Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species

In this study we have identified and characterized dopamine receptor D4 (DRD4) exon III tandem repeats in 33 public available nucleotide sequences from different mammalian species. We found that the tandem repeat in canids could be described in a novel and simple way, namely, as a structure composed of 15- and 12- bp modules. Tandem repeats composed of 18-bp modules were found in sequences from the horse, zebra, onager, and donkey, Asiatic bear, polar bear, common raccoon, dolphin, harbor porpoise, and domestic cat. Several of these sequences have been analyzed previously without a tandem repeat being found. In the domestic cow and gray seal we identified tandem repeats composed of 36-bp modules, each consisting of two closely related 18-bp basic units. A tandem repeat consisting of 9-bp modules was identified in sequences from mink and ferret. In the European otter we detected an 18-bp tandem repeat, while a tandem repeat consisting of 27-bp modules was identified in a sequence from European badger. Both these tandem repeats were composed of 9-bp basic units, which were closely related with the 9-bp repeat modules identified in the mink and ferret. Tandem repeats could not be identified in sequences from rodents. All tandem repeats possessed a high GC content with a strong bias for C. On phylogenetic analysis of the tandem repeats evolutionary related species were clustered into the same groups. The degree of conservation of the tandem repeats varied significantly between species. The deduced amino acid sequences of most of the tandem repeats exhibited a high propensity for disorder. This was also the case with an amino acid sequence of the human DRD4 exon III tandem repeat, which was included in the study for comparative purposes. We identified proline-containing motifs for SH3 and WW domain binding proteins, potential phosphorylation sites, PDZ domain binding motifs, and FHA domain binding motifs in the amino acid sequences of the tandem repeats. The numbers of potential functional sites varied pronouncedly between species. Our observations provide a platform for future studies of the architecture and evolution of the DRD4 exon III tandem repeat, and they suggest that differences in the structure of this tandem repeat contribute to specialization and generation of diversity in receptor function.     

SPATIOTEMPORAL PREDICTION MODELS OF CETACEAN HABITATS IN THE MID-WESTERN NORTH ATLANTIC OCEAN (FROM CAPE HATTERAS, NORTH CAROLINA, U.S.A. TO NOVA SCOTIA, CANADA)

Habitat prediction models were developed for 13 cetacean species of the mid-western North Atlantic Ocean: beaked whale, fin whale, humpback whale, minke whale, pilot whale, sperm whale, bottlenose dolphin, common dolphin, Risso's dolphin, spotted dolphin, whitesided dolphin, and harbor porpoise. Using the multiple logistic regression, sightings of cetaceans during the 1990–1996 summer (June-September) surveys were modeled with oceanographic (sea surface temperature, monthly probability of front occurrence) and topographic (depth, slope) variables for the same period. Predicted habitat maps for June and August were created for each species using a Geographical Information System. The predicted habitat locations matched with current and historic cetacean sighting locations. The model also predicted habitat shifts for some species associated with oceanographic changes. The correct classification rate of the prediction models with 1997–1998 summer survey data ranged from 44% to 70%, of which most of the misclassifications were caused by false positives ( i.e. , absence of sightings at locations where the models predicted).     

Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan

We report the methods and results of molecular genetic identification of the species and, in some cases, geographical origins of whale and dolphin products purchased from retail markets and restaurants in Japan and South Korea. As reported previously (Baker & Palumbi 1994), we used the polymerase chain reaction (PCR) and a portable laboratory to amplify, purify and later sequence a portion of the mitochondrial DNA control region from 16 commercial products purchased in Japan. This ‘spot check’ revealed a surprising variety of species for sale, including minke, fin and humpback whales and one or two species of dolphins sold as ‘kujira’ or whale. In the Korean survey, DNA amplifications were conducted by two of us (C.S.B. and F.C.) working with independent equipment and reagents. The two sets of DNA amplifications were returned to our respective laboratories and sequenced independently for cross-validation. Among the total of 17 species-specific sequences we found a dolphin, a beaked whale, 13 Northern Hemisphere minke whales (representing at least seven distinct individuals) and two whales which are closely related to the recognized sei and Bryde's whales but could not be identified as either using available type sequences. We suggest that these two specimens represent a currently unrecognized species or subspecies of Bryde's whale, possibly the so-called ‘small-form’ reported from the tropical waters of the Indo-Pacific. We conclude that molecular systematic analyses of DNA sequences have tremendous utility for the identification of whale and dolphin products. However, there are certain constraints on the application of these techniques for monitoring whaling or trade in whale products. First, PCR and DNA sequencing can generate misleading artefacts. These can generally be recognized or eliminated through experimental controls. Second, phylogenetic reconstructions of DNA sequences can be misinterpreted if the database of type sequences is inadequate or the taxonomy of the group is incomplete. This constraint is, at present, a more serious obstacle to molecular monitoring of whaling. Our results highlight uncertainties about the taxonomic status of oceanic populations and morphological forms of two species (or species complexes) targeted by legal and illegal hunting, the minke and Bryde's whales. Despite these uncertainties, it is difficult to reconcile some of the species available in Japanese and Korean commercial markets with recent catch records made available to the International Whaling Commission. It is particularly disturbing that two specimens of an unrecognized species or subspecies of baleen whale were for sale in a restaurant in South Korea in October, 1994, 8 years after the acceptance of an international moratorium on commercial whaling.     

