CoChat
Sign Up
Cited by 28

The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance

Yan, Han, Hu, Zhirui, Thomas, Gregg W C, Edwards, Scott V, Sackton, Timothy B, Liu, Jun S·2023·Molecular Biology and Evolution
DOI 10.1093/molbev/msad195PMC PMC10540510
Open this paper in CoChat — free account

Abstract

An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/molbev/msad195

Cites

8 of 8 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 77

  1. Ané, 2007, Bayesian estimation of concordance among gene trees, Mol Biol Evol, 24, 412, 10.1093/molbev/msl170 · DOI
  2. Angelis, 2015, The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times, Curr Zool, 61, 874, 10.1093/czoolo/61.5.874 · DOI · Paper page
  3. Avise, 2008, Hemiplasy: a new term in the lexicon of phylogenetics, Syst Biol, 57, 503, 10.1080/10635150802164587 · DOI
  4. Baum, 2007, Concordance trees, concordance factors, and the exploration of reticulate genealogy, Taxon, 56, 417, 10.1002/tax.562013 · DOI
  5. Bielawski, 2002, Mutation patterns of mitochondrial h-and l-strand DNA in closely related cyprinid fishes, Genetics, 161, 1589, 10.1093/genetics/161.4.1589 · DOI
  6. Blanchette, 2004, Aligning multiple genomic sequences with the threaded blockset aligner, Genome Res, 14, 708, 10.1101/gr.1933104 · DOI · Paper page
  7. Bravo, 2019, Embracing heterogeneity: coalescing the tree of life and the future of phylogenomics, PeerJ, 7, e6399, 10.7717/peerj.6399 · DOI
  8. Chikina, 2016, Hundreds of genes experienced convergent shifts in selective pressure in marine mammals, Mol Biol Evol, 33, 2182, 10.1093/molbev/msw112 · DOI · Paper page
  9. Consortium, 2020, A comparative genomics multitool for scientific discovery and conservation, Nature, 587, 240, 10.1038/s41586-020-2876-6 · DOI · Paper page
  10. Cooper, 2005, Distribution and intensity of constraint in mammalian genomic sequence, Genome Res, 15, 901, 10.1101/gr.3577405 · DOI · Paper page
  11. Cooper, 2005, Distribution and intensity of constraint in mammalian genomic sequence, Genome Res, 15, 901, 10.1101/gr.3577405 · DOI · Paper page
  12. Dai, 2020, Monte Carlo approximation of Bayes factors via mixing with surrogate distributions, J Am Stat Assoc, 117, 1
  13. Degnan, 2009, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trends Ecol Evol, 24, 332, 10.1016/j.tree.2009.01.009 · DOI
  14. Edwards, 2009, Is a new and general theory of molecular systematics emerging?, Evol Int J Org Evol, 63, 1, 10.1111/j.1558-5646.2008.00549.x · DOI · Paper page
  15. Edwards, 2016, Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics, Mol Phylogenet Evol, 94, 447, 10.1016/j.ympev.2015.10.027 · DOI
  16. Espindola-Hernandez, 2022, Genomic signatures of the evolution of a diurnal lifestyle in strigiformes, G3: Genes Genomes Genet, 12, jkac135, 10.1093/g3journal/jkac135 · DOI
  17. Eyre-Walker, 2014, How much of the variation in the mutation rate along the human genome can be explained?, G3: Genes Genomes Genet, 4, 1667, 10.1534/g3.114.012849 · DOI
  18. Felsenstein, 1973, Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters, Syst Biol, 22, 240, 10.1093/sysbio/22.3.240 · DOI
  19. Flouri, 2022, Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent, Mol Biol Evol, 39, msac161, 10.1093/molbev/msac161 · DOI
  20. Flouri, 2018, Species tree inference with BPP using genomic sequences and the multispecies coalescent, Mol Biol Evol, 35, 2585, 10.1093/molbev/msy147 · DOI
  21. Grealey, 2022, The carbon footprint of bioinformatics, Mol Biol Evol, 39, msac034, 10.1093/molbev/msac034 · DOI
  22. Hahn, 2016, Irrational exuberance for resolved species trees, Evolution, 70, 7, 10.1111/evo.12832 · DOI · Paper page
  23. Heled, 2009, Bayesian inference of species trees from multilocus data, Mol Biol Evol, 27, 570, 10.1093/molbev/msp274 · DOI · Paper page
  24. Hiller, 2012, A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species, Cell Rep, 2, 817, 10.1016/j.celrep.2012.08.032 · DOI · Paper page
  25. Hodgkinson, 2011, Variation in the mutation rate across mammalian genomes, Nat Rev Genet, 12, 756, 10.1038/nrg3098 · DOI · Paper page
