DOI: 10.5061/dryad.n2z34tn64
title: Data from: Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals

description: Cetaceans have evolved unique limb structures, such as flippers, due to
 genetic changes during their transition to aquatic life. However, the full
 understanding of the genetic and evolutionary mechanisms behind these
 changes is still developing. By examining 25 limb-related protein-coding
 genes across various mammalian species, we compared genetic changes
 between aquatic mammals, like whales, and other mammals with unique limb
 structures such as bats, rodents, and elephants. Our findings revealed
 significant modifications in limb-related genes, including variations in
 the Hox, GDF5, and EVX genes. Notably, a relaxed selection in several key
 genes was observed, suggesting a lifting of developmental constraints,
 which might have facilitated the emergence of morphological innovations in
 cetacean limb morphology. We also uncovered non-synonymous changes,
 insertions, and deletions in these genes, particularly in the polyalanine
 tracts of HOXD13, which are distinctive to cetaceans or convergent with
 other aquatic mammals. These genetic variations correlated with the
 diverse and specialized limb structures observed in cetaceans, indicating
 a complex interplay of relaxed selection and specific mutations in
 mammalian limb evolution.
description: Annotated orthologous transcripts were retrieved from the
 phylogenomic dataset by McGowen et al. and from Genbank.  We also used the
 OrthoMaM v12 database to check orthologs where possible. The coding
 sequences for the bowhead whale (Balaena mysticetus) came from the public
 platform The Bowhead Whale Genome Resource. For 28 genomes fully or
 partially lacking annotation, the gene sequences were identified by
 reciprocal BLAST+ searches using annotated orthologues of the related
 mammals as queries against reference genome assemblies. Multiple
 alignments for limb-related genes and partial HOXD13 sequences were built
 using translated protein sequences with MAFFT 7.
description: # Data from: Relaxed selection in evolution of genes regulating limb
 development gives clue to variation in forelimb morphology of cetaceans
 and other mammals
 [https://doi.org/10.5061/dryad.n2z34tn64](https://doi.org/10.5061/dryad.n2z34tn64) ## Description of the data and file structure These multiple alignments were used for analysing selection acting on limb-related genes. The full list of species is provided in the table below: | **RESOURCE** | **SOURCE** | **IDENTIFIER** | | :----------------------------------------------- | :--------------------------------------------------------- | :-------------------------------- | | Genome assembly of *Grampus griseus* | DNAZOO \[1,2] | GCA\_028646425.1 | | Genome assembly of *Platanista minor* | Zoonomia Consortium \[3], | GCA\_004363435.1 | | Genome assembly of *Mesoplodon bidens* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004027085.1 | | Genome assembly of *Mesoplodon densirostris* | DNAZOO \[1,2] | Mesoplodon\_densirostris\_HiC | | Genome assembly of *Ziphius cavirostris* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004364475.1 | | Genome assembly of *Lipotes vexillifer* | Zhou et al. \[5] | GCA\_000442215.2 | | Genome assembly of *Pontoporia blainvillei* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004363935.1 | | Genome assembly of\* Inia geoffrensis\* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004363515.1 | | Genome assembly of\* Monodon monoceros\* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004026685.1 | | Genome assembly of *Delphinapterus leucas* | Jones et al. \[6] | GCA\_002288925.3 | | Genome assembly of *Phocoena phocoena* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004363495.1 | | Genome assembly of *Phocoena sinus* | Morin et al. \[8] | GCA\_008692025.1 | | Genome assembly of *Sousa chinensis* | Ming et al. \[9] | GCA\_003521335.2 | | Genome assembly of *Hyperoodon ampullatus* | De Greef et al. \[10 | GCA\_024363105.1 | | Genome assembly of *Neophocaena asiaeorientalis* | Zhou et al. \[11] | GCA\_003031525.2 | | Genome assembly of *Globicephala melas* | The Darwin Tree of Life Project \[12] | GCA\_963455315.1 | | Genome assembly of *Orcinus orca* | The Darwin Tree of Life Project \[12] | GCA\_937001465.1 | | Exon sequences for *Lagenorhynchus obliquidens* | McGowen et al. \[13] | Lobl | | Genome assembly of *Tursiops truncatus* | Foote et al. \[14] | GCA\_000151865.3 | | Genome assembly of *Tursiops aduncus* | Vijay et al. \[15] | GCA\_003227395.1 | | Genome assembly of *Balaenoptera musculus* | Bukhman et al. \[16] | GCA\_009873245.3 | | Genome assembly of *Eubalaena japonica* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004363455.1 | | Genome assembly of *Eubalaena glacialis* | DNAZOO \[1,2] | Eubalaena\_glacialis\_HiC | | Genome assembly of *Balaena mysticetus* | Keane