Ancient and continuing Darwinian selection on insulin-like growth factor II in placental fishes

Abstract

Despite abundant examples of both adaptation at the level of phenotype and Darwinian selection at the level of genes, correlations between these two processes are notoriously difficult to identify. Positive Darwinian selection on genes is most easily discerned in cases of genetic conflict, when antagonistic evolutionary processes such as a Red Queen race drive the rate of nonsynonymous substitution above the neutral mutation rate. Genomic imprinting in mammals is thought to be the product of antagonistic evolution coincident with evolution of the placenta, but imprinted loci lack evidence of positive selection likely because of the ancient origin of viviparity in mammals. To determine whether genetic conflict is a general feature of adaptation to placental reproduction, we performed comparative evolutionary analyses of the insulin-like growth factor II (IGF2) gene in teleost fishes. Our analysis included several members of the order Cyprinodontiformes, in which livebearing and placentation have evolved several times independently. We found that IGF2 is subject to positive Darwinian selection coincident with the evolution of placentation in fishes, with particularly strong selection among lineages that have evolved placentation recently. Positive selection is also detected along ancient lineages of placental livebearing fishes, suggesting that selection on IGF2 function is ongoing in placental species. Our observations provide a rare example of natural selection acting in synchrony at the phenotypic and molecular level. These results also constitute the first direct evidence of parent-offspring conflict driving gene evolution.

Fig. 1.

RNA in situ hybridization detecting IGF2 transcripts in midgestation embryos. (A) Intact gravid ovary from P. prolifica female. (B) Ventral view of H. formosa embryos stained with sense (Upper) and antisense (Lower) probes. (Scale bar, 1 mm.) (C) Zoom C box of antisense from B showing staining of vascular interstices of the pericardial sac. (Scale bar, 0.5 mm.) (D) Zoom D box of sense from B. (Scale bar, 0.5 mm.) pn, portal network; pc, pericardium.

Fig. 2.

Phylogenetic tree for all species used in the PAML analysis. Tree topology inferred from mitochondrial cytochrome b nucleotide sequences generated by Mr. Bayes. 3.1. Species in red represent those with extensive matrotrophy: MI >2. A-M node labels are presented in Table 2.

Fig. 3.

Amino acid sites under positive selection in the IGF2 prohormone in matrotrophic fishes. (A) Schematic of domain structure of the IGF2 peptide sequence. (B) Schematic representation of a portion of IGF2 encompassing all amino acid sites exhibiting a >50% posterior probability (by Bayes Empirical Bayes analysis) of positive selection according to the branch-site models for both extensive matrotrophs (Table 1) and lecithotrophs (Table 3). Gray bars, sites with 50% < posterior probability < 95%; blue bars, sites with posterior probability > 95%: red bars, sites with posterior probability > 99%.

Fig. 4.

IGF2 E domain mutations in Poeciliopsis. (A) Sequence alignment of P. monacha, P. prolifica, and P. lucida illustrating the deletion of the 3′ 15 bases of exon 2 in P. prolifica and P. lucida. The deletion results in the recruitment of sequences that would have been intronic and utilization of a cryptic intronic splice donor site. (B) Conserved site of proteolysis to remove the E domain from the IGF2 prohormone. The nonconservative change (S→A) in P. infans is highlighted in yellow.