  26. Hubisz, 2011, Phast and rphast: phylogenetic analysis with space/time models, Brief Bioinform, 12, 41, 10.1093/bib/bbq072 · DOI · Paper page
  27. Jarvis, 2014, Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, 346, 1320, 10.1126/science.1253451 · DOI · Paper page
  28. Jennings, 2005, Speciational history of Australian grass finches (poephila) inferred from thirty gene trees, Evolution, 59, 2033
  29. Kowalczyk, 2022, Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness, Elife, 11, e76911, 10.7554/eLife.76911 · DOI
  30. Kowalczyk, 2019, Rerconverge: an R package for associating evolutionary rates with convergent traits, Bioinformatics, 35, 4815, 10.1093/bioinformatics/btz468 · DOI · Paper page
  31. Kowalczyk, 2020, Pan-mammalian analysis of molecular constraints underlying extended lifespan, Elife, 9, e51089, 10.7554/eLife.51089 · DOI · Paper page
  32. Lartillot, 2010, A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters, Mol Biol Evol, 28, 729, 10.1093/molbev/msq244 · DOI · Paper page
  33. Lartillot, 2011, A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters, Mol Biol Evol, 28, 729, 10.1093/molbev/msq244 · DOI · Paper page
  34. Levy Karin, 2017, An integrated model of phenotypic trait changes and site-specific sequence evolution, Syst Biol, 66, 917, 10.1093/sysbio/syx032 · DOI · Paper page
  35. Lewis, 2019, Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry, Proc Natl Acad Sci USA, 116, 24174, 10.1073/pnas.1907068116 · DOI
  36. Liu, 1994, The collapsed gibbs sampler in Bayesian computations with applications to a gene regulation problem, J Am Stat Assoc, 89, 958, 10.1080/01621459.1994.10476829 · DOI
  37. Liu, 2008, Monte Carlo strategies in scientific computing
  38. Liu, 2015, Estimating phylogenetic trees from genome-scale data, Ann N Y Acad Sci, 1360, 36, 10.1111/nyas.12747 · DOI
  39. Liu, 2010, A maximum pseudo-likelihood approach for estimating species trees under the coalescent model, BMC Evol Biol, 10, 1, 10.1186/1471-2148-10-302 · DOI · Paper page
  40. Lopes, 2021, Phylogenomic discordance in the eared seals is best explained by incomplete lineage sorting following explosive radiation in the Southern Hemisphere, Syst Biol, 70, 786, 10.1093/sysbio/syaa099 · DOI
  41. Lucaci, 2021, Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes, PLoS ONE, 16, e0248337, 10.1371/journal.pone.0248337 · DOI
  42. Maddison, 1997, Gene trees in species trees, Syst Biol, 46, 523, 10.1093/sysbio/46.3.523 · DOI
  43. Marcovitz, 2016, “reverse genomics” predicts function of human conserved noncoding elements, Mol Biol Evol, 33, 1358, 10.1093/molbev/msw001 · DOI · Paper page
  44. Mattick, 2005, The functional genomics of noncoding RNA, Science, 309, 1527, 10.1126/science.1117806 · DOI
  45. Mayrose, 2011, A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution, Mol Biol Evol, 28, 759, 10.1093/molbev/msq263 · DOI · Paper page
  46. Mendes, 2016, Gene tree discordance causes apparent substitution rate variation, Syst Biol, 65, 711, 10.1093/sysbio/syw018 · DOI · Paper page
  47. Minh, 2020, New methods to calculate concordance factors for phylogenomic datasets, Mol Biol Evol, 37, 2727, 10.1093/molbev/msaa106 · DOI
  48. Minh, 2020, IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era, Mol Biol Evol, 37, 1530, 10.1093/molbev/msaa015 · DOI · Paper page
  49. Mirarab, 2014, Astral: genome-scale coalescent-based species tree estimation, Bioinformatics, 30, i541, 10.1093/bioinformatics/btu462 · DOI
  50. Mölder, 2021, Sustainable data analysis with snakemake, F1000Research, 10
  51. Murrell, 2015, Gene-wide identification of episodic selection, Mol Biol Evol, 32, 1365, 10.1093/molbev/msv035 · DOI
  52. Nguyen, 2015, Iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, 32, 268, 10.1093/molbev/msu300 · DOI · Paper page
  53. O’Connor, 2009, Genotype–phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate, Bioinformatics, 25, i94, 10.1093/bioinformatics/btp231 · DOI
