A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla

Matthias Macé,Brigitte Crouau-Roy

doi:10.1186/1471-2156-9-64

Abstract

BackgroundThe early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia). There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields.Results and discussionWe report a large interstitial insertion in the Y amelogenin locus in most of the Cetartiodactyla lineages (cetaceans and ruminants). This sex-linked size polymorphism is the result of a 460–465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species.When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in Cetartiodactyla whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion.The 1 kbp Amel-Y amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region.ConclusionThe gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the Cetartiodactyla but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science.

Highlights

The early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia)
The 1 kbp amelogenin protein (Amel)-Y amplified fragment is characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Ychromosome sequence markers studied so far but less than the mitochondrial control region
We considered the wellknown amelogenin gene to be of particular interest because parts of it do not recombine between X and Y chromosomes

Summary

Introduction

The early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia). About 240 to 320 million years ago, shortly after the divergence of mammalian and avian lineages, progressive X-Y differentiation began, following chromosomal interstitial rearrangements [1]. This resulted in a partial loss of homology between both chromosomes which reached its maximal extent in primates [2]. Polytomies (unresolved tree nodes) within some Cetartiodactyla taxa [8] highlight areas for further data collection (both species and markers) and phylogenetic research This is a delicate problem within cetaceans, probably due to adaptative radiations within a short period of time [10,11]

Methods

Results

Conclusion