Rapid assessment of adult abundance and demographic connectivity from juvenile kin pairs in a critically endangered species.

The viability of spatially structured populations depends on the abundance and connectivity between subpopulations of breeding adults. Yet, for many species, both are extremely difficult to assess. The speartooth shark is a critically endangered elasmobranch inhabiting tropical rivers with only three adults ever recorded in Australia. Close-kin mark-recapture models, informed by sibling pairs among 226 juveniles, were developed to estimate adult abundance and connectivity in two Australian river systems. Sixty-eight sibling pairs were found, and adult abundance was estimated at 892 for the Adelaide River and 1128 for the Alligator Rivers. We found strong evidence for female philopatry, with most females returning to the same river to pup. Adelaide River males appear largely philopatric, whereas Alligator Rivers males are highly connected to the Adelaide River. From only 4 years of sampling, our results demonstrate that juvenile-only kin pairs can inform simultaneous estimates of abundance and connectivity in a rare and threatened species.

Robust estimates of a high Ne/N ratio in a top marine predator, southern bluefin tuna.

Genetic studies of several marine species with high fecundity have produced "tiny" estimates (≤10-3) of the ratio of effective population size (Ne) to adult census size (N), suggesting that even very large populations might be at genetic risk. A recent study using close-kin mark-recapture methods estimated adult abundance at N ≈ 2 × 106 for southern bluefin tuna (SBT), a highly fecund top predator that supports a lucrative (~$1 billion/year) fishery. We used the same genetic and life history data (almost 13,000 fish collected over 5 years) to generate genetic and demographic estimates of Ne per generation and Nb (effective number of breeders) per year and the Ne/N ratio. Demographic estimates, which accounted for age-specific vital rates, skip breeding, variation in fecundity at age, and persistent individual differences in reproductive success, suggest that Ne/N is >0.1 and perhaps about 0.5. The genetic estimates supported this conclusion. Simulations using true Ne = 5 × 105 (Ne/N = 0.25) produced results statistically consistent with the empirical genetic estimates, whereas simulations using Ne = 2 × 104 (Ne/N = 0.01) did not. Our results show that robust estimates of Ne and Ne/N can be obtained for large populations, provided sufficiently large numbers of individuals and genetic markers are used and temporal replication (here, 5 years of adult and juvenile samples) is sufficient to provide a distribution of estimates. The high estimated Ne/N ratio in SBT is encouraging and suggests that the species will not be compromised by a lack of genetic diversity in responding to environmental change and harvest.

Inferring contemporary and historical genetic connectivity from juveniles.

Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river shark found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis, and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeted sampling in nurseries and juvenile aggregations should be included in the genomic toolbox of threatened species management.