A First Y-Chromosomal Haplotype Network to Investigate Male-Driven Population Dynamics in Domestic and Wild Bactrian Camels

Abstract

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.

Old World camels in a modern world – a balancing act between conservation and genetic improvement

“…The movement of domesticated animals into the habitat of the wild population leads to the transfer of potential pathogens across this domestic-wildlife interface (Walzer et al 2012). Introgression of domestic Bactrian camel genes into wild camels has been demonstrated in mitochondrial (Silbermayr et al 2010) and nuclear DNA (Silbermayr & Burger 2012) as well as the Y-chromosome (Felkel et al 2019).…”

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

“…Together with its inheritance from father to son, it is a highly informative marker for the paternal origin of species, populations or individuals with a much stronger phylogeographic differentiation than observed for mitochondrial or autosomal DNA. The highly informative Y-chromosomal markers are now widely exploited in population-genetic studies of humans (Jobling and Tyler-Smith, 2017; Kivisild, 2017), cattle (Edwards et al, 2011; Xia et al, 2019), horse (Wallner et al, 2017; Wutke et al, 2018; Felkel et al, 2019a) water buffalo (Zhang et al, 2016), sheep (Meadows and Kijas, 2009; Zhang et al, 2014), camel (Felkel et al, 2019b), pigs (Guirao-Rico et al, 2018) and dogs (Natanaelsson et al, 2006; Oetjens et al, 2018).…”

Whole-genome sequencing of 128 camels across Asia reveals origin and migration of domestic Bactrian camels

“…This hypothesis was supported by the presence of Camelid faunal remains at Neolithic sites near Mongolia (MG), although it was unclear these were the domestic as opposed to the wild ones 12 . Nevertheless, molecular studies based on mtDNAs 9,14 and Y chromosomes 15 discovered dramatic sequence variations between the wild and domestic Bactrian camels, suggesting that the extant wild Bactrian camel was a separate lineage 14 . Another possible place of origin was Iran (IRAN) 1 , where early skeletal remains of domestic Bactrian camels (around 2500-3000 BC) were discovered 16 .…”