Integrating multiple analytical approaches to spatially delineate and characterize genetic population structure: an application to boreal caribou (Rangifer tarandus caribou) in central Canada

Abstract

Individual-based clustering (IBC) methods have become increasingly popular for the characterization and delineation of genetic population units for numerous species. These methods delineate populations based on the genetic assumptions of a breeding unit which may provide a better representation of the behaviour of the species. The increasing use of IBC has resulted in the development of several analytical models all of which vary in their theoretical assumptions to infer genetic population structure. In this paper, we report a comparative strategy utilizing three IBC methods to characterize the spatial genetic structure of the boreal population of woodland caribou (Rangifer tarandus caribou) in central Canada. In addition, we implement both tests for isolation-by-distance (IBD) and frequency-based assignment tests to validate the consensus genetic clusters as defined by IBC. We also compare indirect metrics of genetic diversity and gene flow using both a priori defined herds and the IBC defined populations. Although our results show some concordance between both pre-defined herds and IBC derived genetic clusters, the IBC analyses identified a cluster that was cryptic to observation-based caribou herds and found no difference between several adjacent herds. By comparing multiple IBC methods and integrating both IBD and indirect genetic diversity metrics a posteriori, our strategy provides an effective means to delineate wildlife population structure and accurately assess genetic diversity and connectivity.

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

“…DNA sample concentrations were determined by PicoGreen and samples were normalized to 2.5 ng/ul to ensure reliable amplification of samples. Extracted DNA was amplified at nine microsatellite loci following Ball et al, (2007Ball et al, ( , 2010. Amplification reactions contained: 1x PCR buffer; 2.0 mM MgCl; 0.2 μg/ml of BSA; 0.4 μM of each primer pair; 0.2 μM of each dinucleotide triphosphate; 0.5 units of Taq polymerase (Invitrogen Life Technologies); and 5 ng of DNA template.…”

Łeghágots'enetę (learning together): the importance of indigenous perspectives in the identification of biological variation

“…We followed microsatellite genotyping protocols that had been established as part of a long-term caribou genetic database to ensure the production of high quality genetic profiles (Ball 2007, Ball et al 2010, Galpern et al 2012a, Hettinga et al 2012, Klütsch et al 2012. To isolate DNA we swabbed and amplified the mucosal layer covering the caribou fecal pellets.…”

DEVELOPMENT OF MULTIPLEX MICROSATELLITE PANEL TO ASSESS THE PARENTAGE VERIFICATION IN AND DIFFERENTIATION DEGREE OF REINDEER POPULATIONS (Rangifer tarandus)

“…They are used to control the reliability of parentage, determine the degree of inbreeding, to assess breed purity, characterize the biodiversity and the degree of genetic differentiation of breeds and inbreed genetic structures [20][21][22][23]. Currently, there are many publications that demonstrate the applied relevance of STR in the characterization of the reindeer gene pool STR [24][25][26][27][28][29][30][31][32], but the Russian reindeer breeds and population have not been studied yet.…”