Genetic data were used as an indirect means of assessing connectivity among deep‐sea coral populations on seamounts and slopes in the Australian and New Zealand region. We sequenced three DNA regions (16S, ITS and Control Region) in nine deep‐sea coral species from sites spanning thousands of kilometers. Based on haplotype distributions and AMOVA, we found evidence of genetic subdivision across ocean expanses for three species: the scleractinian Desmophyllum dianthus, and the antipatharians Antipathes robillardi and Stichopathes variabilis. Levels of genetic variation were low for the remaining species, including the reef‐forming Solenosmila variablis and Madrepora oculata, and more sensitive molecular markers may be needed to resolve their spatial structure properly. For two species (the scleractinian Stephanocyathus spiniger and the antipatharian Stichopathes filiformis), we found no evidence of genetic subdivision among sites within regions, suggesting sufficient gene flow occurs to maintain genetic homogeneity at scales of tens to hundreds of kilometers. Recognising that some seamount regions and coral populations are, or are not, effectively isolated will be a key component of successful management planning based on marine protected area networks – both within and beyond national jurisdictions.

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.

BackgroundPrey DNA from diet samples can be used as a dietary marker; yet current methods for prey detection require a priori diet knowledge and/or are designed ad hoc, limiting their scope. I present a general approach to detect diverse prey in the feces or gut contents of predators.Methodology/Principal FindingsIn the example outlined, I take advantage of the restriction site for the endonuclease Pac I which is present in 16S mtDNA of most Odontoceti mammals, but absent from most other relevant non-mammalian chordates and invertebrates. Thus in DNA extracted from feces of these mammalian predators Pac I will cleave and exclude predator DNA from a small region targeted by novel universal primers, while most prey DNA remain intact allowing prey selective PCR. The method was optimized using scat samples from captive bottlenose dolphins (Tursiops truncatus) fed a diet of 6–10 prey species from three phlya. Up to five prey from two phyla were detected in a single scat and all but one minor prey item (2% of the overall diet) were detected across all samples. The same method was applied to scat samples from free-ranging bottlenose dolphins; up to seven prey taxa were detected in a single scat and 13 prey taxa from eight teleost families were identified in total.Conclusions/SignificanceData and further examples are provided to facilitate rapid transfer of this approach to any predator. This methodology should prove useful to zoologists using DNA-based diet techniques in a wide variety of study systems.