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Genome-Wide Analysis of SNPs Is Consistent with No Domestic Dog Ancestry in the Endangered Mexican Wolf (Canis lupus baileyi) - PubMed

  • ️Mon Jan 01 2018

Genome-Wide Analysis of SNPs Is Consistent with No Domestic Dog Ancestry in the Endangered Mexican Wolf (Canis lupus baileyi)

Robert R Fitak et al. J Hered. 2018.

Erratum in

Abstract

The Mexican gray wolf (Canis lupus baileyi) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in 3 separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from 3, 2, and 2 founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all 3 captive lineages and cross-lineage wolves, for more than 172000 single nucleotide polymorphisms. We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies.

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Figures

Figure 1.
Figure 1.

Observed heterozygosity in Mexican wolves (Canis lupus baileyi) from 7295 unlinked SNPs. Individual Mexican wolves are shown as a pie chart with slices proportional to each wolf’s predicted ancestry in the 3 captive lineages and ordered by birthdate according to the official studbook (Siminski 2011). The linear regressions that describe the relationship between heterozygosity and birthdate for McBride (dashed line) and cross-lineage (solid line) wolves since the time when the 3 captive populations were merged (vertical dotted line) are shown. MB = McBride, AG = Aragón, GR = Ghost Ranch. See online version for full colors.

Figure 2.
Figure 2.

Principle component analyses of Mexican wolves (Canis lupus baileyi) and other canids (Canis lupus ssp). The first 2 principle components (PC) are shown (A, B) within Mexican wolves and (C, D) among Mexican wolves (MW), domestic dogs (Canis lupus familiaris), North American gray wolves (NAGW), and European gray wolves (EUGW). The proportion of variation explained by each component is shown for (B) Mexican wolves and (D) all canids. Individual Mexican wolves are shown as a pie chart with slices proportional to each wolf’s predicted ancestry in the 3 captive lineages according to the official studbook (Siminski 2011). The solid and dashed arrows in (A) depict Mexican wolves (studbook #547 and #858, respectively) whose predicted ancestries don’t coincide with the clustering in the plot. MB = McBride, AG = Aragón, GR = Ghost Ranch. See online version for full colors.

Figure 3.
Figure 3.

Results of the population clustering analysis from ADMIXTURE. (A) Cross-validation error for different potential numbers of clusters, k, between 1 and 10. Each line represents a different subsample of an equal number (n = 88) of Mexican wolves, gray wolves, and domestic dogs. (B–F) Ancestry plot across all individuals for k = 2–6. Each vertical bar represents an individual with colors corresponding to the proportion of ancestry in the predefined number of clusters, k. (G) Ancestry plot for the supervised analysis, where Mexican wolves were assigned ancestry to either domestic dog, European gray wolf (EUGW) or North American gray wolf (NAGW) parental populations. See online version for full colors.

Figure 4.
Figure 4.

Boxplots of the Z-scores of the f3 statistic for Mexican wolves (MW) when compared with either domestic dog breeds (dog), European gray wolves (EUGW), North American gray wolves (NAGW), or all populations of wolves (wolf). The statistic is in the form f3(X;A,B), where significantly negative values (Z-score ≤ −4) indicate that X is a result of admixture between A and B. Because CL wolves are known to be admixed between the Mexican wolf captive populations, the significantly negative scores for CL wolves are as expected. MB = McBride, AR = Aragón, GR = Ghost Ranch, CL = cross-lineage. See online version for full colors.

Figure 5.
Figure 5.

Local ancestry assignment in Mexican wolves. The proportion of each chromosome assigned to domestic dog ancestry in (A) MB, (B) GR, (C) AG, and (D) CL Mexican wolves. (E) The relationship between the number and length of local ancestry fragments assigned to domestic dogs in Mexican wolves. Mexican wolves are shown as pie charts with slices proportional to each wolf’s predicted ancestry in the 3 captive lineages according to the official studbook (Siminski 2011). (F) Locations of local ancestry fragments in an example Mexican wolf (#431, 100% predicted GR ancestry). Ancestry plots for all individual Mexican wolves can be found in Supplementary Figure S2. See online version for full colors. MB = McBride, AR = Aragón, GR = Ghost Ranch, CL = cross-lineage, NAGW = North American gray wolves, EUGW = European gray wolves.

Figure 6.
Figure 6.

Local ancestry assignment to domestic dogs in simulated Mexican wolves. (A) The proportion of local ancestry assigned per individual to domestic dogs summed across the genome. (B) Scatterplot of the number and mean length of local segments assigned to domestic dog ancestry per individual. In both panels, points represent individual observed Mexican wolves (MW) or individuals from simulated migration schemes (1–13, see Table 2). In (B), groups (MW or schemes 1–13) are bounded by the minimum convex polygon and labeled accordingly. See online version for full colors.

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