Balancing selection, genetic drift, and human‐mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

Abstract

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Conservation Genetics of Mediterranean Brown Trout in Central Italy (Latium): A Multi-Marker Approach

“…Secondly, to deeply characterize population diversity, we genotyped individuals at 11 polymorphic microsatellite loci (STR), namely STR60 and STR73 [44], SSA85 [45], SSOSL417 [46], SSA410UOS and SSA408UOS [47], SSSP2213 [48], OMM1064 [49], SSAD190 [50], Oneµ2 [51], SSA103NVH [52]-see supporting information provided in Talarico et al (2021) for PCR-amplification and genotyping procedures of STR loci. Note that STR and LDH-C1 profiles of a subset of individuals have been already published in [34]; data archived in Dryad doi.org/10.5061/dryad.xsj3tx9fg), although used for purposes other than the present study.…”

“…Lastly, in the final dataset, we included genotypes of the major histocompatibility complex class II DAB locus (hereafter MHC-DAB) for a subset of 156 trout to account for non-neutral genetic variation, as there was evidence for historical and contemporary positive/balancing selection on this gene (data from [34]).…”

“…Firstly, both STR and MHC variation increased with higher LDH-C1 based admixture, so that maximum diversity was found in RAP, TRO, and SIM sites (Figure 2A-D). Although non-native invasive populations/species often undergo a genetic bottleneck and consequently a stochastic loss of genetic diversity, an increase in genetic variability in recipient wild populations can be observed [73][74][75], even for non-neutral loci [34]. This may be due to successive introductions from the same or genetically divergent source populations/stocks-in the case of brown trout, high levels of genetic polymorphism and admixture emerged from the analyses of hatchery strains from Europe and North America [76].…”

“…Conversely, adaptive variation can be inferred through loci that are somehow linked to fitness-related traits such as the highly polymorphic genes of the major histocompatibility complex (MHC), which are directly involved in the immune response against parasites [31]. Specifically, signatures of historical and/or current selection have been demonstrated for the MHC-DAB gene in brown trout (e.g., [32][33][34]), hence making it a candidate locus to reveal natural adaptive variation. However, to the best of our knowledge, brown trout ESUs/MUs have never been defined using both neutral and adaptive marker classes to date.…”

Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers

“…The introgression by restocking practices were evaluated using different molecular markers, such as allozymes or microsatellites. The locus LDH-C * is particularly relevant for its diagnostic role [ 19 , 37 , 38 , 39 , 40 , 41 ], being fixed for the *100 allele in native Southern European populations and for the *90 allele in the North Atlantic populations [ 29 , 41 , 42 , 43 ]. A different introgression degree was reported throughout Southern European rivers, sometimes resulting in the complete replacement of native gene pools [ 19 , 21 , 23 , 44 ] within rivers with unstable hydrological conditions [ 19 , 23 , 39 , 44 ].…”