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Single platform aerial line transect and land-based surveys of Southern Hemisphere Group IV humpback whales were undertaken to provide absoluteabundance estimates of animals migrating northward along the western Australian coast during June–August 2005. The aerial survey was designedto cover the whole period of northward migration but the resulting estimates from that survey alone could only, at best, provide relative abundanceestimates as it was not possible to estimate g(0), the detection probability along the trackline, from the data. Owing to logistical constraints, theland-based survey was only possible for a much shorter period (two weeks during the expected peak of the migration in mid-July). This paperproposes three methods that utilise these complementary data in different ways to attempt to obtain absolute abundance estimates. The aerial linetransect data were used to estimate relative whale density (for each day), allowing absolute abundance from the land-based survey to be estimatedfor the short period of its duration. In turn, the land-based survey allowed estimation of g(0) for the aerial survey. Absolute estimates of abundancefor the aerial survey were obtained by combining the g(0) estimate with the relative density estimates, summing over the appropriate number ofdays. The most reliable estimate of northward migrating whales passing the land station for the period of the land-based survey only was 4,700(95% CI 2,700–14,000). The most reliable estimate for the number of whales passing through the aerial survey region for the duration of that survey(55 days from June through to August) was 10,300 (95% CI 6,700–24,500). This is a conservative estimate because the duration of the aerial surveywas almost certainly shorter than the period of the migration. Extrapolation beyond the end of this survey was considered unreliable, but abundancefrom the estimated start of the migration to the end of the survey (87 days from mid-April to August) was estimated to be 12,800 (95% CI 7,500–44,600). The estimated number of whales depends crucially on the assumed migration and period of migration. Results for different migrationparameters are also presented. The point estimates of abundance, whilst higher than those from a previous survey in 1999 (when adjusted for surveyduration) are not significantly so. The peak of the whales’ distribution was found at c.90m water depth.

Single platform aerial line transect and land-based surveys of Southern Hemisphere Breeding Stock ‘D’ humpback whales Megaptera novaeangliaewere undertaken off Shark Bay, Western Australia to provide absolute abundance estimates of animals migrating northward along the westernAustralian coast. The aerial survey flew a total of 28 flights, of which 26 were completed successfully, from 24 June–19 August 2008. The landbased survey was undertaken from Cape Inscription, Dirk Hartog Island, Shark Bay, during the expected peak of the whales’ northward migration,from 8–20 July. During the first week of the land-based survey, some double count effort was undertaken to provide information on the numbersof pods missed from the land station. The assumed period of northward migration was 2 June–7 September. Estimated abundance of northwardmigrating whales during that time is 34,290 (95% CI: (27,340–53,350)), representing an annual rate of increase of 12.9% (CV = 0.20) since anestimate of 11,500 in 1999. This estimate is based on an estimate of relative abundance of surface-available whales of 10,840 (8,640–16,860), andan estimated g(0) of 0.32. There were considerable practical difficulties encountered during the land-based survey which reduced the effectivenessof the dual-survey approach for estimating g(0) for the aerial survey. Furthermore only about 15% of whales were estimated to be within the visualrange of the land-based station. Alternative approaches for estimating g(0) from these data are therefore also presented, resulting in considerablyhigher estimates of around 0.6–0.7, and yielding a conservative abundance estimate of 17,810 (14,210–27,720).

The history of Australian right whaling is briefly reviewed. Most catching took place in the first half of the 19th century, with a peak inthe 1830s, involving bay whaling by locals and visiting whaleships in winter and whaling offshore in the summer. In the early 20th century,right whales were regarded as at least very rare, if not extinct. The first published scientific record for Australian waters in the 20th centurywas a sighting near Albany, Western Australia, in 1955. Increasing sightings close to the coast in winter and spring led to annual aerialsurveys off southern Western Australia from 1976. To allow for possible effects of coastwise movements, coverage was extended intoSouth Australian waters from 1993. Evidence from 19th century pelagic catch locations, recent sightings surveys, 1960s Soviet catch dataand photographically-identified individuals is beginning to confirm earlier views about likely seasonal movements to and from warm watercoastal breeding grounds and colder water feeding grounds. Increase rates of ca 7-13% have been observed since 1983. Some effects ofdifferent breeding female cohort strength are now beginning to appear. A minimum population size of ca 700 for the period 1995-97 issuggested for the bulk of the ‘Australian’ population, i.e. animals approaching the ca 2,000km of coast between Cape Leeuwin, WesternAustralia and Ceduna, South Australia.

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.

The oceanography of the Perth Canyon, off southwestern Australia, was examined through two major field excursions in austral spring/summer 2003/2004 combined with previous results from field analysis and numerical simulations. Water properties were used to identify water masses and vertical displacement. The field cruises and numerical simulation indicated unique circulation features of the Leeuwin Current and Undercurrent within the canyon associated with the topographic features. The input of nutrients to the euphotic zone occurred sporadically as the Leeuwin Current generally suppressed upwelling, although the Perth Canyon had increased nutrient concentrations within its rims. The distribution of chlorophyll in the surface layers indicated high spatial variability, with a prevalent deep chlorophyll (and phytoplankton biomass) maximum at ~ 80 m. Depth-integrated primary production within the study region ranged from 360 to 760 mg C m− 2 d− 1, which was on average 2.5 times higher than rates measured in continental shelf and offshore waters north of the canyon. Aggregations of krill and other acoustic backscatter targets were concentrated near the head of the canyon at a range of depths, which may have been promoted by the circulation. The findings here are consistent with seasonal variations in wind and insolation, along with variations in the Leeuwin Current, influencing the seasonal changes and mesoscale features within the region, while the canyon promotes localised upwelling, and enhances both pelagic production and physical aggregation of plankton to attract the whales. Canyon processes must be combined with outside factors to allow upwelled nutrients to reach the photic zone. It is concluded that a combination of factors, rather than one factor alone, contributes favourably to the appearance of feeding blue whales in the Perth Canyon during the summer.

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.

Samples of skin tissue were collected by biopsy darting from humpback whales (Megaptera novaeangliae) in six seasonal habitats representing three stocks and four regions: Groups IV (western Australia), V western component (eastern Australia), V eastern component (New Zealand and Tonga) and VI (the Antarctic Peninsula and Gorgona Island, Colombia, South America) of the Southern Hemisphere. A variable section of the mitochondrial DNA control region was amplified and sequenced from 84 of these individuals, distinguishing a total of 48 unique sequences (i. e., mtDNA nucleotypes). Phylogenetic reconstructions suggested that these nucleotypes form three clades, corresponding to those previously described in a world-wide survey of humpback whale mtDNA variation, although bootstrap support for two of the clades was relatively low (