C. Scott Baker

Worldwide structure of mtDNA diversity among Cuvier's beaked whales (Ziphius cavirostris): implications for threatened populations

We present the first description of phylogeographic structure among Cuviers beaked whales (Ziphius cavirostris) worldwide using mitochondrial DNA (mtDNA) control region sequences obtained from strandings (n = 70), incidental fisheries takes (n = 11), biopsy (n = 1), and whale‐meat markets (n = 5). Over a 290‐base pair fragment, 23 variable sites defined 33 unique haplotypes among the total of 87 samples. Nucleotide diversity at the control region was relatively low (π = 1.27%± 0.723%) compared to wide‐ranging baleen whales, but higher than strongly matrifocal sperm, pilot and killer whales. Phylogenetic reconstruction using maximum likelihood revealed four distinct haplotype groups, each of which displayed strong frequency differences among ocean basins, but no reciprocal monophyly or fixed character differences. Consistent with this phylogeographic pattern, an analysis of molecular variance showed high levels of differentiation among ocean basins (FST = 0.14, ΦST = 0.42; P < 0.001). Estimated rates of female migration among ocean basins were low (generally ≤ 2 individuals per generation). Regional sample sizes were too small to detect subdivisions within oceans except in the North Atlantic, where the Mediterranean Sea (n = 12) was highly differentiated due to the presence of two private haplotypes. One market product purchased in South Korea grouped with other haplotypes found only in the North Atlantic, suggesting a violation of current agreements banning international trade in cetacean species. Together, these results demonstrate a high degree of isolation and low maternal gene flow among oceanic, and in some cases, regional populations of Cuviers beaked whales. This has important implications for understanding the threats of human impact, including fisheries by‐catch, direct hunting, and disturbance or mortality from anthropogenic sound.

Estimating the number of whales entering trade using DNA profiling and capture‐recapture analysis of market products

Surveys of commercial markets combined with molecular taxonomy (i.e. molecular monitoring) provide a means to detect products from illegal, unregulated and/or unreported (IUU) exploitation, including the sale of fisheries bycatch and wild meat (bushmeat). Capture‐recapture analyses of market products using DNA profiling have the potential to estimate the total number of individuals entering the market. However, these analyses are not directly analogous to those of living individuals because a ‘market individual’ does not die suddenly but, instead, remains available for a time in decreasing quantities, rather like the exponential decay of a radioactive isotope. Here we use mitochondrial DNA (mtDNA) sequences and microsatellite genotypes to individually identify products from North Pacific minke whales (Balaenoptera acutorostrata ssp.) purchased in 12 surveys of markets in the Republic of (South) Korea from 1999 to 2003. By applying a novel capture‐recapture model with a decay rate parameter to the 205 unique DNA profiles found among 289 products, we estimated that the total number of whales entering trade across the five‐year survey period was 827 (SE, 164; CV, 0.20) and that the average ‘half‐life’ of products from an individual whale on the market was 1.82 months (SE, 0.24; CV, 0.13). Our estimate of whales in trade (reflecting the true numbers killed) was significantly greater than the officially reported bycatch of 458 whales for this period. This unregulated exploitation has serious implications for the survival of this genetically distinct coastal population. Although our capture‐recapture model was developed for specific application to the Korean whale‐meat markets, the exponential decay function could be modified to improve the estimates of trade in other wildmeat or fisheries markets or abundance of living populations by noninvasive genotyping.

How few whales were there after whaling? Inference from contemporary mtDNA diversity

Reconstructing the history of exploited populations of whales requires fitting a trajectory through at least three points in time: (i) prior to exploitation, when abundance is assumed to be at the maximum allowed by environmental carrying capacity; (ii) the point of minimum abundance or ‘bottleneck’, usually near the time of protection or the abandonment of the hunt; and (iii) near the present, when protected populations are assumed to have undergone some recovery. As historical abundance is usually unknown, this trajectory must be extrapolated according to a population dynamic model using catch records, an assumed rate of increase and an estimate of current abundance, all of which have received considerable attention by the International Whaling Commission (IWC). Relatively little attention has been given to estimating minimum abundance (Nmin), although it is clear that genetic and demographic forces at this point are critical to the potential for recovery or extinction of a local population. We present a general analytical framework to improve estimates of Nmin using the number of mtDNA haplotypes (maternal lineages) surviving in a contemporary population of whales or other exploited species. We demonstrate the informative potential of this parameter as an a posteriori constraint on Bayesian logistic population dynamic models based on the IWC Comprehensive Assessment of the intensively exploited southern right whales (Eubalaena australis) and published surveys of mtDNA diversity for this species. Estimated historical trajectories from all demographic scenarios suggested a substantial loss of mtDNA haplotype richness as a result of 19th century commercial whaling and 20th century illegal whaling by the Soviet Union. However, the relatively high rates of population increase used by the IWC assessment predicted a bottleneck that was implausibly narrow (median, 67 mature females), given our corrected estimates of Nmin. Further, high levels of remnant sequence diversity (theta) suggested that pre‐exploitation abundance was larger than predicted by the logistic model given the catch record, which is known to be incomplete. Our results point to a need to better integrate evolutionary processes into population dynamic models to account for uncertainty in catch records, the influence of maternal fidelity on metapopulation dynamics, and the potential for inverse density dependence (an ‘Allee effect’) in severely depleted populations.

