解剖学和形态学
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听力与言语-语言病理学
行为科学
心脏和心血管系统
细胞和组织工程学
临床神经病学
危重症监护医学
牙科,口腔外科和医学
皮肤病学
急诊医学
内分泌学和新陈代谢
肠胃学和肝脏学
老人病学和老年医学
卫生保健科学和服务
血液学
免疫学
传染病
综合和补充性医学
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医学,全科和内科
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生理学
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泌尿学和肾脏学
病毒学
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心理学,临床
abstract::This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species....
journal_title:Systematic biology
pub_type: 杂志文章,评审
doi:10.1093/sysbio/syu048
更新日期:2015-01-01 00:00:00
abstract::When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences foll...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syu051
更新日期:2014-11-01 00:00:00
abstract::Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclea...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt101
更新日期:2014-03-01 00:00:00
abstract::Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level eve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt054
更新日期:2013-11-01 00:00:00
abstract::The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lin...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt034
更新日期:2013-09-01 00:00:00
abstract::We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is...
journal_title:Systematic biology
pub_type: 杂志文章,评审
doi:10.1093/sysbio/syt029
更新日期:2013-09-01 00:00:00
abstract::Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, t...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt009
更新日期:2013-05-01 00:00:00
abstract::In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic o...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys088
更新日期:2013-03-01 00:00:00
abstract::Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys070
更新日期:2013-01-01 00:00:00
abstract::Among models of nucleotide evolution, the Barry and Hartigan (BH) model (also known as the General Markov Model) is very flexible as it allows separate arbitrary substitution matrices along edges. For a given tree, the estimates of the BH model are a set of joint probability matrices, each giving the pairwise frequenc...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys046
更新日期:2012-12-01 00:00:00
abstract::We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 po...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys048
更新日期:2012-10-01 00:00:00
abstract::We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr080
更新日期:2012-10-01 00:00:00
abstract::We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the prob...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys030
更新日期:2012-10-01 00:00:00
abstract::All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark c...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr119
更新日期:2012-05-01 00:00:00
abstract::We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has seve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr118
更新日期:2012-05-01 00:00:00
abstract::We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr101
更新日期:2012-03-01 00:00:00
abstract::Understanding the evolutionary history of species is at the core of molecular evolution and is done using several inference methods. The critical issue is to quantify the uncertainty of the inference. The posterior probabilities in Bayesian phylogenetic inference and the bootstrap values in frequentist approaches meas...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr129
更新日期:2012-03-01 00:00:00
abstract::Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting m...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr100
更新日期:2012-01-01 00:00:00
abstract::Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr073
更新日期:2011-12-01 00:00:00
abstract::Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr052
更新日期:2011-10-01 00:00:00
abstract::Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet, most reconstruction methods like maximum likelihood (ML) do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution. Given tree samples, we propose finding the tr...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr021
更新日期:2011-07-01 00:00:00
abstract::The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confoundin...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq098
更新日期:2011-05-01 00:00:00
abstract::Understanding the origin of island endemics is a central task of historical biogeography. Recent methodological advances provide a rigorous framework to determine the relative contribution of different biogeographic processes (e.g., vicariance, land migration, long-distance dispersal) to the origin of island endemics....
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq046
更新日期:2010-12-01 00:00:00
abstract::A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolutio...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq025
更新日期:2010-07-01 00:00:00
abstract::Ants (Hymenoptera: Formicidae) are conspicuous organisms in most terrestrial ecosystems, often attaining high levels of abundance and diversity. In this study, we investigate the evolutionary history of a major clade of ants, the subfamily Dolichoderinae, whose species frequently achieve ecological dominance in ant co...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq012
更新日期:2010-05-01 00:00:00
abstract::Horizontal gene transfer (HGT) is one of the main mechanisms driving the evolution of microorganisms. Its accurate identification is one of the major challenges posed by reticulate evolution. In this article, we describe a new polynomial-time algorithm for inferring HGT events and compare 3 existing and 1 new tree com...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp103
更新日期:2010-03-01 00:00:00
abstract::Species delimitation and species tree inference are difficult problems in cases of recent divergence, especially when different loci have different histories. This paper quantifies the difficulty of jointly finding the division of samples to species and estimating a species tree without constraining the possible assig...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp077
更新日期:2010-01-01 00:00:00
abstract::The remarkable fossil record of whales and dolphins (Cetacea) has made them an exemplar of macroevolution. Although their overall adaptive transition from terrestrial to fully aquatic organisms is well known, this is not true for the radiation of modern whales. Here, we explore the diversification of extant cetaceans ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp060
更新日期:2009-12-01 00:00:00
abstract::We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp020
更新日期:2009-04-01 00:00:00
abstract::The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because foss...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp012
更新日期:2009-02-01 00:00:00
abstract::Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802580949
更新日期:2008-12-01 00:00:00
abstract::Whereas examples of insular speciation within the endemic-rich Macaronesian hotspot flora have been documented, the phylogeography of recently evolved plants in the region has received little attention. The Macaronesian red fescues constitute a narrow and recent radiation of four closely related diploid species distri...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802302450
更新日期:2008-10-01 00:00:00
abstract::As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802158688
更新日期:2008-06-01 00:00:00
abstract::Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicates the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802172184
更新日期:2008-06-01 00:00:00
abstract::Species complexes undergoing rapid radiation present a challenge in molecular systematics because of the possibility that ancestral polymorphism is retained in component gene trees. Coalescent theory has demonstrated that gene trees often fail to match lineage trees when taxon divergence times are less than the ancest...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802044011
更新日期:2008-04-01 00:00:00
abstract::Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize our understanding of the tree of life. However, problems arise because estimated phylogenies from individual loci often differ because of different histories, systematic bias, or stochastic error. We have developed Concaterpil...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150801910436
更新日期:2008-02-01 00:00:00
abstract::Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, an...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701656378
更新日期:2007-12-01 00:00:00
abstract::Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated netw...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701424553
更新日期:2007-06-01 00:00:00
abstract::Lice in the genus Pectinopygus parasitize a single order of birds (Pelecaniformes). To examine the degree of congruence between the phylogenies of 17 Pectinopygus species and their pelecaniform hosts, sequences from mitochondrial 12S rRNA, 16S rRNA, COI, and nuclear wingless and EF1-alpha genes (2290 nucleotides) and ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701311370
更新日期:2007-04-01 00:00:00
abstract::The dominance of angiosperms has played a direct role in the diversification of insects, especially Coleoptera. The shift to angiosperm feeding from other diets is likely to have increased the rate of speciation in Phytophaga. However, Phytophaga is only one of many hyperdiverse lineages of beetles and studies of host...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701211844
更新日期:2007-02-01 00:00:00