Positive selection and precipitation effects on the mitochondrial NADH dehydrogenase subunit 6 gene in brown hares (Lepus europaeus) under a phylogeographic perspective.

Milomir Stefanović,Csongor István Gedeon,Christoph Beiglböck,Chavdar Dinev Zhelev,Annika Posautz,Zissis Mamuris,Anna Kübber-Heiss,Nevena Veličković,Yasin Demirbaş,Vukan Lavadinović,Ladislav Paule,Mihajla Djan,Franz Suchentrunk,Dejan Beuković

doi:10.1371/journal.pone.0224902

Abstract

Previous studies in hares and jackrabbits have indicated that positive selection has shaped the genetic diversity of mitochondrial genes involved in oxidative phosphorylation, which may affect cellular energy production and cause regional adaptation to different environmental (climatic) pressures. In the present study, we sequenced the NADH dehydrogenase subunit 6 (MT-ND6) gene of 267 brown hares (L. europaeus) from Europe and Asia Minor and tested for positive selection and adaptations acting on amino acid sequences (protein variants). Molecular diversity indices and spatial clustering were assessed by DnaSP, Network, and Geneland, while the presence of selection signals was tested by codeml in PAML, and by using the Datamonkey Adaptive Evolution web server. The SPSS software was used to run multinomial regression models to test for possible effects of climate parameters on the currently obtained protein variants. Fifty-eight haplotypes were revealed with a haplotype diversity of 0.817, coding for 17 different protein variants. The MT-ND6 phylogeographic pattern as determined by the nucleotide sequences followed the earlier found model based on the neutrally evolving D-loop sequences, and reflected the earlier found phylogeographic Late Pleistocene scenario. Based on several selection tests, only one codon position consistently proved to be under positive selection. It did occur exclusively in the evolutionarily younger hares from Europe and it gave rise to several protein variants from the southeastern and south-central Balkans. The occurrence of several of those variants was significantly favored under certain precipitation conditions, as proved by our multinomial regression models. Possibly, the great altitudinal variation in the Balkans may have lead to bigger changes in precipitation across that region and this may have imposed an evolutionarily novel selective pressure on the protein variants and could have led to regional adaptation.

Highlights

Mitochondria play a key role in cellular energy and heat production of organisms
Given the functional importance of some of the peptides encoded by Mitochondrial DNA (mtDNA), and the likely fitness implications of peptide variants, selection on mitochondrial genes may be influenced by environmental conditions affecting metabolic processes [4]
In our study we detected positive selection acting on the mitochondrial NADH subunit 6 (MT-ND6) gene of brown hares (Lepus europaeus) from different biogeographic regions with different regional evolutionary history

Summary

Introduction

Mitochondria play a key role in cellular energy and heat production of organisms. The mitochondrial genome contains thirteen protein-coding genes, which along with a number of nuclear genes encode the protein subunits that make up four out of five complexes of the electron transport chain (ETC) where the oxidative phosphorylation (OXPHOS) pathway occurs [1]. Apart from the D-loop that is usually the most polymorphic part of the mtDNA, MT-ND6 is one of the most polymorphic mitochondrial structural genes in vertebrates [13]. This gene encodes the ND6 subunit that seems to be important for the assembly of Complex I [14]; in humans various point mutations of the MT-ND6 gene affect NADH dehydrogenase activity [15] and are associated with diseases such as Leber’s optic neuropathy, encephalomyopathy, and stroke-like episodes [16]. Certain positions of the MT-ND6 gene seem to be important in physiological adaptations to high altitude regions, as reported for snub-nosed monkey [17], alpine pheasants [9], and Tibetan horses [18]

Methods

Results

Conclusion