Abstract：
:The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character state reconstructions. The MCMC framework provided confidence estimates for the reconstructions of relationships and ancestral character states, which formed the basis for tests of evolutionary hypotheses. Monophyly tests rejected all hypotheses that predicted any clustering of reproductive modes in extant taxa. In addition, a nearest-neighbor statistic could not reject the hypothesis that the vegetative reproductive mode is randomly distributed throughout the group. These results show that transitions between presence and absence of the vegetative reproductive mode within Porpidia s.l. occurred several times and independently of each other. Likelihood reconstructions of ancestral character states at selected nodes suggest that--contrary to previous thought--the ancestor to Porpidia s.l. already possessed the vegetative reproductive mode. Furthermore, transition rates are reconstructed asymmetrically with the vegetative reproductive mode being gained at a much lower rate than it is lost. A cautious note has to be added, because a simulation study showed that the ancestral character state reconstructions were highly dependent on taxon sampling. However, our central conclusions, particularly the higher rate of change from vegetative reproductive mode present to absent than vice versa within Porpidia s.l., were found to be broadly independent of taxon sampling.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Buschbom J,Barker Ddoi
10.1080/10635150600697465subject
Has Abstractpub_date
2006-06-01 00:00:00pages
471-84issue
3eissn
1063-5157issn
1076-836Xpii
V61RT34220484353journal_volume
55pub_type
杂志文章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
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更新日期：2011-12-01 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：:We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally link...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/1063515060081570
更新日期：2006-10-01 00:00:00
abstract：:We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of indiv...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150390197019
更新日期：2003-08-01 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
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更新日期：2013-05-01 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
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journal_title：Systematic biology
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journal_title：Systematic biology
pub_type： 杂志文章,评审
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更新日期：2000-03-01 00:00:00
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
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更新日期：2019-09-01 00:00:00
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...
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更新日期：2017-09-01 00:00:00
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journal_title：Systematic biology
pub_type： 杂志文章
doi：
更新日期：2003-12-01 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：:Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov ch...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150600812544
更新日期：2006-08-01 00:00:00
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
更新日期：2021-01-07 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
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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
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journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150490503053
更新日期：2004-10-01 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
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更新日期：2007-04-01 00:00:00
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...
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journal_title：Systematic biology
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更新日期：2012-12-01 00:00:00
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更新日期：2016-07-01 00:00:00
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journal_title：Systematic biology
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更新日期：1997-09-01 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...
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更新日期：2012-10-01 00:00:00
abstract：:Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the sam...
journal_title：Systematic biology
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更新日期：2006-04-01 00:00:00
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journal_title：Systematic biology
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abstract：:Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the cytochrome oxidase I (COI) mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae). The combinabilit...
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更新日期：1998-06-01 00:00:00
