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BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

Bret R. Larget, Satish K. Kotha, Colin N. Dewey, Cécile Ané
2010 Computer applications in the biosciences : CABIOS  
Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis (Ané et al., 2007) .  ...  The method uses a nonparametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes.  ...  ACKNOWLEDGEMENT We thank David Baum for helpful discussions, and Sarah Friedrich for her skilled help with website design.  ... 
doi:10.1093/bioinformatics/btq539 pmid:20861028 fatcat:suxpycu3wjenje3vqkvlnywyza

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

Yujin Chung, Cécile Ané
2011 Systematic Biology  
With the increasing interest in recognizing the discordance between gene genealogies, various gene tree/species tree reconciliation methods have been developed.  ...  We present here the first attempt to assess and compare two such Bayesian methods, Bayesian estimation of species trees (BEST) and BUCKy (Bayesian untangling of concordance knots), in the presence of several  ...  ACKNOWLEDGMENTS We thank Liang Liu for technical assistance with BEST. Many thanks also to Bret Larget and David Baum for stimulating discussions.  ... 
doi:10.1093/sysbio/syr003 pmid:21368324 fatcat:o3caaknzqjadhh6du6k352tcua

Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo (Caryophyllales) [article]

Abigail Moore, Jurriaan M. de Vos, Lillian P. Hancock, Eric Goolsby, Erika J. Edwards
2017 bioRxiv   pre-print
In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees for the resolution of the sister group of the cacti.  ...  Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply.  ...  One folder contains the analysis pipeline (https://github.com/abigail-Moore/baits-analysis) and a second folder contains scripts for bait design and gene tree/species tree analysis (https://github.com/  ... 
doi:10.1101/145995 fatcat:tv66jeaypvbj5ietjtjd53klwu

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods

Dayana E. Salas-Leiva, Alan W. Meerow, Michael Calonje, M. Patrick Griffith, Javier Francisco-Ortega, Kyoko Nakamura, Dennis W. Stevenson, Carl E. Lewis, Sandra Namoff
2013 Annals of Botany  
These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree -species tree reconciliation, using Cycas as the outgroup.  ...  The specific aim is to evaluate several gene treespecies tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve  ...  Bayes 3 . 1.2; and Bayesian Concordance Analysis (BCA; Ané et al., 2007) with BUCKy v.1.4.2 (Larget et al., 2010) .  ... 
doi:10.1093/aob/mct192 pmid:23997230 pmcid:PMC3806525 fatcat:6ra3ox7g2jhmnnrn6t2efijf6m

Phylogeny and historical biogeography of the cocosoid palms (Arecaceae, Arecoideae, Cocoseae) inferred from sequences of six WRKY gene family loci

Alan W. Meerow, Larry Noblick, Dayana E. Salas-Leiva, Vanessa Sanchez, Javier Francisco-Ortega, Brett Jestrow, Kyoko Nakamura
2014 Cladistics  
We compared parsimony (MP), maximum likelihood (ML), and Bayesian (B) analysis of the supermatrix with three species-tree estimation approaches.  ...  Two B and one ML gene tree-species estimation approaches are incongruent with the supermatrix in a few critical intergeneric clades, but resolve the same infrageneric relationships.  ...  ., 2012) , and Bayesian concordance analysis (BCA; An e et al., 2007) with BUCKy Version 1.4.2 (Larget et al., 2010) .  ... 
doi:10.1111/cla.12100 pmid:34772273 fatcat:zaq27pf27vfg7k43warw532pxm

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Justin L Conover, Nisa Karimi, Noah Stenz, Cécile Ané, Corrinne E Grover, C Skema, Jennifer A Tate, Kirsten Wolff, Samuel A Logan, Jonathan F Wendel, David A Baum
2018 Journal of Integrative Plant Biology  
Gene tree reconciliation and Bayesian concordance analysis suggested a complex history.  ...  Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio).  ...  , a reconciliation method (GRAMPA), Bayesian concordance analysis, and a method based on gene copy number variation.  ... 
doi:10.1111/jipb.12746 pmid:30474311 fatcat:7hkdt575rbg73hvi3byk52mypa

Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction

Cécile Ané
2011 Genome Biology and Evolution  
A high level of systematic bias was found here, highlighting the need for good individual tree building methods, which form the basis for more elaborate gene tree/species tree reconciliation methods.  ...  Simulations show that combining MDL partitioning with Bayesian concordance analysis provides an efficient and robust way to estimate both the vertical inheritance signal and the horizontal phylogenetic  ...  To my knowledge, there is no gene tree/species tree reconstruction method that accounts for or uses the dependence across neighboring gene trees.  ... 
doi:10.1093/gbe/evr013 pmid:21362638 pmcid:PMC3070431 fatcat:otgos5ilrvfenjnqmy7puau73q

