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In Australian waters, southern right whales Eubalaena australis form 2 genetically distinct populations that have shown contrasting patterns of recovery since whaling ceased: a western population in South Australia and Western Australia and an eastern population in southeastern Australia (Tasmania, Victoria and New South Wales). Here, we provide an abundance estimate derived from a breeding female superpopulation mark-recapture model for the southeastern southern right whale population. The population comprises 268 individuals (68 breeding females) and has increased at a rate of 4.7% per annum between 1996 and 2017. There has been no significant change in the annual abundance of mother-calf pairs sighted at the only calving ground (Logans Beach in Victoria) over the last 3 decades. The total number of southern right whales (i.e. all adults and calves) using the southeastern Australian coastline has increased by 7% since 1985. Unlike the population estimate (which was restricted to breeding females sighted prior to the post-breeding southward migration), this estimate is likely to include transiting whales from the southwestern population. The theoretical population model predicts 19 breeding females at Logans Beach in 2018 and 28 in 2028; the actual number of breeding females, as of 2018, is 14. This study provides the first complete estimate of population size and rate of increase of southern right whales along the southeastern Australian coastline. This knowledge is critical for assessing population status and recovery of southern right whales in Australia. It provides a basis for monitoring persistence and responses of the population to environmental stressors.

During the last 2 centuries, southern right whales Eubalaena australis were hunted to near extinction, and an estimated 150 000 were killed by pre-industrial whaling in the 19th century and illegal Soviet whaling in the 20th century. Here we focus on the coastal calving grounds of Australia and New Zealand (NZ), where previous work suggests 2 genetically distinct stocks of southern right whales are recovering. Historical migration patterns and spatially variable patterns of recovery suggest each of these stocks are subdivided into 2 stocks: (1) NZ, comprising NZ subantarctic (NZSA) and mainland NZ (MNZ) stocks; and (2) Australia, comprising southwest and southeast stocks. We expand upon previous work to investigate population subdivision by analysing over 1000 samples collected at 6 locations across NZ and Australia, although sample sizes were small from some locations. Mitochondrial DNA (mtDNA) control region haplotypes (500 bp) and microsatellite genotypes (13 loci) were used to identify 707 individual whales and to test for genetic differentiation. For the first time, we documented the movement of 7 individual whales between the NZSA and MNZ based on the matching of multilocus genotypes. Given the current and historical evidence, we hypothesise that individuals from the NZ subantarctic are slowly recolonising MNZ, where a former calving ground was extirpated. We also suggest that southeast Australian right whales represent a remnant stock, distinct from the southwest Australian stock, based on significant differentiation in mtDNA haplotype frequencies (FST = 0.15, p < 0.01; ΦST = 0.12, p = 0.02) and contrasting patterns of recovery. In comparison with significant differences in mtDNA haplotype frequencies found between the 3 proposed stocks (overall FST = 0.07, ΦST = 0.12, p < 0.001), we found no significant differentiation in microsatellite loci (overall FST = 0.004, G’ST = 0.019, p = 0.07), suggesting ongoing or recent historical reproductive interchange.

Most known concentrations of humpback whales in the southern hemisphere were exploited by commercial whaling operations, first on tropical breeding grounds during the 19th cen- tury and then in Antarctic feeding areas and along migratory corridors during the 20th century. How- ever, whaling logbooks of 19th century whalers show almost no records of catches in some regions of current concentration, notably eastern Polynesia, suggesting that humpback whales were formerly absent from these regions or that the locations of their primary concentrations were unknown to early whalers. Here we investigate the population structure of humpback whales across the South Pacific and eastern Indian oceans, with an interest in the origins of whales in eastern Polynesia, using an extensive collection of mitochondrial DNA (mtDNA) sequences obtained from living whales on 6 breeding grounds: New Caledonia, Tonga, Cook Islands, eastern Polynesia (Society Islands of French Polynesia), Colombia and Western Australia. From a total of 1112 samples we sequenced 470 bp of the mtDNA control region, revealing 115 unique haplotypes identified by 71 variable sites. We found significant differentiation, at both the haplotype and nucleotide level (FST = 0.033; ΦST = 0.022), among the 6 breeding grounds and for most pair-wise comparisons. The differentiation of the eastern Polynesia humpback whales is consistent with the hypothesis of a relic subpopulation, rather than vagrancy or colonization from known neighboring breeding grounds. Regardless of their origin, it seems probable that islands of eastern Polynesia are now the primary breeding grounds for hump- back whales feeding in management Area VI (170 to 120° W) of the Antarctic, as defined by the Inter- national Whaling Commission.