Naive binning improves phylogenomic analyses

Bayzid, Shamsuzzoha; Warnow, Tandy

doi:10.1093/bioinformatics/btt394

Cited by 149 publications

(128 citation statements)

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“…Simulation studies show that species trees estimated with summary methods can be less accurate than species trees estimated with concatenation, even in the presence of substantial ILS (11,27,28). A main reason for this disparity in performance is poor phylogenetic signal (e.g., because of short sequence lengths) in individual genes, which is a potential problem for coalescent-based summary methods (28,29). Moreover, many realistic biological conditions (including short branches in gene trees) make completely accurate gene tree estimation from limited sequence data highly unlikely (30).…”

Section: Resultsmentioning

confidence: 99%

“…Summary methods are by far the most frequently used method for species tree estimation and have produced good results on some biological data sets (14,15); however, for other data sets, the summary methods have not been able to produce highly supported trees (25), even with a large quantity of data (26). Simulation studies show that species trees estimated with summary methods can be less accurate than species trees estimated with concatenation, even in the presence of substantial ILS (11,27,28). A main reason for this disparity in performance is poor phylogenetic signal (e.g., because of short sequence lengths) in individual genes, which is a potential problem for coalescent-based summary methods (28,29).…”

Section: Resultsmentioning

confidence: 99%

“…Although it is not known how summary methods are affected when only some of the loci have low signal, coalescentbased summary methods have reduced accuracy on data sets where all the gene sequence alignments are short (28).…”

Section: Resultsmentioning

confidence: 99%

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab

Bayzid

Boussau

et al. 2014

Science

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Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although coalescent-based species tree estimation methods can have good accuracy in the presence of ILS, they are sensitive to gene tree estimation error. We propose a pipeline that uses bootstrapping to evaluate whether two genes are likely to have the same tree, then it groups genes into sets using a graph-theoretic optimization and estimates a tree on each subset using concatenation, and finally produces an estimated species tree from these trees using the preferred coalescent-based method. Statistical binning improves the accuracy of MP-EST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab

Bayzid

Boussau

et al. 2014

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“…This is an exciting time. Many long existing controversies are in the process of being resolved by an unparalleled amount of data [6,8,9]. Phylogenomics, a dream just a few decades ago, is now changing the face of molecular phylogenetics.…”

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confidence: 99%

Selecting Molecular Markers for a Specific Phylogenetic Problem

Russo¹,

Aguiar²,

Àlex³

et al. 2017

MOJPB

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Submit Manuscript | http://medcraveonline.com of new technologies and the subsequent accessibility of refined methods due to cost reduction contributed to an immeasurable expansion of molecular facilities worldwide [1]. The rate of sequence submission has recently intensified for three primary reasons: the numerous and successful DNA barcoding projects [2,3], the advent of Next Generation Sequencing [4] and the subsequent decrease in prices for molecular sequencing services [5].As a consequence, genetic data repositories such as GenBank have been doubling in size every 18 months [6], rising from 606 sequences in the first 1982 release to close to 200 million sequences in the 218 th release in February 2017. Molecular data from more than 260 thousand nominal species is now widely accepted as a paramount source of biological information in all life sciences [7]. This is an exciting time. Many long existing controversies are in the process of being resolved by an unparalleled amount of data [6,8,9]. Phylogenomics, a dream just a few decades ago, is now changing the face of molecular phylogenetics. It is a revolution second only to the introduction of molecules in the field of phylogenetics in the 1960's.However, the availability of large number of sequences is not necessarily associated with an accurate estimation of phylogenies, due to analytical errors associated with very large sets of sequence data [10][11][12]. Hence, the contentious matter of molecular marker sampling is inhibiting this new breakthrough. Different genes may yield strikingly contradictory topological patterns for a given diversity group [13,14]. Thus, the selection of suitable markers is critical in obtaining accurate estimates, but it is not a straightforward task. In this review, we aim to provide some guidelines for newcomers weighing the suitability of particular molecular markers for a given phylogenetic problem. Homology in Molecular MarkersIn phylogenetic reconstruction, as in comparative biology studies, the single most important concern lies in the matter of homology, a concept that occupies a central position in evolutionary biology [15]. Homology is a qualitative term, defined by equivalence of parts due to inherited common origin [16][17][18].Homology has been more recently defined as the relationship that binds all states of a single character and sets them apart from the states of other characters, supporting the logical equivalence of the notions of homology and synapomorphy (for review see [19]). The comparison of homologous sequences is critical in a phylogenetic analysis, because only homologous characters may reveal the actual phylogenetic pattern.Nevertheless, a number of authors erroneously refer to homology as a synonym for similarity. Molecular biologists are particularly prone to this error, as they assert that 'two sequences share 70% homology' (for reviews on this problem see [15,20]). Two sequences might show 70% similarity, if 7 out of 10 aligned base pairs are identical between them.In molecular sequences, the high...

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“…Not surprisingly, the gene tree / species tree 'dilemma' has received a lot of attention in recent years, and consequently a plethora of species tree reconstruction methods have been published (Chaudhary, Bansal, et al 2010; e.g., Heled and Drummond 2010;Liu, Yu, et al 2010;Boussau, Szollosi, et al 2013;De Oliveira Martins, Mallo, et al 2014;Mirarab and Warnow 2015; see Mallo, de Oliveira Martins, et al 2014a for a review). Although several benchmarks of species tree methods have been carried out (Leache and Rannala 2011; Yang and Warnow 2011;Bayzid and Warnow 2013;Mirarab, Bayzid, et al 2014) they have generally focused on single causes of phylogenetic discordance. Nevertheless, ILS, GDL and HGT can act simultaneously during genome evolution yielding synergistic evolutionary scenarios (Mallo, De Oliveira Martins, et al 2014b) and therefore it would be convenient to consider them all together.…”

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confidence: 99%

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

Mallo

Martins

Posada

2015

Preprint

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We present here a fast and flexible software -SimPhy-for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer -all three potentially leading to the species tree/gene tree discordance-and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoalSim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.. CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/021709 doi: bioRxiv preprint first posted online Jun. 30, 2015; 3 Recent advances in sequencing technologies have furnished the expansion of genomewide phylogenetic studies, unveiling not only extensive phylogenomic incongruence (Jeffroy, Brinkmann, et al. 2006;Salichos and Rokas 2013) but also bringing back to the spotlight the consideration of how ancestral polymorphisms sort within populations (Edwards 2009). Indeed, it is well known that gene and species phylogenies can be inconsistent due to evolutionary processes like incomplete lineage sorting (ILS), gene duplication and loss (GDL) and horizontal gene transfer (HGT) (Goodman, Czelusniak, et al. 1979;Pamilo and Nei 1988; Takahata 1989;Maddison 1997;Page and Charleston 1997). Not surprisingly, the gene tree / species tree 'dilemma' has received a lot of attention in recent years, and consequently a plethora of species tree reconstruction methods have been published (Chaudhary, Bansal, et al. 2010; e.g., Heled and Drummond 2010;Liu, Yu, et al. 2010;Boussau, Szollosi, et al. 2013;De Oliveira Martins, Mallo, et al. 2014;Mirarab and Warnow 2015; see Mallo, de Oliveira Martins, et al. 2014a for a review). Although several benchmarks of species tree methods have been carried out (Leache and Rannala 2011; Yang and Warnow 2011;Bayzid and Warnow 2013;Mirarab, Bayzid, et al. 2014) the...

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Naive binning improves phylogenomic analyses

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 149 publications

References 27 publications

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Selecting Molecular Markers for a Specific Phylogenetic Problem

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

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