et al. \[17] | | | Genome assembly of *Balaenoptera physalus* | Wolf et al. \[18] | GCA\_023338255.1 | | Genome assembly of *Balaenoptera ricei* | DNAZOO \[1,2] | Balaenoptera\_ricei\_HiC | | Genome assembly of *Balaenoptera bonaerensis* | Kishida et al. \[19] | GCA\_000978805.1 | | Genome assembly of *Balaenoptera acutorostrata* | The Darwin Tree of Life Project \[12] | GCA\_949987535.1 | | Genome assembly of *Megaptera novaeangliae* | Tollis et al. \[20] | GCA\_004329385.1 | | Genome assembly of *Kogia breviceps* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004363705.1 | | Genome assembly of *Physeter catodon* | Fan et al. \[21] | GCA\_002837175.3 | | Genome assembly of *Hippopotamus amphibius* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004027065.1 | | Genome assembly of *Ovis aries* | Li et al.\[22] | GCA\_022416915.1 | | Genome assembly of *Bos taurus* | The Bovine Genome Sequencing and Analysis Consortium \[23] | GCA\_000003205.7 | | Genome assembly of *Sus scrofa* | Warr et al. \[24] | GCA\_000003025.4 | | Genome assembly of *Felis catus* | Buckley et al. \[25] | GCA\_000181335.2 | | Genome assembly of *Ailuropoda melanoleuca* | Fan et al. \[26] | GCA\_002007445.2 | | Genome assembly of *Ursus arctos* | Taylor et al. \[27] | GCA\_003584765.2 | | Genome assembly of *Enhydra lutris* | Jones et al. \[28] | GCA\_002288905.2 | | Genome assembly of *Odobenus rosmarus* | Foote et al. \[14] | GCA\_000321225.1 | | Genome assembly of *Zalophus californianus* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004024565.1 | | Genome assembly of *Mirounga anguirostris* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004023865.1 | | Genome assembly of *Rhinolophus ferrumequinum* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_007922735.1 | | Genome assembly of *Myotis myotis* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004026985.1 | | Genome assembly of *Macrotus californicus* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_007922815.1 | | Genome assembly of *Pteropus vampyrus* | Lindblad-Toh et al. \[29] | GCA\_000151845.2 | | Genome assembly of *Condylura cristata* | Foley et al. \[4] | GCA\_000260355.1 | | Genome assembly of *Scalopus aquaticus* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004024925.1 | | Genome assembly of *Mus musculus* | Church et al. \[30] | GCA\_000001635.27 | | Genome assembly of *Jaculus jaculus* | Foley et al. \[4] | GCA\_000280705.1 | | Genome assembly of *Cavia porcellus* | Lindblad-Toh et al. \[29] | GCA\_000151735.1 | | Genome assembly of *Castor canadensis* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004027675.1 | | Genome assembly of *Heterocephalus glaber* | Kim et al. \[31], Keane et al. \[32] | GCA\_000230445.1 GCA\_000247695.1 | | Genome assembly of *Otolemur garnettii* | Lindblad-Toh et al. \[29] | GCA\_000181295.1 | | Genome assembly of *Homo sapiens* | Human Genome Project \[33] | GCA\_000001405.40 | | Genome assembly of *Loxodonta africana* | Lindblad-Toh et al. \[29] | GCA\_000001905.1 | | Genome assembly of *Elephas maximus* | Tollis et al.\[34] | GCA\_014332765.1 | | Genome assembly of *Elephantulus edwardii* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004027355.1 | | Genome assembly of *Orycteropus afer* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004365145.1 | | Genome assembly of *Dugong dugon* | DNAZOO \[1,2] | Dugong\_dugon\_HiC | | Genome assembly of *Trichechus manatus* | Foote et al. \[14] | GCA\_000243295.1 | | Genome assembly of *Tolypeutes matacus* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004027955.1 | | Genome assembly of *Dasypus novemcinctus* | Lindblad-Toh et al. \[29] | GCA\_030445035.2 | | Genome assembly of *Choloepus didactylus* | Zoonomia Consortium \[3], Foley et al. \[4] | GCA\_004027855.1 | Note: The dataset does not contain sequences from the unpublished *Platanista gangetica* genome, which were used in the analysis with the permission of Dr. Siddiki A. Z. and coauthors. Users interested in obtaining these sequences should contact Dr. Siddiki A. Z. and coauthors directly for permission and access. ### Files and variables #### File: Control\_genes.zip **Description:** This zip archive contains alignments of coding sequences of genes, unrelated to limb development in fasta format #### File: Limb\_related\_genes.zip **Description:** This zip archive contains alignments of coding nucleotide sequences and protein sequences of limb-related genes in fasta format ## Code/software Jalview program (Waterhouse et al., 2009) or any other multiple sequence alignment viewer can be used to visualize alignments. ## Access information Data was derived from the following sources: * NCBI database, DNAZOO Resource, The Bowhead Whale Genome Resource, phylogenomic dataset by McGowen et al., 2020.  **The references for the individual genome assemblies** 1\. 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