DOI: 10.5061/dryad.xksn02vgp
title: Genetic diversity and relatedness among African Painted dogs in North America

description: African painted dogs (Lycaon pictus, APD) are highly endangered, with
 fewer than 7,000 remaining in nature. Captive breeding programs can
 preserve a genetically diverse population and provide a source of
 individuals for re-introductions. However, most programs are initiated
 from few founders and suffer from low genetic diversity and inbreeding.
 The aims of this study were to use molecular markers to assess genetic
 variation, inbreeding, and relatedness among APDs in the North American
 captive population, to use these data to realign studbook records, and to
 compare these data to wild populations and to the European captive
 population to facilitate development of a global management plan. We
 sequenced mitochondrial and major histocompatibility (MHC) class II loci,
 and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in
 North America. We identified three likely studbook errors and resolved ten
 cases of uncertain paternity. Overall, microsatellite heterozygosity was
 higher than reported in Europe, but effective population size estimates
 were lower. Mitochondrial sequence variation was extremely limited, and
 there were fewer MHC haplotypes than in Europe or the wild. Although the
 population did not show evidence of significant inbreeding overall,
 several individuals shared high relatedness values, which should be
 incorporated into future breeding programs.
description: Samples from 109 African
 painted dogs (61 males: 48 females) were obtained from 34 captive breeding
 institutions in North America. Blood was collected on FTA Elute collection
 cards (GE Healthcare, Pittsburgh PA, USA) according to the manufacturer’s
 instructions, and FTA cards were stored and shipped at room temperature.
 DNA was extracted from the FTA Elute cards according to the manufacturer’s
 instructions, eluted into 180 ml 1X Tris-EDTA, and stored at either 4˚C or
 -20˚C. We included negative controls with DNA extractions to monitor for
 contamination. To
 assess neutral genetic diversity,<strong> </strong>we
 genotyped each individual at 14 physically unlinked microsatellite loci,
 which we amplified in five multiplexes: (1) Pez12, FH2054, FH2611, (2)
 Pez8, FH2010, (3) FH3399, FH3965, (4) FH2785, FH2658, Pez15, and (5)
 CXX155, CXX250, CXX263 and CXX366 (Ostrander et al. 1993,
 1995, Francisco et al. 1996, Neff et
 al. 1999, Breen et al. 2001, Guyon et
 al. 2003, Eichmann et al. 2006).
 Amplification conditions have been described in detail previously (Miller-Butterworth et al. 2019).
 Fragment analysis was performed using an Applied Biosystems genetic
 analyzer (model 3730 XL; Waltham, MA) at the Penn State Genomics Core
 Facility, University Park, PA. One negative control (deionized water) and
 two previously genotyped samples were included on every plate to monitor
 for contamination and to ensure consistency across electrophoretic
 runs. Allele
 sizes were called using GeneMarker software (SoftGenetics, State College,
 PA, USA), based on a known DNA size standard (GeneScan 500 LIZ Dye Size
 Standard; ThermoFisher Scientific).  Each locus was amplified
 independently two to four times to confirm each genotype, and putative
 homozygotes were accepted only if the same single allele was observed in
 at least three independent PCRs. Thereafter, a consensus multilocus
 genotype was generated for each individual. Breen et al. 2001. Genome
 research <strong>11</strong>:1784-1795. Eichmann et al.
 2006. International Congress Series
 <strong>1288</strong>:813-815. Francisco et
 al. 1996.  Mammalian Genome
 <strong>7</strong>:359-362. Guyon et al.
 2003. Proceedings of the National Academy of Sciences
 <strong>100</strong>:5296-5301. Miller-Butterworth et al. 2019. Mammal Research:1-5. Neff et al. 1999. Genetics <strong>151</strong>:803-820. Ostrander et al. 1995. Mammalian Genome <strong>6</strong>:192-195. Ostrander et al. 1993. Genomics <strong>16</strong>:207-213.
description: The first column lists the ID of the dog. The first row gives the
 names of the 14 loci. Allele sizes (in base pairs) are listed for the 14
 loci, two columns per locus. Unknown genotypes (missing data) are listed
 as zeros.