Partitioned Likelihood Support and the Evaluation of Data Set Conflict

Lee, M. S. Y.; Hugall, Andrew F.

doi:10.1080/10635150390132650

Cited by 81 publications

(58 citation statements)

References 43 publications

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“…The probability of 15 or more of 20 independent gene trees agreeing by chance is extremely low (P ϭ 2 ϫ 10 Ϫ9 ; binomial test using equiprobable trees null model). A number of loci that fail to support ratite polyphyly in individual analyses show hidden support (31,32) in combined analyses (Table S3). Thus, the phylogenetic signal is widespread in the nuclear genome and any attempt to explain ratite polyphyly as an artifact must invoke a genome-wide systematic bias.…”

Section: Resultsmentioning

confidence: 99%

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Phylogenomic evidence for multiple losses of flight in ratite birds

Harshman

Braun

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

194

227

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Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.convergence ͉ flightlessness ͉ Paleognath ͉ homoplasy ͉ vicariance biogeography

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Section: Resultsmentioning

confidence: 99%

“…In contrast, Bayesian posterior probabilities can overestimate the probability that a clade is correct (e.g., 66). We also assessed branch (Bremer) support as well as hidden support and conflict for specific branches (31,32).…”

Section: Methodsmentioning

confidence: 99%

Phylogenomic evidence for multiple losses of flight in ratite birds

Harshman

Braun

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

194

227

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“…In parsimony, this question is often addressed using partitioned Bremer support (Baker and DeSalle, 1997); a likelihood analogue, partitioned likelihood support (Lee and Hugall, 2003), has also been developed. In either approach, for each bipartition on the optimal tree, a new tree search is performed with the constraint that the resulting tree not have that bipartition.…”

Section: Phylogenetic Analysis: Combined Analysismentioning

confidence: 99%

Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation (PhD Dissertation)

O’Meara

2008

Nat Prec

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Abstract1) Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. 2) Species delimitation and species tree inference are difficult problems in the case of recent divergences, especially when different loci have different histories. I quantify the difficulty of the problem and introduce a non-parametric method for simultaneously dividing anonymous samples into different species and inferring a species tree, using individual gene trees as input. This heuristic method seeks to both minimize gene tree – species tree discordance and excess population structure within a species. Analyses suggest that the method may provide useful insights for systematists working at the species level with molecular data.3) The phylogeny of Myrmecocystus ants is estimated using nine loci, finding that none of the three subgenera are monophyletic, implying repeated evolution of foraging times and particular morphologies. A new partitioned likelihood program, MrFisher, is created from MrBayes to aid analysis of multilocus datasets without assuming priors. Simulations show that using a partitioned likelihood approach in the presence of rate heterogeneity and missing data, as is common in supermatrix analyses, can recover correct branch lengths where non-partitioned likelihood gives predictably biased estimates of branch lengths but the correct topology.4) Evolution of foraging time and coevolution of behavior and morphology in Myrmecocystus ants is examined. New models for reconstructing discrete states along branches of a tree and for examining continuous trait evolution and coevolution with discrete traits are developed and implemented. Foraging transitions between diurnal and nocturnal foraging evidently go through crepuscular intermediates. There is some evidence for increased rates of morphological character evolution associated with changes in foraging regime, but little evidence for particular optimum values for morphological traits associated with foraging.

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“…O suporte dos ramos foi estimado por "bootstrap" de 100 réplicas com 10 adições aleatórias de seqüências para ambas as análises em MP e ML. Análise Bayesiana (BA) com amostragem pelo algoritmo da cadeia de "Markov Chain Monte Carlo" (MCMC) foi implementada no MrBayes 3.0 com verossimilhança particionada (Lee & Hugall, 2003). O modelo de substituição escolhido para cada partição gênica da análise de ML foi também imposto na análise Bayesiana.…”

Section: 14) Análises Filogenéticasunclassified

“…Monte Carlo" (MCMC) no MrBayes 3.0 com verossimilhança particionada (Lee & Hugall, 2003). Para cada partição gênica foi definido no MrBayes 3.0 o modelo de substituição selecionado pela análise dos dados com o programa MODELTEST 3.0 .…”

Section: 5) Análises Filogenéticasunclassified

Filogenia molecular e biogeografia: jacus e jacutingas (Cracidae)

Grau¹

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Partitioned Likelihood Support and the Evaluation of Data Set Conflict

Cited by 81 publications

References 43 publications

Phylogenomic evidence for multiple losses of flight in ratite birds

Phylogenomic evidence for multiple losses of flight in ratite birds

Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation (PhD Dissertation)

Filogenia molecular e biogeografia: jacus e jacutingas (Cracidae)

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