Paternity assignment and demographic closure in the New Zealand southern right whale EMMA L. CARROLL,* SIMON J. CHILDERHOUSE,† MARK CHRISTIE,‡ SHANE LAVERY,* NATHALIE PATENAUDE,§ ALANA ALEXANDER, – ROCHELLE CONSTANTINE,* DEBBIE STEEL, – LAURA BOREN** and C. SCOTT BAKER* – *School of Biological Sciences, University of Auckland, 3A Symonds St, Auckland 1010, New Zealand, †Australian Marine Mammal Centre, Australian Antarctic Division, 203 Channel Highway, Kingston Tasmania 7050, Australia, ‡Department of Zoology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA, §LGL Limited, Environmental Research Associates, King City, Ontario L7B 1A6, Canada, –Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, 2030 SE Marine Science Drive, Newport, OR 97365, USA, **New Zealand Department of Conservation, National Office, 18-32 Manners St, Wellington 6011, New Zealand Abstract The identification and characterization of reproductively isolated subpopulations or ‘stocks’ are essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and ‘gametic recapture’ to examine the reproductive autonomy of southern right whales (Eubalaena australis) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother–calf pairs from skin biopsy samples, using sex-specific markers, 13 microsatellite loci and mtDNA haplotypes. We constructed DNA profiles for 314 adult males, representing 30% of the census male abundance of the NZ stock, previously estimated from genotypic mark-recapture modelling to be 1085 (95% CL 855, 1416). Under the hypothesis of demographic closure and the assumption of equal reproductive success among males, we predict: (i) the proportion of paternities assigned will reflect the proportion of the male population sampled and (ii) the gametic mark–recapture (GMR) estimate of male abundance will be equivalent to the census male estimate for the NZ stock. Consistent with these predictions, we found that the proportion of assigned paternities equalled the proportion of the census male population size sampled. Using the sample of males as the initial capture, and paternity assignment as the recapture, the GMR estimate of male abundance was 1001 (95% CL 542, 1469), similar to the male census estimate. These findings suggest that right whales returning to the NZ calving ground are reproductively autonomous on a generational timescale, as well as isolated by maternal fidelity on an evolutionary timescale, from others in the Indo-Pacific region. Keywords: gametic mark recapture, geneflow, population structure Received 1 March 2012; revision received 29 April 2012; accepted 10 May 2012 Introduction Defining population structure is critical for the effective management of species, particularly those that have undergone exploitation. However, characterization of population structure can be problematic in marine spe- cies with large effective population sizes, particularly when there are no obvious barriers to geneflow. Here we focus on the southern right whale (Eubalaena austral- is), which was subject to extensive commercial whaling in the nineteenth century and illegal Soviet whaling in the twentieth century (IWC 2001; Tormosov et al. 1998). The species was targeted on both its high-latitude, Correspondence: Emma Carroll, Fax: + 64 (0)9 373 7417; E-mail: ecar026@aucklanduni.ac.nz Ó 2012 Blackwell Publishing Ltd Molecular Ecology (2012) 21, 3960–3973 doi: 10.1111/j.1365-294X.2012.05676.x