Multilocus inference of species trees and DNA barcoding

Diego Mallo, David Posada
2016 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Consensus methods build a tree with compatible gene tree bipartitions weighted by their frequencies while BUCKy does so using concordance factors.  ...  Some rely on the optimization of a gene tree-species tree reconciliation cost (GTP; [29] ).  ... 
doi:10.1098/rstb.2015.0335 pmid:27481787 pmcid:PMC4971187 fatcat:fovihzzjfrbepn4eys3rvlfuvm

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A Smith, Michael J Moore, Joseph W Brown, Ya Yang
2015 BMC Evolutionary Biology  
For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods  ...  The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets.  ...  Other methods that explicitly address topological concordance include concordance analysis as implemented in BUCKy [14, 20, 21] .  ... 
doi:10.1186/s12862-015-0423-0 pmid:26239519 pmcid:PMC4524127 fatcat:2krxuc7ilnbcjbrnkppovbw5di

Speciation genes are more likely to have discordant gene trees [article]

Richard J Wang, Matthew W Hahn
2018 bioRxiv   pre-print
Here, we formally analyze whether genealogies from loci participating in Dobzhansky-Muller (DM) incompatibilities are more likely to be concordant with the species tree under incomplete lineage sorting  ...  Contrary to existing verbal models, we find that reproductively isolating loci that follow the DM model are often more likely to have discordant gene trees.  ...  BUCKy: gene tree/species tree 624 reconciliation with Bayesian concordance analysis. Bioinformatics, 26(22), 2910-2911.625 doi:10.1093/bioinformatics/btq539 626 Liénard, M. A., Araripe, L.  ... 
doi:10.1101/244822 fatcat:znhu3d75vzhudi46uwu5vczkwy

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

Rebecca T. Kimball, Edward L. Braun
2014 PeerJ  
Here we present analyses of a multi-locus data matrix comprising over 6 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 7 46 galliform taxa with all gene  ...  The increased sampling of unlinked 8 nuclear genes provided strong bootstrap support for all but a small number of relationships. 9 Coalescent-based methods to combine individual gene trees and analyses  ...  BUCKy: Gene tree/species tree 588 reconciliation with Bayesian concordance analysis. Bioinformatics 26:2910-2911. 589 Liu, L, Yu, L. 2011. Estimating species trees from unrooted gene trees.  ... 
doi:10.7717/peerj.361 pmid:24795852 pmcid:PMC4006227 fatcat:zbi3deknbbdavbx355ltop4yr4

Phylogenomic terraces: presence and implication in species tree estimation from gene trees [article]

Ishrat Tanzila Farah, Md Muktadirul Islam, Kazi Tasnim Zinat, Atif Hasan Rahman, Md Shamsuzzoha Bayzid
2020 bioRxiv   pre-print
score, extra lineage score, etc.) with respect to a collection of gene trees.  ...  Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores.  ...  BUCKy: Gene tree/species tree 541 reconciliation with the Bayesian concordance analysis. Bioinf, 26(22):2910-2911, for gene trees under coalescence.  ... 
doi:10.1101/2020.04.19.048843 fatcat:qlmewjqjrzhp7i27437lzm7fce

Optimal markers for the identification of Colletotrichum species [article]

Willie Anderson dos Santos Vieira, Priscila Alves bezerra, Anthony Carlos da Silva, Josiene Silva Veloso, Marcos Paz Saraiva Câmara, Vinson Patrick Doyle
2019 bioRxiv   pre-print
Bayesian concordance analyses.  ...  Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA).  ...  BUCKy: Gene tree/species tree 929 reconciliation with the Bayesian concordance analysis. Bioinformatics 26P., Rozas, J.,2009.  ... 
doi:10.1101/659177 fatcat:bmmc36fkcjhs7pqtzi7qsqcsfm

Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

Jeffrey P. Rose, Ricardo Kriebel, Larissa Kahan, Alexa DiNicola, Jesús G. González-Gallegos, Ferhat Celep, Emily M. Lemmon, Alan R. Lemmon, Kenneth J. Sytsma, Bryan T. Drew
2021 Frontiers in Plant Science  
However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance.  ...  We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology.  ...  BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.  ... 
doi:10.3389/fpls.2021.767478 pmid:34899789 pmcid:PMC8652245 fatcat:fbahjrhw4vdznkudhpnweuvqsu

Why concatenation fails in the anomaly zone [article]

Fábio K Mendes, Matthew W Hahn
2017 bioRxiv   pre-print
One such strategy - the concatenation of gene alignments - can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage  ...  of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting.  ...  BUCKy: Gene tree/species tree reconciliation with 563" Bayesian concordance analysis. Bioinformatics 26:2910-2911. 564" Leaché A., Harris R., Rannala B., Yang Z. 2014.  ... 
doi:10.1101/116509 fatcat:6d6ny64ksbf7ffwrfyzosepffq
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