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

Sabine Felkel,Adiya Yadamsuren,Battsesteg Chuluunbat,Chris Walzer,Pamela A Burger,Gottfried Brem,Barbara Wallner,Bernard Faye

doi:10.3389/fgene.2019.00423

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.

Highlights

The male-specific region (MSY) of the mammalian Y chromosome is transferred directly from the father to the son without recombination
Trimmed Illumina short reads from nine wild and five domestic Bactrian camel genomes were derived from an ongoing project (FWF P24706-B25; PI: PB) to detect signatures of selection related to domestication in Old World camelids
We used 11,987,466 read pairs not mapping to the female Bactrian camel reference genome as input for the de novo assembly and classified the resulting 22,398 contigs of the raw assembly into single copy (scY), multi copy (mcY), and nonMSY regions

Summary

Introduction

The male-specific region (MSY) of the mammalian Y chromosome is transferred directly from the father to the son without recombination. A Prime Y-Phylogeny in Bactrian Camels single nucleotide variants (SNVs) on the MSY can be combined into haplotypes and robust MSY haplotype phylogenies can be built using the principle of maximum parsimony (reviewed in Jobling and Tyler-Smith, 2017) Such MSY backbone phylogenies based on biallelic markers (Skaletsky et al, 2003) became recently available in dogs (Oetjens et al, 2018), cattle (Chen H. et al, 2018) and horses (Wallner et al, 2017; Felkel et al, 2018). We described in detail the need to accurately define single copy regions in the assembly (Felkel et al, 2019) to unambiguously call variants in these regions only With this approach (de novo assembly and SNV calling in single copy MSY regions) we elevated the resolution and accuracy of paternal lineage tracing in horses to a level similar to that in humans (Wallner et al, 2017; Felkel et al, 2019), where MSY haplotype (HT) trajectories are well described (Jobling and Tyler-Smith, 2017)

Methods

Results

Conclusion