DOI: 10.5061/dryad.280gb5mqd
title: Novel genomic insights into body size evolution in cetaceans and a resolution of Peto’s Paradox

description: Cetaceans (whales, dolphins, and porpoises) have undergone a radical
 transformation from the typical terrestrial mammalian body plan to a
 streamlined one while exhibited dramatic inter-specific size
 ranges. However, the molecular
 mechanisms underlying the diversifying evolution of
 cetacean body size are largely unknown. Here, by using genome and
 phenotypic data from 22 cetaceans,
 we seek to investigate the genome-wide
 gene-phenotype correlation and to explore the genetic
 basis under the high diversity of body size in cetaceans. Results
 of the functional enrichment showed that body size-related genes
 in cetaceans were enriched in pathways associated with immunity, cell
 growth, and metabolism, suggesting their potential roles in the
 diversifying evolution of body size in cetaceans. A series
 of genes was also found coevolution with body size that are
 mainly involved in immune surveillance, tumor suppression function, and
 development of ‘cheater’ tumors. This in turn suggests that the
 genes play a role in tumor control and thus resolve
 Peto’s paradox, a finding that the expansion in body size and thereby cell
 number does not correlate with increases in cancer incidence in larger
 whales. The present study could provide novel insights into the
 evolution of great body size variation in cetaceans.
description: Gene Multi-alignments
 data All the gene sets
 were aligned at the codon level using the Prank program with the option
 ‘-codon.’ All alignments have been deposited at Dryad. After the
 alignments were generated, the Gblocks program was used to trim
 potentially unreliable and gap regions. The parameters used were
 relatively strict to obtain as many bases as possible with the sequence
 type being codon (‘-t = c -b1=5 -b2=6 -b3=8 -b4=5 -b5’). The *html file
 showed the trim detail for each gene.
description: Supplementary
 data Table S1–4.
 Phenotype data and sequencing data used in this study. Table S5. PGLS
 results for genes with significant correlations between evolutionary rate
 (dN/dS) and body size (body length and body size, respectively).
 Table S6.
 Summary of an enrichment analysis of candidate genes in three p-value
 categories by DAVID. Table S7.
 Enrichment results for PAGs and NAGs by DAVID. Table S8. Summary
 of positive selection in cetaceans. Code 1.cds_prepare 01Getfa_gbk.pl: If input is gbk file, this script is used to extract cds, protein sequence and gene name. 02gff2cds.pl: If input is gff file, this script is used to extract cds, protein sequence and gene name. 03rm_sort_gene.pl: Delete the sequence with length &lt; 150bp. 04Select_longest.pl: If there are more than one transcript for a gene, select the longest one. 2.paml_result 05collect.paml.Freeratio.pl: Used to batch collect dn/ds value from free ratio result. 3.pgls 06write1stepR.pl: Used to prepare script of PGLS in R. 07getresults.pl: Used to batch extract info from result of pgls. 08step23writeR.pl: Used to prepare script of two step verification in R. 09setpgls.pl: Used to batch extract info from result of two step verification.