IDENTIFICATION OF WHALE SPECIES BY LIQUID CHROMATOGRAPHIC ANALYSIS OF SARCOPLASMIC PROTEINS

Liquid chromatography (LC) was applied to identify whale species by analyzing water-soluble sarcoplasmic proteins in skeletal muscles. Twenty-five samples from four baleen whale species (fin whale, sei whale, Bryde's whale, and minke whale) and eight toothed whale species (sperm whale, Baird's beaked whale, short-finned pilot whale, Dall's porpoise, northern right whale dolphin, Pacific white-sided dolphin, common dolphin, and striped dolphin) were analyzed. Water-soluble sarcoplasmic proteins were extracted from each sample and analyzed using a UV-VIS spectrophotometric detector at 280 nm and a pho-todiode array detector. The chromatographic profiles of each sample showed distinctive qualitative and quantitative characteristics for each whale species, making species identification possible. A photodiode array detector was useful for further accurate identification of whale species by obtaining the absorption spectra of separated protein peaks. These results suggest that the LC method is readily applicable to rapid, simple, and reliable identification of whale species.     

Associations between seabirds and cetaceans: a review

(1) Seabird-cetacean associations involve many genera.
(2) Some seabirds/cetaceans associate with more species than others, e.g. minke and pilot whales, Common dolphins and porpoises amongst cetaceans, and gannet & kittiwake amongst seabirds. Killer whale, sperm whale, shag and cormorant have not been recorded in associations, in the N.E. Atlantic.
(3) All observed associations would be predicted on the basis of the diets of the associated species.
(4) Most associations are probably opportunistic or incidental, as a result of concentration of shared prey.
(5) Some species, however, may associate more regularly, e.g. minke & pilot whales, Common dolphin and porpoise amongst cetaceans and gannet amongst seabirds. It is not possible to say which derives benefit from the association, but on theoretical grounds it is most likely to be the seabird.
(6) Minke and pilot whales may drive towards the surface food normally out of reach of seabirds, particularly Procellariformes. Common dolphins feed by herding fast-moving fish shoals into tight groups which will be a more concentrated food source for diving sea-birds, such as gannets, and make food more accessible to other species. Porpoises may achieve the same result with inshore shoals of sprats and sand eels, particularly for auks and kittiwakes, and terns.     

Cetacean mitochondrial DNA control region: sequences of all extant baleen whales and two sperm whale species

The sequence of the mitochondrial control region was determined in all 10 extant species commonly assigned to the suborder Mysticeti (baleen or whalebone whales) and to two odontocete (toothed whale) species (the sperm and the pygmy sperm whale). In the mysticetes, both the length and the sequence of the control region were very similar, with differences occurring primarily in the first approximately 160 bp of the 5' end of the L-strand of the region. There were marked differences between the mysticete and sperm whale sequences and also between the two sperm whales. The control region, less its variable portion, was used in a comparison including the 10 mysticete sequences plus the same region of an Antarctic minke whale specimen and the two sperm whales. The difference between the minke whales from the North Atlantic and the Antarctic was greater than that between any acknowledged species belonging to the same genus (Balaenoptera). The difference was similar to that between the families Balaenopteridae (rorquals) and Eschrichtiidae (gray whales). The findings suggest that the Antarctic minke whale should have a full species status, B. bonaerensis. Parsimony analysis separated the bowhead and the right whale (family Balaenidae) from all remaining mysticetes, including the pygmy right whale. The pygmy right whale is usually included in family Balaenidae. The analysis revealed a close relationship between the gray whale (family Eschrichtiidae) sequence and those of the rorquals (family Balaenopteridae). The gray whale was included in a clade together with the sei, Bryde's, fin, blue, and humpback whales. This clade was separated from the two minke whale types, which branched together.      

