Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples.
High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9-25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2-9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics.
NIBIO-Norwegian Institute of Bioeconomy Research. Electronic address: siv.grethe.aarnes@nibio.no.
Siv Grethe
SG
Aarnes
NIBIO-Norwegian Institute of Bioeconomy Research.
Snorre B
SB
Hagen
Faculty of Health Sciences, Oslo and Akershus University College, Oslo Norway.
Rune
R
Andreassen
NIBIO-Norwegian Institute of Bioeconomy Research.
Julia
J
Schregel
NIBIO-Norwegian Institute of Bioeconomy Research.
Per M
PM
Knappskog
Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK.
Frank
F
Hailer
Foothills Research Institute, 1176 Switzer Drive, Box 6330, Hinton, AB T7V 1X6, Canada.
Gordon
G
Stenhouse
Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Frankfurt am Main, Germany.
Axel
A
Janke
NIBIO-Norwegian Institute of Bioeconomy Research.
Hans Geir
HG
Eiken
D000818:Animals; D005243:Feces; D006197:Hair; D006801:Humans; D057230:Limit of Detection; D018895:Microsatellite Repeats / Q000235:genetics*; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D001503:Ursidae / Q000235:genetics*; D014998:Y Chromosome
Conservation genetics; Microsatellite; Non-invasive genetic sampling; Population genetics; Wildlife forensics; Y-chromosome