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 ancestral effective population sizes. Suggestions to increase the number of loci and the number of individuals per taxon have been proposed; however, phylogenetic methods to adequately analyze these data in a coalescent framework are scarce. We compare two approaches to estimating lineage (species) trees using multiple individuals and multiple loci: the commonly used partitioned Bayesian analysis of concatenated sequences and a modification of a newly developed hierarchical Bayesian method (BEST) that simultaneously estimates gene trees and species trees from multilocus data. We test these approaches on a phylogeny of rapidly radiating species wherein divergence times are likely to be smaller than effective population sizes, and incomplete lineage sorting is known, in the rodent genus, Thomomys. We use seven independent noncoding nuclear sequence loci (total approximately 4300 bp) and between 1 and 12 individuals per taxon to construct a phylogenetic hypothesis for eight Thomomys species. The majority-rule consensus tree from the partitioned concatenated analysis included 14 strongly supported bipartitions, corroborating monophyletic species status of five of the eight named species. The BEST tree strongly supported only the split between the two subgenera and showed very low support for any other clade. Comparison of both lineage trees to individual gene trees revealed that the concatenation method appears to ignore conflicting signals among gene trees, whereas the BEST tree considers conflicting signals and downweights support for those nodes. Bayes factor analysis of posterior tree distributions from both analyses strongly favor the model underlying the BEST analysis. This comparison underscores the risks of overreliance on results from concatenation, and ignoring the properties of coalescence, especially in cases of recent, rapid radiations.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Belfiore NM,Liu L,Moritz Cdoi
10.1080/10635150802044011subject
Has Abstractpub_date
2008-04-01 00:00:00pages
294-310issue
2eissn
1063-5157issn
1076-836Xpii
792380183journal_volume
57pub_type
杂志文章abstract::Although calyptraeid gastropods are not well understood taxonomically, in part because their simple plastic shells are the primary taxonomic character, they provide an ideal system to examine questions about evolution in the marine environment. I conducted a phylogenetic analysis of calyptraeid gastropods using DNA se...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390235430
更新日期:2003-10-01 00:00:00
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
更新日期:2019-09-01 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::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::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::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::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::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::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::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
更新日期:2016-09-01 00:00:00
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
更新日期:2020-09-01 00:00:00
abstract::Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390196948
更新日期:2003-06-01 00:00:00
abstract::Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study,...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2003-12-01 00:00:00
abstract::Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351501753462876
更新日期:2001-11-01 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::The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before a...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/46.3.464
更新日期:1997-09-01 00:00:00
abstract::How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids an...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500234625
更新日期:2005-10-01 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::Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage o...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351599260085
更新日期:1999-09-01 00:00:00
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
更新日期:2020-09-03 00:00:00
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
更新日期:2016-01-01 00:00:00
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
更新日期:2016-07-01 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::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::Comprehensive phylogenetic analyses utilize data from distinct sources, including nuclear, mitochondrial, and plastid molecular sequences and morphology. Such heterogeneous datasets are likely to require distinct models of analysis, given the different histories of mutational biases operating on these characters. The ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351502753475853
更新日期:2002-02-01 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::The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of co-evolution but little is known about the history of the interaction, and understanding the origin of functionally dioecious fig pollination has been...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2001-04-01 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::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
更新日期:2018-11-01 00:00:00
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
更新日期:2019-03-01 00:00:00