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. 2024 Jun 10;14(6):e11573.
doi: 10.1002/ece3.11573. eCollection 2024 Jun.

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

Elif Bozlak  1   2 , Kisun Pokharel  3 , Melak Weldenegodguad  3 , Antti Paasivaara  4 , Florian Stammler  5 , Knut H Røed  6 , Juha Kantanen  3 , Barbara Wallner  1
Affiliations

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

Elif Bozlak et al. Ecol Evol. .

Abstract

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.

Keywords: caribou; haplotypes; population genetics; reindeer; uniparental markers.

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Conflict of interest statement

The authors declare no competing interest.

Figures

FIGURE 1
FIGURE 1
MSY assembly – strategy and results. (a) Flowchart showing the generation of the assembly and results. The plot shows the average percentage of each contig (in total 53,855) covered in males versus females. (b) Basic statistics of the first assembly and the final contig set “reindeerY1320.” For reindeerY1320 the length of single‐copy‐Y (scY), multi‐copy‐Y (mcY), and non‐Y is given.
FIGURE 2
FIGURE 2
Distribution and types of sampled individuals, Y‐chromosomal and mtDNA trees. (a) Geographic regions of sample collection were plotted with ggOceanMaps package in R (4.2.2.). Different shapes refer to subspecies. Sample names reflect sampling location – type of animal (wild/domestic) – subspecies. Sample details are given in Table S1. (b, c) Y‐chromosomal and mtDNA parsimony trees of 55 male Rangifer tarandus samples rooted with a moose. The two well‐separated clades (NA and EuroBeringian) are marked. Trees are collapsed for major haplogroups (uncollapsed versions are in Figure S3). The proposed EuroBeringian Expansion event in Y‐chromosomal tree, related to population growth after the LGM is shown in the gray area and the calibration point (CP) for dating is marked. Maximum likelihood (ML) trees with bootstrap values are given in Figure S4.
FIGURE 3
FIGURE 3
Y‐chromosomal tree with split dates estimated by BEAST and illustration summarizing the distribution of Y‐HTs in Eurasian samples. (a) Dating estimates are given on each node with 95% confidence intervals in parenthesis. Branching points after the EuroBeringian/NA are named hierarchically and the full information is provided in Table S6. The five haplogroups (HG) including mostly domesticated animals (DR1, DR2, DR3, DN1, DF1) and the Finnish forest reindeer HG (WWF) are marked. (b) Icons represent the HTs, with size proportional to the number of carriers. The combination of icon colors and shapes refers to subspecies and type (wild/semi‐domestic). Lines delineate the HT topology (full topology given in Figure S5), whereas dashed lines link HGs observed in geographically distant locations.
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