DOI: 10.5061/dryad.q2bvq83r2
title: Convergent evolution and predictability of gene copy numbers associated with diets in mammals

description: Convergent evolution, the evolution of the same or similar phenotypes in
 phylogenetically independent lineages, is a widespread phenomenon in
 nature. If the genetic basis for convergent evolution is predictable to
 some extent, it may be possible to infer organismic phenotypes and
 adaptability based on genome sequence data. While repeated amino acid
 changes have been studied in association with convergent evolution,
 relatively little is known about the potential contribution of repeated
 gene copy number changes. In this study, we explore whether certain gene
 copy number changes are linked to diet shifts in mammals and assess if
 trophic ecology can be inferred from the copy numbers of a specific set of
 genes. Using 86 mammalian genome sequences, we identified several genes
 with higher copy numbers in herbivores, carnivores, and omnivores, even
 after phylogenetic corrections. We were able to confirm previous findings
 on genes such as amylase, olfactory receptor, and xenobiotic metabolism
 genes, and identify novel genes whose copy numbers correlate with dietary
 patterns. For example, omnivores exhibited higher copy numbers of genes
 encoding gene expression regulators. We also established a discriminant
 function based on the copy numbers of 13 genes that can help predict
 trophic ecology based on genome sequence data. These findings highlight a
 possible association between convergent evolution and repeated copy number
 changes in specific genes, suggesting the potential to develop a method
 for predicting animal ecology and adaptability from genome sequence data.
description: The publicly available data were used. The scripts for processing
 the data are uploaded here.
description: This README file was generated on 2023-11-28 by Jun Kitano. GENERAL
 INFORMATION 1. Title of Dataset: Analysis of convergent evolution and
 predictability of gene copy numbers associated with diets in mammals 2.
 Author Information Principal Investigator Contact Information Name: Jun
 Kitano Institution: National Institute of Genetics Address: Mishima,
 Shizuoka, Japan Email: [jkitano@nig.ac.jp](mailto:jkitano@nig.ac.jp) 3.
 Date of data collection: 2022-2023 4. Geographic location of data
 collection: Mishima, Japan 5. Information about funding sources that
 supported the collection of the data: NIG Summer Internship Program, JSPS
 Kakenhi (23KJ0483, 22H04925, and 22H04983), JST CREST (JPMJCR19S2 and
 JPMJCR20S2), and MEXT (JPMXD1521474594). SHARING/ACCESS INFORMATION 1.
 Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain 2. Links to publications that cite or use the data: Wilhoit,
 K., Yamanouchi, S., Chen. B.Y., Yamasaki., Y.Y., Ishikawa, A., Inoue, J.,
 Iwasaki, W., and Kitano, J.(2024). Convergent evolution and predictability
 of gene copy numbers associated with diets in mammals. 1. Links to other
 publicly accessible locations of the data: None 2. Links/relationships to
 ancillary data sets: None 3. Was data derived from another source? Yes A.
 If yes, list source(s): Dryad database (doi:10.5061/dryad.qd450 and
 doi.org/10.5061/dryad.tb03d03) and an original paper (doi:
 10.1098/rspb.2014.2103). 4. Recommended citation for this dataset:
 Gainsbury AM, Tallowin OJS, Meiri S. 2018. An updated global data set for
 diet preferences in terrestrial mammals: testing the validity of
 extrapolation. Mamm. Rev. 48:160–167. doi:10.5061/dryad.qd450. Upham NS,
 Esselstyn JA, Jetz W. 2019. Inferring the mammal tree: Species-level sets
 of phylogenies for questions in ecology, evolution, and conservation. PLoS
 Biol. 17:e3000494. doi.org/10.5061/dryad.tb03d03. Tucker MA, Rogers TL.
 2014. Examining predator-prey body size, trophic level and body mass
 across marine and terrestrial mammals. Proc. Biol. Sci. 281. doi:
 10.1098/rspb.2014.2103. DATA & FILE OVERVIEW 1. File List: A)
 herbivore.tsv B) carnivore.tsv C) omnivore.tsv D)
 Data_Preparation_Script_Median.R E) Mammal_Data.xlsx F)
 Phylogenetic_Tree_Script_Median.R G)
 RAxML_bipartitions.result_FIN4_raw_rooted_wBoots_4098mam1out_OK.newick H)
 PhyloTree.newick I) Phylogenetic_Correction_Script_Median.R J) DFA.R K)
 Corrected DFA Table.csv 1. Relationship between files, if important: None
 2. Additional related data collected that was not included in the current
 data package: None 3. Are there multiple versions of the dataset? Yes A.
 If yes, name of file(s) that was updated: PFDA.R PhyloTree_ultra.newick
 phylo_dfa_selected.csv go_random_select.R herbivore.btaurus.csv
 omnivore.hsapiens.csv i. Why was the file updated? For the revision of the
 paper, we conducted additional analyses. ii. When was the file updated?
