CAAStools: a Toolbox to Identify and Test Convergent Amino Acid Substitutions

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2023 Oct 17

PMID 37846039

Authors

Fabio Barteri

Alejandro Valenzuela

Xavier Farre

David de Juan

Gerard Muntane

Borja Esteve-Altava

Arcadi Navarro

Affiliations

Soon will be listed here.

Abstract

Motivation: Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes.

Results: Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user.

Availability And Implementation: CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples.

Citing Articles

WGCCRR: a web-based tool for genome-wide screening of convergent indels and substitutions of amino acids.

Dong Z, Wang C, Qu Q Bioinform Adv. 2024; 4(1):vbae070.

PMID: 38808070 PMC: 11132816. DOI: 10.1093/bioadv/vbae070.

References

Xu S, He Z, Guo Z, Zhang Z, Wyckoff G, Greenberg A . Genome-Wide Convergence during Evolution of Mangroves from Woody Plants. Mol Biol Evol. 2017; 34(4):1008-1015. DOI: 10.1093/molbev/msw277. View

Royer-Carenzi M, Didier G . A comparison of ancestral state reconstruction methods for quantitative characters. J Theor Biol. 2016; 404:126-142. DOI: 10.1016/j.jtbi.2016.05.029. View

Rodrigue N, Philippe H, Lartillot N . Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci U S A. 2010; 107(10):4629-34. PMC: 2842053. DOI: 10.1073/pnas.0910915107. View

Zou Z, Zhang J . No genome-wide protein sequence convergence for echolocation. Mol Biol Evol. 2015; 32(5):1237-41. PMC: 4408410. DOI: 10.1093/molbev/msv014. View

Rey C, Gueguen L, Semon M, Boussau B . Accurate Detection of Convergent Amino-Acid Evolution with PCOC. Mol Biol Evol. 2018; 35(9):2296-2306. PMC: 6106957. DOI: 10.1093/molbev/msy114. View

Besnard G, Muasya A, Russier F, Roalson E, Salamin N, Christin P . Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Mol Biol Evol. 2009; 26(8):1909-19. DOI: 10.1093/molbev/msp103. View

Li G, Wang J, Rossiter S, Jones G, Cotton J, Zhang S . The hearing gene Prestin reunites echolocating bats. Proc Natl Acad Sci U S A. 2008; 105(37):13959-64. PMC: 2544561. DOI: 10.1073/pnas.0802097105. View

Farre X, Molina R, Barteri F, Timmers P, Joshi P, Oliva B . Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span. Mol Biol Evol. 2021; 38(11):4948-4961. PMC: 8557403. DOI: 10.1093/molbev/msab219. View

Kowalczyk A, Meyer W, Partha R, Mao W, Clark N, Chikina M . RERconverge: an R package for associating evolutionary rates with convergent traits. Bioinformatics. 2019; 35(22):4815-4817. PMC: 6853647. DOI: 10.1093/bioinformatics/btz468. View

10.

Muntane G, Farre X, Rodriguez J, Pegueroles C, Hughes D, de Magalhaes J . Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis. Mol Biol Evol. 2018; 35(8):1990-2004. PMC: 6063263. DOI: 10.1093/molbev/msy105. View

11.

Castoe T, de Koning A, Kim H, Gu W, Noonan B, Naylor G . Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci U S A. 2009; 106(22):8986-91. PMC: 2690048. DOI: 10.1073/pnas.0900233106. View

12.

Saputra E, Kowalczyk A, Cusick L, Clark N, Chikina M . Phylogenetic Permulations: A Statistically Rigorous Approach to Measure Confidence in Associations in a Phylogenetic Context. Mol Biol Evol. 2021; 38(7):3004-3021. PMC: 8233500. DOI: 10.1093/molbev/msab068. View

13.

Zhang J, Kumar S . Detection of convergent and parallel evolution at the amino acid sequence level. Mol Biol Evol. 1997; 14(5):527-36. DOI: 10.1093/oxfordjournals.molbev.a025789. View

14.

Thomas G, Hahn M . Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals. Mol Biol Evol. 2015; 32(5):1232-6. PMC: 4408409. DOI: 10.1093/molbev/msv013. View

15.

Shen X, Pu Z, Chen X, Murphy R, Shen Y . Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes. Front Genet. 2019; 10:925. PMC: 6785628. DOI: 10.3389/fgene.2019.00925. View

16.

He Z, Xu S, Zhang Z, Guo W, Lyu H, Zhong C . Convergent adaptation of the genomes of woody plants at the land-sea interface. Natl Sci Rev. 2021; 7(6):978-993. PMC: 8289059. DOI: 10.1093/nsr/nwaa027. View

17.

Rey C, Lanore V, Veber P, Gueguen L, Lartillot N, Semon M . Detecting adaptive convergent amino acid evolution. Philos Trans R Soc Lond B Biol Sci. 2019; 374(1777):20180234. PMC: 6560273. DOI: 10.1098/rstb.2018.0234. View

18.

Zhang G, Li C, Li Q, Li B, Larkin D, Lee C . Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014; 346(6215):1311-20. PMC: 4390078. DOI: 10.1126/science.1251385. View

19.

Kosakovsky Pond S, Poon A, Velazquez R, Weaver S, Hepler N, Murrell B . HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Mol Biol Evol. 2019; 37(1):295-299. PMC: 8204705. DOI: 10.1093/molbev/msz197. View

20.

Foote A, Liu Y, Thomas G, Vinar T, Alfoldi J, Deng J . Convergent evolution of the genomes of marine mammals. Nat Genet. 2015; 47(3):272-5. PMC: 4644735. DOI: 10.1038/ng.3198. View