Abstract. Superpopulation capture-recapture models are useful for estimating the abundance of long-lived, migratory species because they are able to account for the fluid nature of annual residency at migratory destinations. Here we extend the superpopulation POPAN model to explicitly account for heterogeneity in capture probability linked to reproductive cycles (POPAN-s). This extension has potential application to a range of species that have temporally variable life stages (e.g., non-annual breeders such as albatrosses and baleen whales) and results in a significant reduction in bias over the standard POPAN model. We demonstrate the utility of this model in simultaneously estimating abundance and annual population growth rate (k) in the New Zealand (NZ) southern right whale (Eubalaena australis) from 1995 to 2009. DNA profiles were constructed for the individual identification of more than 700 whales, sampled during two sets of winter expeditions in 1995-1998 and 2006-2009. Due to differences in recapture rates between sexes, only sex-specific models were considered. The POPAN-s models, which explicitly account for a decrease in capture probability in non-calving years, fit the female data set significantly better than do standard superpopulation models (DAIC . 25). The best POPAN-s model (AIC) gave a superpopulation estimate of 1162 females for 1995-2009 (95% CL 921, 1467 and an estimated annual increase of 5% (95% CL À2%, 13%). The best model (AIC) gave a superpopulation estimate of 1007 males (95% CL 794, 1276) and an estimated annual increase of 7% (95% CL 5%, 9%) for 1995-2009. Combined, the total superpopulation estimate for 1995-2009 was 2169 whales (95% CL 1836, 2563). Simulations suggest that failure to account for the effect of reproductive status on the capture probability would result in a substantial positive bias (þ19%) in female abundance estimates.

Historically, the range of the southern right whale (SRW) included winter calving grounds around the North and South Islands (mainland) of New Zealand (NZ) and in the NZ subantarctic Auckland and Campbell Islands. Due to extensive whaling in the 19th and 20th centuries, no SRW was seen around mainland NZ for nearly four decades (1928–1963). Here we present evidence for the regular use of the mainland NZ wintering ground, presumably from a remnant population that persisted in the NZ subantarctic Auckland and Campbell Islands. SRWs have been sighted every year around mainland NZ since 1988, with 125 sightings during the focus of this work: from 2003 to 2010. There were 28 cow‐calf pairs sighted around mainland NZ from 2003 to 2010, compared with 11 sightings from 1991 to 2002. Furthermore, two females, identified by DNA profiles, were sighted with calves around mainland at 4 yr intervals: the first evidence of female site fidelity to the mainland NZ calving ground. Individual identification from photographs of natural markings and DNA profiles provided information on within‐year movements and residency around the mainland, and further evidence for exchange between the mainland and subantarctic wintering grounds. Despite these promising signs, the distribution of NZ SRWs remains primarily concentrated in the NZ subantarctic.

Abstract.Since its near extermination by sealing, the New Zealand fur seal (Arctocephalus forsteri) has been recolonising areas of its former range throughout New Zealand and Australia. This study examined fur seal population growth over four breeding seasons spanning 2002–05 at the Ohau Point and Lynch’s Reef colonies in Kaikoura and the Horseshoe Bay and Te Oka Bay colonies on Banks Peninsula, on the east coast of New Zealand. Estimates of pup numbers were made using mark–recapture techniques and condition indices were used to assess the body condition of pups in each colony. We found that the Ohau Point and Te Oka Bay colonies are growing exponentially (32% and 47% per annum respectively), reaching nearly 600 pups at Ohau Point and 300 pups at Te Oka Bay, whereas Horseshoe Bay appears stable. Pups born at Ohau Point are consistently heavier and in better condition than their Banks Peninsula counterparts despite the faster rate of growth observed at Te Oka Bay. An El Niño event in 2003 coincided with a drop in mass and condition at the Banks Peninsula colonies, but not at the Kaikoura colony. This discrepancy between colonies in response to environmental conditions suggests that colony-specific variables at Kaikoura may provide more favourable conditions for rearing pups than on Banks Peninsula.

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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.