The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and high-altitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system. Lineage-specific analysis of mitochondrial protein evolution revealed a significant effect of purifying selection in the concatenated protein-coding genes in domestic Bactrian camels. The estimated dN/dS < 1 in the concatenated protein-coding genes suggested purifying selection as driving force for shaping mitogenome diversity in camels. Additional analyses of the functional divergence in amino acid changes between species-specific lineages indicated fixed substitutions in various genes, with radical effects on the physicochemical properties of the protein products. The evolutionary time estimates revealed a divergence between domestic and wild Bactrian camels around 1.1 [0.58–1.8] million years ago (mya). This has major implications for the conservation and management of the critically endangered wild species, Camelus ferus.

Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack secondary bottlenecks associated with breed development. By resequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, here we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pandomestication setand overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication.

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro-ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization.

Polymorphic markers on the male-specific part of the Y chromosome (MSY) provide useful information for tracking male genealogies. While maternal lineages are well studied in Old World camelids using mitochondrial DNA, the lack of a Y-chromosomal reference sequence hampers the analysis of male-driven demographics. Recently, a shotgun assembly of the horse MSY was generated based on short read next generation sequencing data. The haplotype network resulting from single copy MSY variants using the assembly as a reference revealed sufficient resolution to trace individual male lines in this species. In a similar approach we generated a 3.8 Mbp sized assembly of the MSY of Camelus bactrianus. The camel MSY assembly was used as a reference for variant calling using short read data from eight Old World camelid individuals. Based on 596 single nucleotide variants we revealed a Y-phylogenetic network with seven haplotypes. Wild and domestic Bactrian camels were clearly separated into two different haplogroups with an estimated divergence time of 26,999 ± 2,268 years. Unexpectedly, one wild camel clustered into the domestic Bactrian camels' haplogroup. The observation of a domestic paternal lineage within the wild camel population is concerning in view of the importance to conserve the genetic integrity of these highly endangered species in their natural habitat.

Argali sheep is an ungulate, which inhabits the north, west, south and central regions of Mongolia. There are two major populations (Altai and Gobi) in Mongolia, but their taxonomic classification as subspecies is often disputed among researchers. Furthermore, there is no recent study about the population genetic structure of argali sheep in Mongolia. In the present study, we have investigated genetic diversity and difference between Altai and Gobi argali populations using mitochondrial control region hyper variable segment (HVS) sequence (598bp) and 3 microsatellite markers. Mitochondrial HVS haplotype analysis showed high haplotype diversity (0.982±0.012) and low nucleotide diversity (0.02589). In microsatellite analysis, total of 9 alleles were found across all loci while mean Ho were 0.59±0.13 for Altai and 0.53±0.1 for Gobi populations, indicating low allelic diversity with moderate heterozygosity. Neighbor-joining tree separated haplotypes into two clusters, Altai and Gobi population, implying distinct genetic difference between the two subspecies. Additionally, Pairwise FST and Kimura-2 parameter showed 0.127 and 0.0413±0.0068, respectively. These genetic distance analyses hinted genetic difference between Altai and Gobi populations are in subspecies level. In summary, mitochondrial HVS and microsatellite analysis demonstrated that Altai and Gobi populations had low genetic diversity but might be genetically distinct from each other in subspecies level, suggesting conservation should be separately managed.

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