Abstract
Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species.
Highlights
Interspecific hybridization is common in nature (Mallet 2005; Abbott et al 2013), especially among species in early stages of speciation or in secondary contact (Via 2009; Ellegren et al 2012)
Studies of genetic admixture are most powerful when they use diagnostic species-specific markers, that is markers that are highly differentiated between the two parental species (Moccia et al 2007; Hohenlohe et al 2011)
By generating sequencing data from both species’ genomes, screening markers for repeat differences can be performed in silico, thereby saving tremendously on the laborious process of screening loci in the laboratory. We developed such a strategy for comparing the repeat sequences generated by whole-genome shotgun sequencing of two hybridizing avian sister species, to identify a suite of diagnostic markers for high-resolution identification of pure and admixed individuals in an avian hybrid zone
Summary
Interspecific hybridization is common in nature (Mallet 2005; Abbott et al 2013), especially among species in early stages of speciation or in secondary contact (Via 2009; Ellegren et al 2012). Wild hybrids are a mosaic of phenotypes and genotypes, creating challenges for their taxonomic identification and confusion about their conservation status (Stronen and Paquet 2013). Studies of genetic admixture are most powerful when they use diagnostic species-specific markers, that is markers that are highly differentiated between the two parental species (Moccia et al 2007; Hohenlohe et al 2011). Current sequencing technologies present solutions to the challenges of identifying diagnostic markers, through efficient development of large genomewide panels of SNPs or microsatellite loci. Despite the advent and potential power of large SNP panels, there are many research questions, including those involving genetic hybrid indices, that can be effectively addressed with a carefully selected suite of highly informative microsatellite markers
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