Analysis of the C4 genes in baleen whales using a human cDNA probe

We have used a human C4 cDNA probe to investigate the complement component C4 gene in four members of the family Balaenopteridae: fin whale (Balaenoptera physalus), sei whale (B. borealis), minke whale (B. acutorostrata), and bryde's whale (B. edeni). Restriction mapping of genomic DNA from the first three species suggests the presence of only one locus in these species, and also shows that the C4 genes in the three species are very similar. We have used 14 restriction endonucleases to investigate the restriction fragment length polymorphism (RFLP) of fin whales, 13 enzymes for sei whales, and 8 enzymes for the minke whale. No polymorphism was seen in DNA from the five minke whale samples, but Rsa I and Taq I restriction enzymes gave polymorphism in fin and sei whales whereas Hind III and Msp I restriction enzymes showed polymorphism in sei whales only. Only one bryde's whale sample was available for investigation. The study of DNA available from mother-fetus pairs from the two polymorphic species demonstrated a simple, two-allele transmission of RFLP alleles.     

An analysis of sightings of Cetacea in British waters

An analysis is carried out of all documented sightings of cetaceans in British waters between 1950–1975, received by the Cetacean Group. Two major problems which must be taken into account in such an analysis are difficulties of specific identification and bias from uneven coverage.
The results show that porpoises are present in coastal waters for much of the year. The pattern of movements for this species is rather confused. Most dolphin species show peak numbers in summer, earliest in the north of Britain and later further south. Risso's dolphins may enter British waters rather earlier in spring than other species. Killer whales occur off the west coast of Britain and Ireland mainly between June-September. Pilot whales are seen in North Britain at most times of the year but otherwise enter British waters along the west coast in spring. Bottle-nosed whales and the larger whale species, including the Rorquals, are found only on the north and west coasts in summer and early autumn. For all species, herd size increases at the same time as increase in the numbers of sightings reported. Different species have different herd sizes with the largest occurring amongst porpoise and all dolphin species except Risso's dolphin, and the smallest amongst the large whale species. Herds may be accompanied by young individuals in spring-late summer, depending on the species.     

Anisakis spp. in toothed and baleen whales from Japanese waters with notes on their potential role as biological tags

In this study, Anisakis nematodes isolated from toothed and baleen whales from localities around Japan were molecularly (PCR-RFLP) identified. In Wakayama, common bottlenose dolphins (Tursiops truncatus) were infected with A. simplex sensu stricto (s.s.), A. typica and A. pegreffii, while A. typica was the only species found in pantropical spotted dolphin (Stenella attenuata) and striped dolphin (S. coeruleoalba). Offshore common minke whales (Balaenoptera acutorostrata) and sei whales (B. borealis) were almost exclusively infected with A. simplex s.s.. However, in common minke whales from two Hokkaido localities, mature worms mostly consisted of A. simplex s.s. in some individuals and of A. pegreffii in others, but immature worms were mainly A. simplex s.s.. Gross and histopathological examination on gastric mucosa attached by anisakids resulted in mild and superficial reactions by the two baleen whale species in contrast to severe inflammatory reaction associated with ulcer formations by common bottlenose dolphin. Host specificity and adaptability of Anisakis spp. in these baleen and toothed whales were discussed from the points of view of adult worm size, worm population and pathological reactions by hosts. Interestingly, most of the common minke whales predominantly harboring mature A. pegreffii adults belonged to the Yellow Sea – East China Sea stock (J stock), which migrates through the Sea of Japan, whereas most of those mainly parasitized by mature A. simplex s.s. adults were from the Okhotsk Sea – West Pacific stock (O stock), mostly inhabiting the Pacific side, suggesting that these sibling species may have utility as biological tags to differentiate whale stocks. These results represent the first definitive host records for A. pegreffi in the Northwestern Pacific Ocean.     

Interspecific relationships in density among the whale community in the Antarctic

Interspecific relationships in density among a whale community in Antarctic feeding grounds were examined using the sightings data derived from the systematic surveys conducted between 1978/1979 and 1987/1988. A clear difference in densities against the physiographic variables (the sea floor-slope type) was identified between baleen whales and toothed whales. Densities of sperm whales and ziphiids were low in the waters over the continental shelf where minke whales' densities were highest. This led to an apparent negative correlation in the density between minke and sperm whales, and minke whale and ziphiids. A significant positive correlation in density between minke and blue whales was identified. No association in density between minke and humpback whales was observed. Distribution of killer whales shows strong positive correlation with that of minke whales. The positive correlation existed between minke and blue whales, and minke and killer whales even when the effect of environmental variables was excluded. Analysis also revealed that the environmental variables, including physiographic variables, are major factors affecting the distributions and density of whales, especially between baleen whales and toothed whales. Accepted: 8 December 1999     

