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Kovach AI, Walsh J, Ramsdell J, et al. Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone. Ecol Evol. 2015;5(11):2267-83doi: 10.1002/ece3.1514.
Kovach, A. I., Walsh, J., Ramsdell, J., & Kelley Thomas, W. (2015). Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone. Ecology and evolution, 5(11), 2267-83. https://doi.org/10.1002/ece3.1514
Kovach, Adrienne I, et al. "Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone." Ecology and evolution vol. 5,11 (2015): 2267-83. doi: https://doi.org/10.1002/ece3.1514
Kovach AI, Walsh J, Ramsdell J, Kelley Thomas W. Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone. Ecol Evol. 2015 Jun;5(11):2267-83. doi: 10.1002/ece3.1514. Epub 2015 May 13. PMID: 26078861; PMCID: PMC4461426.
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Ecol Evol. 2015 Jun;5(11):2267-83. doi: 10.1002/ece3.1514. Epub 2015 May 13.

Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone.

Ecology and evolution

Adrienne I Kovach, Jennifer Walsh, Jordan Ramsdell, W Kelley Thomas

Affiliations

  1. Department of Natural Resources and the Environment, University of New Hampshire Durham, New Hampshire, 03824.
  2. Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire Durham, New Hampshire, 03824.

PMID: 26078861 PMCID: PMC4461426 DOI: 10.1002/ece3.1514

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.

Keywords: Admixture; Ammodramus; diagnostic markers; hybridization; next-generation sequencing

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