  54. O’Connor, 2013, Evolutionary modeling of genotype–phenotype associations, and application to primate coding and non-coding mtDNA rate variation, Evol Bioinform, 9, EBO–S11600, 10.4137/EBO.S11600 · DOI
  55. Ogilvie, 2017, Starbeast2 brings faster species tree inference and accurate estimates of substitution rates, Mol Biol Evol, 34, 2101, 10.1093/molbev/msx126 · DOI · Paper page
  56. Partha, 2017, Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling, eLife, 6, e25884, 10.7554/eLife.25884 · DOI · Paper page
  57. Partha, 2019, Robust method for detecting convergent shifts in evolutionary rates, Mol Biol Evol, 36, 1817, 10.1093/molbev/msz107 · DOI · Paper page
  58. Pollard, 2010, Detection of nonneutral substitution rates on mammalian phylogenies, Genome Res, 20, 110, 10.1101/gr.097857.109 · DOI · Paper page
  59. Pond, 2005, Hyphy: hypothesis testing using phylogenies, Bioinformatics, 21, 676, 10.1093/bioinformatics/bti079 · DOI · Paper page
  60. Prudent, 2016, Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences, Mol Biol Evol, 33, 2135, 10.1093/molbev/msw098 · DOI · Paper page
  61. Rannala, 2003, Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci, Genetics, 164, 1645, 10.1093/genetics/164.4.1645 · DOI
  62. Rannala, 2017, Efficient Bayesian species tree inference under the multispecies coalescent, Syst Biol, 66, 823, 10.1093/sysbio/syw119 · DOI
  63. Sackton, 2019, Convergent regulatory evolution and loss of flight in paleognathous birds, Science, 364, 74, 10.1126/science.aat7244 · DOI · Paper page
  64. Saito, 2015, The precision-recall plot is more informative than the roc plot when evaluating binary classifiers on imbalanced datasets, PLoS ONE, 10, e0118432, 10.1371/journal.pone.0118432 · DOI · Paper page
  65. Simmons, 2022, Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds, Mol Phylogenet Evol, 167, 107344, 10.1016/j.ympev.2021.107344 · DOI
  66. Singh, 2009, Strong evidence for lineage and sequence specificity of substitution rates and patterns in drosophila, Mol Biol Evol, 26, 1591, 10.1093/molbev/msp071 · DOI
  67. Smith, 2020, Phylogenetics is the new genetics (for most of biodiversity), Trends Ecol Evol, 35, 415, 10.1016/j.tree.2020.01.005 · DOI · Paper page
  68. Smith, 2015, Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection, Mol Biol Evol, 32, 1342, 10.1093/molbev/msv022 · DOI
  69. Stamatakis, 2014, Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033 · DOI · Paper page
  70. Sun, 2021, Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits, Mol Biol Evol, 38, 486, 10.1093/molbev/msaa240 · DOI
  71. Tong, 2022, Genomic signatures of recent convergent transitions to social life in spiders, Nat Commun, 13, 1, 10.1038/s41467-022-34446-8 · DOI
  72. Venkat, 2018, Multinucleotide mutations cause false inferences of lineage-specific positive selection, Nat Ecol Evol, 2, 1280, 10.1038/s41559-018-0584-5 · DOI
  73. Yang, 1997, On the estimation of ancestral population sizes of modern humans, Genet Res (Camb), 69, 111, 10.1017/S001667239700270X · DOI
  74. Yang, 1997, PAML: a program package for phylogenetic analysis by maximum likelihood, Comput Appl Biosci, 13, 555
  75. Yang, 2002, Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci, Genetics, 162, 1811, 10.1093/genetics/162.4.1811 · DOI
  76. Zhang, 2005, Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level, Mol Biol Evol, 22, 2472, 10.1093/molbev/msi237 · DOI · Paper page
  77. Zhu, 2021, Complexity of the simplest species tree problem, Mol Biol Evol, 38, 3993, 10.1093/molbev/msab009 · DOI

Cited by

Sorted by citations

Metadata

Authors
Yan, H., Hu, Z., Thomas, G. W. C., Edwards, S. V., Sackton, T. B., & Liu, J. S.
Affiliations
  • Department of Statistics, Harvard University, Cambridge, MA, USA
  • Informatics Group, Harvard University, Cambridge, MA, USA
  • Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2023-09-01
Volume
40
Issue
9
ISSN
  • 0737-4038
  • 1537-1719
DOI
10.1093/molbev/msad195
PMC
PMC10540510
Cited by
28
References
8
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor, 3 d)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review