00:00:00

  • Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits.

    abstract::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 proces...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syz005

    authors: Tarasov S

    更新日期:2019-09-01 00:00:00

  • Restriction-Site-Associated DNA Sequencing Reveals a Cryptic Viburnum Species on the North American Coastal Plain.

    abstract::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. Here, we focus on the Viburnum nudum c...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syy084

    authors: Spriggs EL,Eaton DAR,Sweeney PW,Schlutius C,Edwards EJ,Donoghue MJ

    更新日期:2019-03-01 00:00:00

  • Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

    abstract::Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynami...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syy048

    authors: Duchene S,Bouckaert R,Duchene DA,Stadler T,Drummond AJ

    更新日期:2019-03-01 00:00:00

  • A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics.

    abstract::As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceede...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syy026

    authors: Singhal S,Hoskin CJ,Couper P,Potter S,Moritz C

    更新日期:2018-11-01 00:00:00

  • An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution.

    abstract::Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associ...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syx032

    authors: Levy Karin E,Wicke S,Pupko T,Mayrose I

    更新日期:2017-11-01 00:00:00

  • Efficient Bayesian Species Tree Inference under the Multispecies Coalescent.

    abstract::We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruni...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw119

    authors: Rannala B,Yang Z

    更新日期:2017-09-01 00:00:00

  • Different from Trees, more than Metaphors: Branching Silhouettes-Corals, Cacti, and the Oaks.

    abstract::There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syx039

    authors: Podani J

    更新日期:2017-09-01 00:00:00

  • Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species.

    abstract::We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Mar...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw063

    authors: Dalquen DA,Zhu T,Yang Z

    更新日期:2017-05-01 00:00:00

  • Incomplete Lineage Sorting in Mammalian Phylogenomics.

    abstract::The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among genes, and the related issue of whether to account for ILS in species tree reconstruction, are matters of intense controversy. Here, focusing on full-genome data in placental mammals, we empirically test two assumptions underlying current u...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw082

    authors: Scornavacca C,Galtier N

    更新日期:2017-01-01 00:00:00

  • Taxonomic Quality of Species Descriptions Varies over Time and with the Number of Authors, but Unevenly among Parasitic Taxa.

    abstract::Although concerns are being raised about a potential shortage of taxonomists and systematists, recent analyses suggest instead that the number of researchers involved in taxonomic descriptions is higher than ever and that the average number of new species described annually per taxonomist has declined in recent decade...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw053

    authors: Poulin R,Presswell B

    更新日期:2016-11-01 00:00:00

  • Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera.

    abstract::Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many group...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw031

    authors: Morard R,Escarguel G,Weiner AK,André A,Douady CJ,Wade CM,Darling KF,Ujiié Y,Seears HA,Quillévéré F,de Garidel-Thoron T,de Vargas C,Kucera M

    更新日期:2016-09-01 00:00:00

  • Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

    abstract::The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpi...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw039

    authors: O'Connor A,Wills MA

    更新日期:2016-09-01 00:00:00

  • Testing for Independence between Evolutionary Processes.

    abstract::Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for th...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw004

    authors: Behdenna A,Pothier J,Abby SS,Lambert A,Achaz G

    更新日期:2016-09-01 00:00:00

  • Gene Tree Discordance Causes Apparent Substitution Rate Variation.

    abstract::Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide da...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syw018

    authors: Mendes FK,Hahn MW

    更新日期:2016-07-01 00:00:00

  • The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?

    abstract::Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions ...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv084

    authors: Murray GG,Weinert LA,Rhule EL,Welch JJ

    更新日期:2016-03-01 00:00:00

  • Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host.

    abstract::Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provi...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv070

    authors: Pérez-Escobar OA,Balbuena JA,Gottschling M

    更新日期:2016-01-01 00:00:00

  • How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards.

    abstract::Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolve...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv058

    authors: Streicher JW,Schulte JA 2nd,Wiens JJ

    更新日期:2016-01-01 00:00:00

  • A Skull Might Lie: Modeling Ancestral Ranges and Diet from Genes and Shape of Tree Squirrels.

    abstract::Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they ...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv054

    authors: Pečnerová P,Moravec JC,Martínková N

    更新日期:2015-11-01 00:00:00

  • Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.

    abstract::The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and reso...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv031

    authors: Dececchi TA,Balhoff JP,Lapp H,Mabee PM

    更新日期:2015-11-01 00:00:00

  • Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci.

    abstract::Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv035

    authors: Brassac J,Blattner FR

    更新日期:2015-09-01 00:00:00

  • Multilocus Phylogeny of the Afrotropical Freshwater Crab Fauna Reveals Historical Drainage Connectivity and Transoceanic Dispersal Since the Eocene.

    abstract::Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensiv...

    journal_title:Systematic biology

    pub_type: 杂志文章

    doi:10.1093/sysbio/syv011

    authors: Daniels SR,Phiri EE,Klaus S,Albrecht C,Cumberlidge N

    更新日期:2015-07-01 00:00:00

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