Estimating the species tree for Hawaiian Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution

Willyard, Ann; Wallace, Lisa E.; Wagner, Warren L.; Weller, Stephen G.; Sakai, Ann K.; Nepokroeff, Molly

doi:10.1016/j.ympev.2011.04.001

Cited by 39 publications

(64 citation statements)

References 107 publications

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“…For tree-based comparisons, we propose the following thresholds as an indication of strongly supported incongruence between cpDNA and nrDNA data sets: MP BS70% and PP0.95 and/or ML70%. The weakly supported clades are considered as potential conflicts [39] and need further examination by sampling additional molecular loci.…”

Section: Identification Of Significant Incongruencementioning

confidence: 99%

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Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

Wang

Chen

2014

Sci. China Life Sci.

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Correct combination of plastid (cp) and nuclear (nr) DNA data for plant phylogenetic reconstructions is not a new issue, but with an increasing number of nrDNA loci being used, it is of ever greater practical concern. For accurately reconstructing the phylogeny and evolutionary history of plant groups, correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data. We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011. Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets, or did not address in detail possible reasons for incongruence between the two data sets. By reviewing various methods, we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data, which includes four steps: identifying significant incongruence, determining conflicting taxa, providing possible interpretations for incongruence, and reconstructing the phylogeny after treating incongruence. Particular attention is given to explanation of the cause of incongruence. We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data. combined analysis, plastid DNA, incongruence, nuclear DNA, phylogenetics Citation:Wang W, Li HL, Chen ZD. Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement.

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Section: Identification Of Significant Incongruencementioning

confidence: 99%

“…Morphological evidence for hybridization represents only a probable hypothesis. Nevertheless, if the hybrid nature of a species is supported by artificial and/or field experiments, this can be considered as robust evidence for hybridization [39,63,64].…”

Section: Provision Of Possible Interpretations For Incongruencementioning

confidence: 99%

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

Wang

Chen

2014

Sci. China Life Sci.

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“…69 This was in the light of probable introgression events in the data set, 69 which is a violation of the assumption of the coalescent model that no gene flow occurs after speciation. An empirical study of Hawaiian flowering plants in the genus Schiedea found well supported but different inferred with BEST and traditional concatenation approaches 70 indicating some or all methods were positively misleading compared to the true tree. This finding may be a result of reticulate evolution in Schiedea and a violation of the coalescent model's primary assumption.…”

Section: Reviewmentioning

confidence: 99%

“…This finding may be a result of reticulate evolution in Schiedea and a violation of the coalescent model's primary assumption. 70 Recent studies suggest that at least under certain conditions, BCA and *BEAST may be better alternatives to BEST. Chung and Ané 45 showed BCA, as implemented by BUCKy 43,44 outperformed BEST when horizontal gene transfer was the primary cause of gene tree discordance, and it seems that this conclusion may be extrapolated for *BEAST and STEM as the presence of horizontal gene transfer violates the primary assumption of the coalescent model.…”

Section: Reviewmentioning

confidence: 99%

Species tree inference in the age of genomics

Whelan

2011

Trends Evol Biol

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Species trees are an essential tool in conservation and evolutionary biology. In phylogenomics, not only is data choice (e.g. using unlinked orthologs rather than paralogs) an important systematic consideration, but the choice of phylogenetic algorithm is also important. Since individual gene phylogenies can differ from the true species phylogeny, new methods have been proposed for species tree estimation using multiple unlinked genes. Improvements in genome sequencing technologies have increased the amount of data available to researchers and this has increased the utility of multi-locus species tree inference methods. The Bayesian methods BEST and *BEAST that incorporate a coalescent model to account for gene tree and species tree conflict offer promising advances in species tree inference directly from DNA sequences. Methods that infer species trees from gene trees rather than directly from sequence data such as STAR, STEAC, NJ st and the likelihood method STEM have been recently developed as computationally efficient alternatives. Bayesian concordance analysis, which has been shown to perform well when horizontal gene transfer is the cause of gene tree and species tree conflict, is also discussed. Furthermore, methods for species delimitation including a non-parametric species tree inference method that does not require a priori species assignments can remove subjectivity from species delimitation. Here, I review the assumptions, required inputs, and the performance of these methods under simulation and in recent empirical studies. Researchers in many disciplines should understand the methods available for phylogenomic species tree inference in order to enhance evolutionary and conservation studies.

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“…Polytomies, alternatively called multifurcations, refer to vertices in a phylogenetic tree that have more than two direct descendants. A hard polytomy refers to an event during which an ancestral species gave rise to more than two offspring species at the same time [25], whereas a soft polytomy represents ambiguous evolutionary relationships as a result of insufficient information [26]. Recent research in biology and evolution [27] has shown that the majority of tree space in typical phylogenetic studies consists of multifurcating trees, and that multifurcations can introduce irresolvable problems for certain well-known tree-search algorithms (such as NNI algorithm [5]).…”

Section: Introductionmentioning

confidence: 99%

A fixed-parameter algorithm for the maximum agreement forest problem on multifurcating trees

Shi

Wang

Yang

et al. 2015

Sci. China Inf. Sci.

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The Maximum Agreement Forest (MAF) problem on two given phylogenetic trees is an important NP-hard problem in the field of computational biology. In this paper, we study the parameterized version of the MAF problem: given two unrooted (multifurcating) phylogenetic trees T 1 and T 2 with the same leaf-label set L, and a parameter k, either construct an agreement forest of at most k trees for T 1 and T 2 , or report that no such a forest exists. Whether there is a fixed-parameter tractable algorithm for this problem was posed as an open problem several times in the literature. In this paper, we resolve this open problem by presenting a parameterized algorithm of running time O(4 k n 5 ) for the problem.

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Estimating the species tree for Hawaiian Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution

Cited by 39 publications

References 107 publications

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

Species tree inference in the age of genomics

A fixed-parameter algorithm for the maximum agreement forest problem on multifurcating trees

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