Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Abstract

The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large‐scale introductions of commercial strains (C‐lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M‐lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C‐lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C‐lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time‐ and cost‐effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

“…A recent population genetics study on mud crab ( Rhithropanopeus harrisii ) also concluded that analyzing even a few individuals from each population with RADseq can be highly informative (Forsström, Ahmad, & Vasemägi, ). Alternatives to RADseq‐based approach include, for instance, reduced sets of SNP loci, which can perform nearly as well as thousands of loci in highly diverged populations (Henriques et al, ). In addition, increased resolution can be achieved by sequencing a large number of microsatellites first identified with a whole genome sequence scan (Bradbury et al, ).…”

“…Alternatives to RADseq-based approach include, for instance, reduced sets of SNP loci, which can perform nearly as well as thousands of loci in highly diverged populations (Henriques et al, 2018). In addition, increased resolution can be achieved by sequencing a large number of microsatellites first identified with a whole genome sequence scan (Bradbury et al, 2018).…”

Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod

“…In order to increase statistical power to resolve weak population genetic structure, a select panel of loci with higher than average level of genetic differentiation is often employed (André et al, ; Banks, Eichert, & Olsen, ; Henriques et al, ; Johansen et al, ; Jorde, Kleiven, et al, ; Larson, Seeb, Pascal, Templin, & Seeb, ; Nielsen et al, ; Russello, Kirk, Frazer, & Askey, ). Such a high‐graded panel is likely to include loci under divergent selection, raising concerns over their reliability as a tool for inferring demographic population structure (Luikart, England, Tallmon, Jordan, & Taberlet, ; Nielsen, Hansen, & Meldrop, ).…”

Leveraging targeted sequencing for non-model species: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica

“…The low sample sizes for lcWGR also contributed to the AFS shift since the likelihood of a rare variant to be included was initially low . To minimize 11 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 sample bias on the estimation of population genetic parameters (Albrechtsen, Nielsen & Nielsen, 2010;Fumagalli, 2013) and on the design of a reduced set of SNPs (Anderson, 2010;Ding et al, 2011;Henriques et al, 2018;Mariette et al, 2002), a larger sample size would be required. However, in some cases with non-model organisms, large initial sample sizes may be challenging due to costs or unavailability of collections.…”

“…Most important information for population and conservation genetic studies can be achieved with traditional molecular methods that do not require whole genome sequencing of populations (Allendorf, 2017;Bowden et al, 2012;Fischer et al, 2017;Peterson et al, 2012). Targeted enrichment protocols are alternatives to whole-genome re-sequencing (WGR) (Henriques et al, 2018;Meek & Larson, 2019;Milano et al, 2013). These protocols enable amplification of specific genomic regions that contain previously discovered variation.…”