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Bannasch, Anita M. Oberbauer, Juan F. There is considerable interest in the genetics of wolves Canis lupus because of their close relationship to domestic dogs C. This includes wolf populations in Southeast Alaska for which we determined genotypes of wolves at single nucleotide polymorphism SNP loci. There is differentiation of SNP allele frequencies between the species wolves, coyotes, and dogs , although differentiation is relatively low between some wolf and coyote populations.
There are varying levels of differentiation among populations of wolves, including low differentiation of wolves in interior Alaska, British Columbia, and the northern US Rocky Mountains.
There is considerable differentiation of SNP allele frequencies of wolves in Southeast Alaska from wolves in other areas. However, wolves in Southeast Alaska are not a genetically homogeneous group and there are comparable levels of genetic differentiation among areas within Southeast Alaska and between Southeast Alaska and other geographic areas.
SNP variation and other genetic data are discussed regarding taxonomy and management. Understanding the genetics of the wolf Canis lupus is important because of its close relationship to the domestic dog C. The genetic variation inherent in wolf progenitors permitted concerted selection and the development of more than dog breeds that display great phenotypic divergence.
Comparative studies of the genetic underpinnings of wolves and dogs can help understanding the basis of phenotypic variation, genealogy, and phylogeny of both species Honeycutt ; vonHoldt et al. In this article, we describe the genetic variation of wolves and compare it with that of dogs and of coyotes C. This is an important topic because of the uncertain systematic relationships and taxonomy of canid taxa in North America Chambers et al.
Recent assessment of wolf genetic profiles have been used for both basic science genomics, systematics, taxonomy, and population genetics, e. Our study contributes to the basic science of North American canid systematics and taxonomy and also has relevance to conservation and management.
The emergence of novel genetic methods utilizing large numbers of genetic markers single nucleotide polymorphisms SNP allows greater resolution of relationships and ancestry of populations than previous methods.
For example, vonHoldt et al. The taxonomy of wolves in other regions is also uncertain, including Southeast Alaska and coastal British Columbia. Wolf populations in this region are relatively intact compared to other areas of North America in which wolves were exterminated or greatly reduced in numbers.
Morphological analyses suggested the wolves in Southeast Alaska were a distinct subspecies C.
However, C. North American wolf Canis lupus sampling locations and subspecies distribution Adapted from Nowak , and Chambers et al. Genetic studies have shown that wolves in southeast Alaska are genetically differentiated from wolves in other areas, including mitochondrial DNA mtDNA haplotypes that vary in frequency between wolves in Southeast Alaska and other North American locations Leonard et al.
Analysis of 12 nuclear microsatellite loci show allele frequency differences between wolves in Southeast Alaska and wolves in the continental areas, although there are few private alleles in Southeast Alaska Weckworth et al. An extensive study of variation of 14 microsatellite loci of North American wolves also showed differentiation of Southeast Alaska from other populations Carmichael et al.
Knowles described variation at SNP that showed differentiation of wolves from interior Alaska and Canada and 10 wolves from Southeast Alaska. These studies indicate there is genetic differentiation of wolves in Southeast Alaska and wolves in other areas. However, the numbers of wolves sampled and loci assessed have been limited.
New methods developed in dogs i. In this article, we describe the population genetics of wolves, coyotes, and dogs with SNP genotype data obtained using the IlluminaK CanineBeadChip. Our primary objective is to quantify the genetic differentiation of wolves within southeast Alaska and among wolves, coyotes, and dogs in several areas in North America, with a secondary objective to assess the data with regard to taxonomy and management.
All of the wolf and coyote samples were obtained from legal harvest or animal control and research. We refer to the populations by geographic locations shown in Table 1. All of the samples are from wild coyotes and wolves, except the New Mexico wolves spent part of their lives captive and part of their lives wild, and are descendants of a captive-bred population started with 7 founders from Mexico M.
We refer to wolves from the 6 Southeast Alaska locations collectively as Southeast Alaska wolves, and wolves from interior Alaska, Montana, Idaho, and Wyoming as northern wolves. Wolves from Idaho, Montana, and Wyoming are considered northern wolves because they originated from animals transplanted from the northern wolf C.
Wolves in interior Alaska are also considered northern wolves Chambers et al.
Wolves from British Columbia are considered C. Numbers and locations of samples and observed heterozygosity of wolves, coyotes, and dogs that were genotyped with the IlluminaK CanineBeadChip. The PCoA analysis shows the individual animal relatedness graphically in multidimensions. The PCoA was performed under assumptions of an additive model and a dominant model. Separate PCoA analyses were done for all 3 species wolf, coyote, and dog and for only wolves. The fixation index algorithm was performed by calculating genetic distance based on all markers after quality control and filtering using Cochran—Mantel—Haenszel statistics CMH test with SVS.
This quantifies whether differences of allele frequencies measured as F st among populations within a group e. Consistent results were obtained by using the lowest standard error estimated with the cross validation method Alexander et al. Of the SNPs analyzed, SNP passed the quality control analysis and resulted in reliable genotypes of wolves, dogs, and coyotes SNP genotype data have been deposited in the Dryad data archive. The other 48, SNP were removed from the analysis.
One of each linked pair was removed from the analysis resulting in a final set of SNP that were used in the population genetic analysis. PCoA considering genetic distances between individuals Supplementary Table 1 online shows graphically the interspecies and interpopulation relationships for the SNP loci Supplementary Figure 3 online.
Within the dog cluster, the mixed breed dogs cluster separately from the poodles. Some wolves occur close to or overlap with coyotes in the PCoA graph, particularly some wolves from Idaho, Montana, and Wyoming and coyotes from Maine.