GENETIC STRUCTURE, DIVERSITY, AND HISTORICAL DEMOGRAPHY OF NEW ZEALAND'S DUSKY DOLPHIN (LAGENORHYNCHUS OBSCURUS )

Abstract Although generally limited to coastal waters of South America, South Africa, and New Zealand, dusky dolphins (Lagenorhynchus obscurus) show high potential for dispersal over large distances. In New Zealand, photographic identification data indicate a seasonal shift in residency of dolphins between Kaikoura and the Marlborough Sounds as well as changes in group size and behavior. The effect of this seasonal variation on the genetic structure of New Zealand’s dusky dolphins was examined by sequencing a 473–base pair fragment of the mitochondrial DNA control region for 169 individuals from 4 regions along the New Zealand coast. A neighbor-joining phylogeny and an analysis of molecular variance did not support genetic subdivision among regions (ϕsr = −0.041, P = 0.13). However, nested-clade analysis demonstrated significant evidence for contiguous range expansion and fragmentation along the New Zealand coast. Seasonal movement patterns from Kaikoura to either Otago or the Marlborough Sounds and West Coast are presented as an alternative explanation of nested clade results. New Zealand–wide diversity indices and rate of substitution among sites were used to estimate effective female population size. Lineages-through-time analysis was used to test hypotheses of population growth. Structure of the neighbor-joining phylogeny, the nested haplotype network, and results of the lineages-through-time analysis suggest that the New Zealand dusky dolphin population underwent at least 1, if not 2, historical population expansions.

How many protected minke whales are sold in Japan and Korea? A census by microsatellite DNA profiling

Products from the protected East Sea/Sea of Japan (‘J’ stock) minke whales (Balaenoptera acuturostrata) are sold widely on the commercial markets of Japan and Korea despite the protection of this stock since 1986. To determine the minimum number of individual whales for sale, genotypes from six microsatellite loci were used to profile North Pacific (NP) minke whale products purchased on these markets between December 1997 and October 1999. Genotype differences showed that 99 NP minke whale products from the Japanese market represented 86 unique individuals. Of these, 33.7% were of likely J-stock origin based on mitochondrial (mt) DNA haplotypes. In Korea, genotyping showed that 23 NP minke products from March 1999 represented 18 individuals, and 19 products from October 1999 represented 16 individuals. No matches were found between the two sampling periods, giving a total of 34 unique individuals. A frequency-of-capture model suggests that 98 minke whales were present on the Korean market over the two brief sampling periods. No genotype matches were confirmed between the two countries, indicating that undocumented exploitation of this depleted stock must be additive, and greater than previously assumed.

Lack of divergence in the mitochondrial cytochrome b gene between Macruronus species (Pisces: Merlucciidae) in the Southern Hemisphere

Abstract Two species of grenadier, the blue grenadier (or hoki) Macruronus novaezelandiae and the Patagonian grenadier M. magellanicus, have been recorded in the Southern Hemisphere with disjunct distributions along southern Australia‐New Zealand and southern Chile‐Argentina, respectively. The extent of genetic difference between these two putative species was examined using partial sequences (n = 44; 405 bp) of the mitochondrial DNA cytochrome b gene in a phylogenetic analysis and in an analysis of molecular variance (AMOVA). Our analysis showed a lack of genetic differentiation between species (FST = ‐0.02275, F ST = ‐0.00250) and among stocks. This absence of genetic differences is consistent with recent larval and adult morphology data suggesting that the two species should be synonymised. A comparable lack of genetic isolation has been observed in other closely related taxa (genera Merluccius and Micromesistius) with similar disjunct distributions across the Southern Hemisphere.