Combining mitochondrial and nuclear data for pedigree reconstruction in absence of genealogical information: analysis of a captive population of the endemic and endangered mexican prairie dog

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Ex situ conservation aims to maintain healthy captive populations that eventually can be used as source populations for reintroductions to the wild. It is fundamental to develop adequate breeding and reproduction programs that minimize the loss of genetic variation, but in many cases a studbook is lacking or unavailable. Nevertheless, molecular data allows the identification of relationships among captive individuals, but care is needed as erroneous parentage allocations are common. Here, we used nuclear and mitochondrial molecular data to reconstruct the pedigree of a captive population (Museo del Desierto, Saltillo, Coahuila, Mexico), of the endemic and endangered Mexican prairie dog (Cynomys mexicanus). This captive population was founded by five individuals from the same wild population. This captive population lacks a studbook; therefore, relatedness estimates would allow designing a breeding strategy to minimize the loss of genetic diversity and inbreeding. We analyzed 18 individuals and used 10 nuclear microsatellite loci to reconstruct a pedigree based on five different relatedness coefficients. We also incorporated sequence data from the mitochondrial control region (854 bp) to verify each relationship. The relatedness coefficients obtained with each method and the parental assignments varied among methods. However, mitochondrial information allowed verifying the relationships for several individuals. We propose a breeding scheme based on individual genetic variation, relatedness and in breeding coefficient to maximize the preservation.