3.1 Genetic diversity of the European mink captive populations
The microsatellite markers analysis demonstrated an overall population
allelic richness per locus of 2.69 with an average of 2.49 in the
western population, and 2.82 in the eastern population. Heterozygosity
values were lower in the western population compared to eastern
population (Table 1). Bayesian assignment recovered two genetic clusters
within our population, and no admixture pattern were detected. All
individuals clustered according to populations, corresponding to the two
different breeding facilities. The offspring with parents of each
population was assigned to the western population according to
clustering (p(Kwestern)=0.975). Multilocus
heterozygosity was slightly higher in eastern than western populations
(Kruskal-Wallis: χ2=3.4761; p-value=0.0623), but the
inbreeding coefficient (F) was not (Kruskal-Wallis:
χ2=0.085714; p-value=0.7697). Overall, sex and birth
location had no significant effect on neutral markers’ diversity and
richness. PERMANOVA on genetic distance based on the microsatellite
markers detected no variation according to E-mink population, sex and
birth location (Table 2).
Raw MHC amplicon sequencing data consisted of 3,084,478 raw reads with
an average length of 230 base pairs for MCH-I and 130 base pairs for
MHC-II. After processing, we characterized 13 MHC-I motifs (amino acid
sequences) and 6 MHC-II motifs. The average number of motifs per
individual was 5.3 and 3.08 (range: 2-9; 2-4) for MHC-I and MHC-II genes
respectively, indicating the presence of at least five and two copies
for the two regions. For the MHC-I gene, three motifs were strictly
present in the eastern E-mink, and one motif in the western population.
Comparatively, no motifs were unique to eastern E-mink for MHC-IIex2
gene, and three were strictly found in western E-mink (Figure 1).
Spearman correlation tests allowed us to detect haplotype blocks for
both genes, mostly attributed to the eastern population (with the motifs
Mulu:MHC-I*0003, Mulu:MHC-I*0008, Mulu:MHC-I*0012, Mulu:MHC-I*0013 and
Mulu:MHC-I*0015 for MHC-I and Mulu:DRB*90701, EU263553 for MHC-II) and
western E-mink (Mulu:MHC-I*0007, Mulu:MHC-I*0009 and Mulu:MHC-I*0011 for
MHC-I, KM371114_EU263551, EU263558_LC055119, EU263550_EU263557 and
EU263554_EU263552_EU263556 for MHC-II, Figure S2 & Table S2). Most of
the variation encountered in both genes was expressed in amino acid
residues that influence the binding of CD4 and CD8 glycoproteins
involved in antigen presentation for adaptive immunity (Figure S3).
Motif richness and divergence (Faith’s PD) were significantly higher in
the western population compared to eastern E-mink for MHC-II gene
(Kruskal-Wallis: χ2=13.456, p-value=0.0002;
χ2=8.0614, p-value=0.0045; respectively). However, for
MHC-I, divergence was higher in eastern E-mink compared to the western
population, but not motif richness (Kruskal-Wallis:
χ2=5.0097, p-value=0.0252;
χ2=1.5456, p-value=0.2138, respectively). No changes
in motif richness nor divergence were observed according to sex for the
two genes. However, we did observe significant variation in MHC-II
richness according to birth location (Kruskal-Wallis:
χ2=10.854, p-value=0.0125), and a Dunn test with
Benjamini-Hochberg correction only detected higher motif richness for
the MHC-II gene in captive-born E-mink in Spain compared to the EEP
(Dunn: Z=-2.748, adjusted p-value=0.0358). PERMANOVA detected a
significant influence of E-mink sex for MHC-I genetic distance, as well
an influence of mink population close to the significance threshold
(Figure S5), whereas E-mink population was the only variable influenced
MHC-II composition variation (Table 2). Finally, Mantel tests showed a
positive correlation between MHC class I and neutral markers distances
(Mantel: r=0.2761, p-value=0.001).