 2024 Oct 10th
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: herbivore.tsv, carnivore.tsv, and
 omnivore.tsv 1. Number of variables: 348 2. Number of cases/rows: 77
 (herbivore.tsv), 19 (carnivore.tsv), and 61 (omnivore.tsv) 3. Variable
 List: group_id: orthologous gene ID pMCMC: significance test after
 phylogenetic correction positive.median: median copy number of the target
 category (eg. herbivore) negative.median: median copy number of the
 non-target category (eg. non-herbivore) ratio: Ratio of the median copy
 number of the target category divided by that of the non-target category
 *.tag: protein sequence identification number *.len: translated amino acid
 length *.prod: gene product *.gcn: gene copy number ## Abbreviations of
 species names Acijub*: Acinonyx jubatus Ailmel*: Ailuropoda melanoleuca
 Balacusca*: Balaenoptera acutorostrata Bisbisbis*: Bison bison Bosmut*:
 Bos mutus Bostar*: Bos taurus Bubbub*: Bubalus bubalis Caljac*: Callithrix
 jacchus Calurs*: Callorhinus ursinus Cambac*: Camelus bactrianus Camdro*:
 Camelus dromedarius Canlupfam*: Canis lupus Caphir*: Capra hircus Carsyr*:
 Carlito syrichta Cersimsim*: Ceratotherium simum Chlsab*: Chlorocebus
 sabaeus Chrasi*: Chrysochloris asiatica Colangpal*: Colobus angolensis
 palliatus Concri*: Condylura cristata Dasnov*: Dasypus novemcinctus
 Delleu*: Delphinapterus leucas Desrot*: Desmodus rotundus Echtel*:
 Echinops telfairi Eleedw*: Elephantulus edwardii Enhlutken*: Enhydra
 lutris Eptfus*: Eptesicus fuscus Equasi*: Equus asinus asinus Equcab*:
 Equus caballus Equprz*: Equus przewalskii Erieur*: Erinaceus europaeus
 Eumjub*: Eumetopias jubatus Felcat*: Felis catus Glomel*: Globicephala
 melas Gorgorgor*: Gorilla gorilla Hiparm*: Hipposideros armiger Homsap*:
 Homo sapiens Lagobl*: Lagenorhynchus obliquidens Lepwed*: Leptonychotes
 weddellii Lipvex*: Lipotes vexillifer Loxafr*: Loxodonta africana Lyncan*:
 Lynx canadensis Macmul*: Macaca mulatta Manjav*: Manis javanica Minnat*:
 Miniopterus natalensis Mondom*: Monodelphis domestica Monmon*: Monodon
 monoceros Musmus*: Mus musculus Musputfur*: Mustela putorius furo Myoluc*:
 Myotis lucifugus Neoasiasi*: Neomonachus schauinslandi Neosch*:
 Neophocaena asiaeorientalis Neovis*: Neovison vison Nomleu*: Nomascus
 leucogenys Odorosdiv*: Odobenus rosmarus Odovirtex*: Odocoileus
 virginianus Orcorc*: Orcinus orca Ornana*: Ornithorhynchus anatinus
 Oryafeafe*: Orycteropus afer Orycun*: Oryctolagus cuniculus Otogar*:
 Otolemur garnettii Oviari*: Ovis aries Panpar*: Panthera pardus Pantig*:
 Panthera tigris altaica Pantro*: Pan troglodytes Phacin*: Phascolarctos
 cinereus Phycat*: Phyllostomus discolor Phydis*: Physeter catodon Ponabe*:
 Pongo abelii Pteale*: Pteropus alecto Ptevam*: Pteropus vampyrus Pumcon*:
 Puma concolor Ratnor*: Rattus norvegicus Rouaeg*: Rousettus aegyptiacus
 Sarhar*: Sarcophilus harrisii Sorara*: Sorex araneus Sursur*: Suricata
 suricatta Susscr*: Sus scrofa Trimanlat*: Trichechus manatus Turtru*:
 Tursiops truncatus Ursame*: Ursus americanus Ursarc*: Ursus arctos
 Ursmar*: Ursus maritimus Vicpac*: Vicugna pacos Vomurs*: Vombatus ursinus
 Vulvul*: Vulpes vulpes Zalcal*: Zalophus californianus 1. Missing data
 codes: Empty cells indicate that the orthologous gene was not found. 2.
 Specialized formats or other abbreviations used: None
 \#########################################################################
 # Data\_Preparation\_Script\_Median.R R script for preparation of diet and
 copy number data used for the subsequent analysis
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Mammal_Data.xlsx 1. Number of variables: 5
 2. Number of cases/rows: 86 3. Variable List: * binomial: ID for the
 species * species: species names * CommonName: common names for the
 species * TrophicLevel: categorial classification of trophic ecology *
 TrophicPosition: quantitative data on the trophic position. NA, not
 available. 4. Missing data codes: NA (data not available) 5. Specialized
 formats or other abbreviations used: None
 \#########################################################################
 # Phylogenetic\_Tree\_Script\_Median.R R script for preparation of the
 phylogenetic tree
 \#########################################################################
 #
 RAxML\_bipartitions.result\_FIN4\_raw\_rooted\_wBoots\_4098mam1out\_OK.newick Input file of a mammalian phylogenetic tree in newick format \######################################################################### # PhyloTree.newick Output file of Phylogenetic_Tree_Script_Median.R in newick format \######################################################################### # Phylogenetic\_Correction\_Script\_Median.R R script for phylogenetic correction \######################################################################### # DFA.R R script for discriminant function analysis \######################################################################### DATA-SPECIFIC INFORMATION FOR: Corrected DFA Table.csv This is an input file for DFA.R. 1. Number of variables: 42 2. Number of cases/rows: 86 3. Variable List: * binomial: ID for the species * diet: categorial classification of trophic ecology * habitat: categorial classification of habitat * Columns 4-42 indicate the copy numbers of each orthologous gene ID 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None \######################################################################### # PFDA.R R script for phylogenetic flexible discriminant function analysis \######################################################################### # PhyloTree\_ultra.newick Input tree file of PFDA.R in newick format \######################################################################### # phylo\_dfa\_selected.csv Input file of PFDA.R containing diet and gene copy number data \######################################################################### # go\_random\_select.R R script for repeating GO analysis 1o times using randomly selected genes \######################################################################### # herbivore.btaurus.csv Input file containing *Bos taurus* gene names of herbivore-high genes for go_random_select.R \######################################################################### # omnivore.hsapiens.csv Input file containing *Homo sapiens *gene names of omnivore-high genes for go_random_select.R