Some of the Montana, Wyoming, and Idaho wolves and 1 British Columbia wolf occur scattered outside the primary clusters of wolves. Graph of first 2 coordinate axes of principal components analysis PCoA of wolf individual genetic distances for single nucleotide polymorphism SNP loci. Cross validation values ranged from 0. However, low cross validation values from 0.
Wolves, dogs, and coyotes are in different clusters, and coyotes and dogs cluster separately from wolves in the NJ tree Figure 4. This topology occurs in either an unrooted tree or a mid-point rooted tree, and regardless of which coyote and dog populations are included or excluded from the NJ analysis.
However, the individual animal genetic distances used in the PCoA analysis were also subjected to NJ analysis and in this case wolves and dogs cluster together, separately from coyotes Supplementary Figure 5 online. Comparisons of F st indicate the level of differentiation among the locations within Southeast Alaska is comparable to differentiation between Southeast Alaska and populations from other geographic areas Table 2.
The other group for which intragroup and intergroup variation can be compared is northern wolves.
This indicates that SNP differentiation among populations of northern wolves is low relative to differentiation among areas within Southeast Alaska, and northern wolves and British Columbia wolves are a relatively homogeneous group. For the comparisons of populations with only 1 sampling location i. These relationships are shown graphically in the NJ tree Figure 4 in which wolves from Southeast Alaska occur in a cluster with wolves from British Columbia and northern wolves, while Minnesota wolves and New Mexico wolves cluster separately.
In our study and others Vaysse et al. These SNP data represent variation across the canid genome including coding and noncoding regions, synonymous and nonsynonymous substitutions, and not specifically gene regions that are under selection or selectively neutral.
We found greater heterozygosity in dogs than in wolves or coyotes, which may be because of ascertainment bias. Other assays of SNP developed in dogs had similar levels of variation in dog, wolf, and coyote but lower variation in more distantly related canids vonHoldt et al.
The levels of observed heterozygosity we report Table 1 are comparable to those for wolves 0. The New Mexico wolves we sampled have low heterozygosity compared with other wolves, perhaps reflecting their origin from only 7 founding animals Hedrick and Fredrickson ; and Maine and Connecticut coyotes have high heterozygosity compared with other coyotes, perhaps reflecting their mixed coyote—wolf ancestry Kays et al.
Phylogenetic analyses show that dogs and wolves share a more recent common ancestry than either does with coyotes Bardeleben et al. However, there are contrasting relationships of these 3 species depending on the genetic markers and analysis used. Phylogenetic analyses of 6 nuclear gene sequences also group dogs and coyotes separately from wolves Figure 1 of Bardeleben et al. This indicates that caution is advisable when interpreting genetic relationships with molecular markers.
Wolves, coyotes, and dogs are known to hybridize in captivity and the wild e. Assessment of interspecies hybridization is beyond the scope of our study, but we note that the coyotes in the northeast United States i. This may be due to some wolf ancestry in northeast US coyotes due to hybridization Kays et al. Wolves in Southeast Alaska are not a genetically homogeneous group and there is as much or more genetic differentiation among locations within Southeast Alaska as there is between other areas Table 2.
This includes significantly more differentiation among areas in Southeast Alaska than among populations of northern wolves in interior Alaska and the northern Rocky Mountain states. This pattern is likely due to the recent post-glacial colonization of Southeast Alaska, and island and mountainous geography resulting in limited gene flow within Southeast Alaska and between Southeast Alaska and other regions Weckworth et al.
The SNP variation among locations in Southeast Alaska shows different relationships, depending on the analysis used. These differences reflect the different assumptions and characteristics of each method. However, the mean F st between the wolves in GMU2 and the other 5 Southeast Alaska locations is not significantly different than the mean F st among the other 5 locations. This indicates that although the wolves in GMU2 show a degree of differentiation Weckworth et al.
These genetic data combined with data on demographics and movements can help managers understand the relationships of wolves in Southeast Alaska. There is considerable differentiation of SNP allele frequencies between wolves in Southeast Alaska and wolves in other areas. There is also relatively low differentiation of wolves in British Columbia and northern wolves, including wolves in the northern US Rocky Mountains that originated from transplants of northern wolves from British Columbia and Alberta Forbes and Boyd , The SNP data indicate that wolves in Minnesota and New Mexico have relatively high allele frequency differentiation from other wolf populations, consistent with other SNP data vonHoldt et al.
The subspecies taxonomy of wolves in Southeast Alaska is uncertain as some authors Nowak , ; Chambers et al. It is also important to note that our analysis of allele frequency differentiation with clustering algorithms is not a phylogenetic analysis Felsenstein Allele frequencies vary due to population genetic factors mutation, drift, selection, gene flow , and not necessarily phylogeny.
Because taxonomy is based on phylogeny Mayr ; Avise and Ball , such analyses may not be applicable to formal taxonomic designations. However, SNP data can provide relevant information regarding the extent of gene flow and ancestry of populations and hence aid in assessment of species and subspecies phylogeny Decker et al. MtDNA haplotype frequencies of wolves in Southeast Alaska also indicate a degree of isolation, but the haplotypes are not monophyletic and haplotypes of wolves in Southeast Alaska also occur in other areas Leonard et al.
These results indicate that wolves in Southeast Alaska are not a genetically isolated or monophyletic population, and do not support a subspecies designation of wolves in Southeast Alaska. Our data and those of vonHoldt et al. However, extant and historic samples show that Mexican wolves lack mtDNA monophyly, share haplotypes with wolves in other areas and with coyotes, Leonard et al.
These factors indicate that designation of a Mexican wolf subspecies is of questionable validity.