Evolutionary genetics of the suiformes as reconstructed using mtDNA sequencing

Abstract

We have amplified and sequnced the entire mitochondrial DNA cytochromeb gene from four species of Suidae: babirusa, warthog, bearded pig, and some specimens belonging to different subspecies and populations of wild and domestic pigs (Sus scrofa). These sequences were aligned with additional mammalian sequences retrieved from the literature and were used to obtain phylogenetic trees of the Suiformes (Artiodactyla). Several species of Carnivora, Perissodactyla. Cetacea, and other Artiodactyla were used as outgroups. Molecular phylogenetic relationships among the Suiformes reflect their current taxonomy: Hippopotamidae, Tayassuidae, and Suidae are separated by deep genetic gaps, and the division of the Suidae into the subfamilies Babyrousinae., Phacochoerinae, and Suinae has strong genetic correlates. Cytochromeb sequences show differences among Asian and Western populations ofSus scrofa, agreeing with other genetic information (karyotypes blood groups, and protein variability). The two Italian subspecies of wild boar have unique mtDNA cytochromeb haplotypes. The evolutionary rates of cytochromeb sequences are different at transitions versus transversions as well as at first, second, and third positions of codons. Therefore, these classes of substitutions reached different levels of mutational saturation. Only transversions and the conservative first and second position substitutions are linearly related to genetic distances among the Suiformes. Therefore, divergence times were computed using unsaturated conserved nucleotide substitutions and calibrated using paleontological divergence times between some Artiodactyla. Transversions apparently evolve at remarkably regular rates in ungulate taxa which have accumulated less than 20% estimated sequence divergence, corresponding to about 40–45 million years of independent evolution. Molecular, information suggests that Hippopotamidae and Tayassuidae are not closely related (as stated by Pickford, 1986, 1989, 1993) and that the origin of babirusa and warthog (about 10–19 and 5–15 million years ago, respectively) is more recent than supported by current evolutionary reconstructions. The inferred origin of bearded pig is about 2.1 million years old, and genetic divergence among differentSus scrofa populations is probably a Pleistocene event. The addition of new sequences of Suiformes does not help in resolving the phylogenetic position ofHippopotamus amphibius, which shows weak but recurrent linkages with the cetacean evolutionary lineage.