Population genomics of grey wolves and wolf-like canids in North America.

Mikkel-Holger S Sinding,Rune Dietz,Filipe G Vieira,Shyam Gopalakrishan,Anders J Hansen,Thomas Sicheritz-Ponten,Love Dalén,Mads Peter Heide Jørgensen,Jose A Samaniego Castruita,M Thomas P Gilbert,Lutz Bachmann,Morten Meldgaard,Bent Petersen,Christian Sonne,Johan Brus Mikkelsen,Øystein Wiig,Ulf Marquard-Petersen,Katrine Raundrup

doi:10.1371/journal.pgen.1007745

Abstract

North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified “Polar wolf” population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.

Highlights

Grey wolves (Canis lupus) currently occupy a wide range of habitats across North America, including the tundra, taiga, desert, plain, and boreal forest
Using admixture graphs (Fig 2), we modelled the genomic makeup of red, Eastern timber and Great Lakes wolves, as composed of genomic variation found in North American grey wolves and coyotes
We find that Mexican wolves have the same cladistic ancestry as other American grey wolves, and note that ancient samples will be highly relevant in addressing whether the last common ancestors of North American wolves were within or outside the continent

Summary

Introduction

Grey wolves (Canis lupus) currently occupy a wide range of habitats across North America, including the tundra, taiga, desert, plain, and boreal forest. Analysing ~40–50,000 SNPs from genotype arrays, the hitherto most comprehensive studies have identified seven North American grey wolf populations and ecotypes, which are referred to as West Forest, Boreal Forest, Arctic, High Arctic, British Columbia, Atlantic Forest, and Mexican wolves [1,2]. While this represents a major step forward in terms of describing the population structure, much remains to be learned. Nuclear DNA-based studies remain to include the full range of North American continental populations, omitting, for example, the Greenland wolves, despite mitochondrial DNA evidence suggesting it might represent an isolated population [3]. Dog-ascertained markers may not be able to reveal the full genetic structure of wolves, and underestimate their true genetic diversity [7]

Methods

Results

Discussion

Conclusion