Evolution of exon 1 of the dopamine D4 receptor (DRD4) gene in primates

The dopamine D4 receptor (DRD4) gene exhibits a large amount of expressed polymorphism in humans. To understand the evolutionary history of the first exon of DRD4-which in humans contains a polymorphic 12bp tandem duplication, a polymorphic 13bp deletion, and other rare variants-we examined the homologous exon in thirteen other primate species. The great apes possess a variable number of tandem repeats in the same region as humans, both within and among species. In this sense, the 12bp tandem repeat of exon 1 is similar to the 48bp VNTR of exon 3 of DRD4, previously shown to be polymorphic in all primate species examined. The Old World monkeys show no variation in length, and a much higher conservation of amino acid sequence than great apes and humans. The New World monkeys show interspecific differences in length in the region of the 12bp polymorphism, but otherwise show the higher conservation seen in Old World monkeys. The different patterns of variation in monkeys compared to apes suggest strong purifying selective pressure on the exon in these monkeys, and somewhat different selection, possibly relaxed selection, in the apes.     

Assessing changes in numbers and distribution of large whale entanglements in Newfoundland and Labrador,Canada1

Entanglements of large whales in commercial fisheries in Newfoundland and Labrador, Canada, have been consistently recorded since 1979, as part of a program aimed at releasing captured animals and reducing costs to fishermen. This data set represented an opportunity to identify fisheries posing particular entanglement risks to local whale populations. Data were assessed over the periods 1979–1992 and 1993–2008, corresponding to distinct phases in fisheries distribution and intensity. Between 1979 and 2008, 1,209 large whale entanglements were recorded in Newfoundland and Labrador. These were mostly humpback whales (Megaptera novaeangliae; 80%) and minke whales (Balaenoptera acutorostrata; 15%). Dramatic declines in reported inshore whale entanglement rates were observed following the 1992 moratorium on Atlantic cod (Gadus morhua) fisheries. Recently, more entanglements have been reported further offshore, largely due to expansion of fisheries targeting snow crab (Chionoecetes opilio). For all whale species, entanglement rates and associated mortality rates varied considerably in different fishing gear. Fractions of humpback and minke whales found dead in different fishing gear differed substantially, with minke whales far more likely to be found dead than humpback whales.     

Allelic variation of the dopamine receptor D4 gene polymorphic region in gibbons

We examined the tandem repeat sequence of the dopamine receptor D4 (DRD4) gene in 73 individuals derived from 8 species of gibbons (genusHylobates) in an attempt to assess the variability of this gene in gibbon species.H. syndactylus (subgenusSymphalangus) andH. concolor (subgenusNomascus), which were inferred to have diverged at an early time within the family Hylobatidae, shared only long repeat (7–8) alleles. On the other hand, DRD4 was highly polymorphic in gibbons of the subgenusHylobates, with 4-, 5-, 6-, 7-, and 8-repeat alleles being recognized. In this subgenus, 4- and 5-repeat alleles were found in the species distributed mainly in the southern islands such as Sumatra, Java, and Borneo but not in the species inhabiting the Asian continent. Sequence analysis indicated that the repeat structure of the gibbon DRD4 gene was quite complex but most of the 48-bp units could be classified into several groups across the species based on sequence similarities. However, the sequence of the 7-repeat allele ofH. muelleri was unique, since the repeat units had low similarities to other units of gibbons.     

Evolutionary strategies of odontocete brain development

The development of the brain was studied in several species of toothed whales (harbour porpoise, spotted dolphin, narwhal, and sperm whale). As embryos, odontocetes show the general mammalian bauplan. The olfactory bulb, lacking in adult toothed whales, forms in embryos but then disappears in early fetal development. In contrast, the terminal nerve persists and shows a great increase in neuron number. Some components of the limbic system are reduced while others grow to become relatively large. The pyramidal tract is inconspicuous. The auditory system and the extrapyramidal system show rapid size increase. In the sperm whale, growth of the telencephalic hemispheres relative to the size of the brain as a whole (telencephalization) and expansion of the cortical areas (neocorticalization) are greater than in other mammals. Increases in the diameters of the cranial nerves seem to be correlated with their presumed functional roles in the postnatal animal.     

