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 communities. This group has also produced some of the world's most successful invasive ants. We use an extensive molecular data set ( approximately 9 kb of sequence data from 10 nuclear genes, covering 48 dolichoderine species and 6 outgroup taxa) to infer the phylogenetic relationships, divergence dates, and biogeographic history of these ants. We evaluate the effects of data partitioning and outgroup composition on phylogenetic inference by estimating relationships under a series of increasingly partitioned data sets and by running analyses both with and without Aneuretus simoni, a rare and localized species that is the nearest living relative of Dolichoderinae. We also examine the effects of excluding 2 data partitions with significant base composition heterogeneity. Our results reveal 4 well-supported and mutually exclusive clades of dolichoderines, corresponding to 4 newly defined tribes: Bothriomyrmecini (B), Dolichoderini (D), Leptomyrmecini (L), and Tapinomini (T). All Bayesian and likelihood analyses yield the same unrooted (ingroup-only) topology, ((D,L),(B,T)), with the outgroups attaching either on the Dolichoderini branch or on the Tapinomini branch. Placement of the root is highly sensitive to choice of model partition and to inclusion/exclusion of Aneuretus. Bayes' factors strongly favor the more partitioned models, and in these Tapinomini is recovered as sister to the remaining dolichoderines, but only if Aneuretus is included. Exclusion of Aneuretus precludes recovery of this topology in all but the most highly partitioned Bayesian analyses and then only with nonsignificant support, underscoring the importance of relict, taxonomically isolated taxa for phylogenetic inference. Removal of 2 partitions with heterogeneous base composition also markedly increases support for placement of the root on the Tapinomini branch. Our divergence date estimates and biogeographic analyses indicate that crown-group dolichoderines arose about 65 million years ago (Ma), although this was preceded by a substantial period (30 million years) of stem group evolution. The 4 extant tribes are estimated to have crown-group origins in the late Paleocene or Eocene (40-60 Ma). Tapinomini and Bothriomyrmecini originated in the Paleotropics and subsequently dispersed to other biogeographic regions. Crown-group Leptomyrmecini arose and diversified in the Neotropics, but they also gave rise to one clade that colonized Australia about 30 Ma and subsequently experienced a massive radiation on that continent. This event occurred later than the diversification of dolichoderines in the northern hemisphere, so that by the time dolichoderines came to dominate the Australian fauna they had already declined in abundance in the Holarctic region.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Ward PS,Brady SG,Fisher BL,Schultz TRdoi
10.1093/sysbio/syq012subject
Has Abstractpub_date
2010-05-01 00:00:00pages
342-62issue
3eissn
1063-5157issn
1076-836Xpii
syq012journal_volume
59pub_type
杂志文章abstract::The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology....
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490264699
更新日期:2004-02-01 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::Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a h...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2001-06-01 00:00:00
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
更新日期:2020-07-08 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::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::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::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::Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 spec...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490888840
更新日期:2004-12-01 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::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::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::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
更新日期:2021-01-01 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::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::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::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
更新日期:2021-01-07 00:00:00
abstract::Randomization tests allow the formulation and statistical testing of null hypotheses about the quality of entire data sets or the quality of fit between the data and particular phylogenetic hypotheses. Randomization tests of phylogenetic hypotheses based on the concepts of split support and split conflict are describe...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351598260662
更新日期:1998-12-01 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::In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean estimation procedure. In the ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500433722
更新日期:2006-04-01 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::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::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::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::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::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::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::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
更新日期:2016-11-01 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::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
更新日期:2020-09-17 00:00:00