Estimation of minke whale abundance from an acoustic line transect survey of the Mariana Islands

The minke whale is one of the most abundant species of baleen whales worldwide, yet is rarely sighted in subtropical waters. In the North Pacific, they produce a distinctive sound known as the “boing,” which can be used to acoustically localize individuals. A vessel‐based survey using both visual and passive acoustic monitoring was conducted during the spring of 2007 in a large (616,000 km²) study area encompassing the Mariana Islands. We applied line transect methods to data collected from a towed hydrophone array to estimate the abundance of calling minke whales in our study area. No minke whales were sighted, but there were hundreds of acoustic detections of boings. Computer algorithms were developed to localize calling minke whales from acoustic recordings, resulting in over 30 independent localizations, a six‐fold increase over those estimated during the survey. The two best estimates of abundance of calling minke whales were determined to be 80 and 91 animals (0.13 and 0.15 animals per 1,000 km2, respectively; CV = 34%). These are the first density and abundance estimates for calling minke whales using towed hydrophone array surveys, and the first estimates for this species in the Mariana Islands region. These are considered minimum estimates of the true number of minke whales in the study area.     

Future recovery of baleen whales is imperiled by climate change

Historical harvesting pushed many whale species to the brink of extinction. Although most Southern Hemisphere populations are slowly recovering, the influence of future climate change on their recovery remains unknown. We investigate the impacts of two anthropogenic pressures—historical commercial whaling and future climate change—on populations of baleen whales (blue, fin, humpback, Antarctic minke, southern right) and their prey (krill and copepods) in the Southern Ocean. We use a climate–biological coupled “Model of Intermediate Complexity for Ecosystem Assessments” (MICE) that links krill and whale population dynamics with climate change drivers, including changes in ocean temperature, primary productivity and sea ice. Models predict negative future impacts of climate change on krill and all whale species, although the magnitude of impacts on whales differs among populations. Despite initial recovery from historical whaling, models predict concerning declines under climate change, even local extinctions by 2100, for Pacific populations of blue, fin and southern right whales, and Atlantic/Indian fin and humpback whales. Predicted declines were a consequence of reduced prey (copepods/krill) from warming and increasing interspecific competition between whale species. We model whale population recovery under an alternative scenario whereby whales adapt their migratory patterns to accommodate changing sea ice in the Antarctic and a shifting prey base. Plasticity in range size and migration was predicted to improve recovery for ice‐associated blue and minke whales. Our study highlights the need for ongoing protection to help depleted whale populations recover, as well as local management to ensure the krill prey base remains viable, but this may have limited success without immediate action to reduce emissions.     

The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: evidence for reduction of the functional proportions in cetaceans

An olfactory receptor (OR) multigene family is responsible for the well-developed sense of smell possessed by terrestrial tetrapods. Mammalian OR genes had diverged greatly in the terrestrial environment after the fish-tetrapod split, indicating their importance to land habitation. In this study, we analysed OR genes of marine tetrapods (minke whale Balaenoptera acutorostrata, dwarf sperm whale Kogia sima, Dall's porpoise Phocoenoides dalli, Steller's sea lion Eumetopias jubatus and loggerhead sea turtle Caretta caretta) and revealed that the pseudogene proportions of OR gene repertoires in whales were significantly higher than those in their terrestrial relative cattle and also in sea lion and sea turtle. On the other hand, the pseudogene proportion of OR sequences in sea lion was not significantly higher compared with that in their terrestrial relative (dog). It indicates that secondary perfectly adapted marine vertebrates (cetaceans) have lost large amount of their OR genes, whereas secondary-semi-adapted marine vertebrates (sea lions and sea turtles) still have maintained their OR genes, reflecting the importance of terrestrial environment for these animals.     

Are Antarctic minke whales unusually abundant because of 20th century whaling?

Severe declines in megafauna worldwide illuminate the role of top predators in ecosystem structure. In the Antarctic, the Krill Surplus Hypothesis posits that the killing of more than 2 million large whales led to competitive release for smaller krill‐eating species like the Antarctic minke whale. If true, the current size of the Antarctic minke whale population may be unusually high as an indirect result of whaling. Here, we estimate the long‐term population size of the Antarctic minke whale prior to whaling by sequencing 11 nuclear genetic markers from 52 modern samples purchased in Japanese meat markets. We use coalescent simulations to explore the potential influence of population substructure and find that even though our samples are drawn from a limited geographic area, our estimate reflects ocean‐wide genetic diversity. Using Bayesian estimates of the mutation rate and coalescent‐based analyses of genetic diversity across loci, we calculate the long‐term population size of the Antarctic minke whale to be 670 000 individuals (95% confidence interval: 374 000–1 150 000). Our estimate of long‐term abundance is similar to, or greater than, contemporary abundance estimates, suggesting that managing Antarctic ecosystems under the assumption that Antarctic minke whales are unusually abundant is not warranted.