Biologically threatened dolphins and whales

Among the several threats to which free-ranging cetaceans are exposed, a number of biological noxae are believed to represent a serious hazard to their health and conservation on a global scale, with special emphasis on the Mediterranean Sea. These pathogens include viral agents such as Morbillivirus, which during the last 25 years have caused dramatic epidemics and die-offs among several aquatic mammal species and populations worldwide, as well as Herpesvirus, protozoan agents such as Toxoplasma gondii and bacterial pathogens such as Brucella spp.     

Conservation genetics of whales and dolphins

Whales and dolphins (cetaceans) are found in all the world's oceans and in some of the major rivers, yet little is known about the distribution and behaviour of many species. At the same time, cetaceans are under threat from a variety of pressures including direct and indirect takes, pollution, and competition for habitat and prey. To ensure their long-term survival it will be necessary to preserve genetic diversity through the identification and protection of differentiated populations, the assessment of variation within local populations, and through a better understanding of reproductive and dispersal behaviour. The application of molecular genetic techniques is helping to provide answers to some of these previously intractable questions. Early results suggest few consistent patterns. Obvious geographic boundaries correlate to genetic distance in some species, and not in others. Furthermore, morphological variation within species can be fairly extensive without correlating to genetic distance, or relatively minor between morphotypes that are as genetically distinct as some species. These examples emphasize the need for further study.     

Population biology, social behavior and communication in whales and dolphins

The baleen whales differ from the toothed whales and dolphins in life history and in social organization. Even though they grow to a larger size, young baleen whales tend to develop more rapidly than dolphins and toothed whales. Except for the mother-calf bond, most groups of baleen whales are short-lived, lasting only for hours, and individual-specific associations appear to be exceptions to the norm. Most toothed whales live in more structured groups, in which young animals have a long period of dependency and social learning. The communication signals described for different cetacean species have functions suited to the interactions that predominate in their societies.     

Hearing loss in stranded odontocete dolphins and whales

The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB) or profound (>90 dB) hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.     

Post-mortem investigations on stranded dolphins and porpoises from Hong Kong waters

Stranded cetaceans reported from the territorial waters of Hong Kong during the period May 1993 to March 1998 were examined to establish factors that may have contributed to their death. During the current study, 28 Indo-Pacific hump-backed dolphins (Sousa chinensis), 32 finless porpoises (Neophocaena phocaenoides), and four bottlenose dolphins (Tursiops truncatus) were necropsied. Bacteria (15 species) were isolated from nine animals. Of these bacteria, 47% were of possible fecal origin reflecting the high level of sewage contamination in Hong Kong's waters. One finless porpoise displayed wounds caused by a shark attack, and two female finless porpoises presented prolapsed uteri. At least 10 finless porpoises showed evidence of moderate to heavy lungworm infections (Halocercus pingi), and this appears to have been a factor contributing to death in at least six animals. Evidence suggesting blunt traumatic injury (probably caused by boat collisions) was found in six cetaceans (three finless porpoises and three hump-backed dolphins). Signs of fishery-related mortality were detected in at least nine animals (six hump-backed dolphins, two finless porpoises, and one bottlenose dolphin). Of these two human-caused mortality types, pre-existing disease or bacterial infection were detected in 29% of cases. Results indicate that human factors may have played a significant role in the death of at least 15 animals (32% of hump-backed dolphins, 15% of finless porpoises, and 25% of bottlenose dolphins).     

Evolution of group size in the dolphins and porpoises: interspecific consistency of intraspecific patterns

I investigated group size variability in dolphins and porpoisesusing intraspecific comparisons. Explanatory factors consideredin the analysis were variables of the physical environment,the diet, and the life history of the species. Open habitatand small body size were viewed as increasing predation risk.This pattern was apparent in Risso's dolphins (Grampus griseus) and weakly apparent in bottlenose dolphins (Tursiops spp.).Group size was negatively correlated with body size in pilotwhales (Globicephala spp.) and positively correlated with theopenness of habitat in killer whales (Orcinus orca), stripeddolphins (Stenella coeruleoalba), and common dolphins (Delphinus spp.). No such relationship was found for harbor and Dall'sporpoises (Phocoena phocoena, P. dalli). Group size also seemedto vary depending on other physical measures of the habitat,which may indirectly reflect diet; group size showed U-shapedpatterns if related to temperature. The predictive power ofvariables comprising detailed prey information on group sizewas variable. For example, pilot whales had smaller group sizes when they fed more on mesopelagic fish and less on mesopelagiccephalopods, and common dolphins had larger groups if theyfed on varying types of fish. In most Delphinoidea species,group size could be described by the variables considered inthis study. But each species showed its own pattern of correlationsbetween group size and a specific set of explanatory variables. Thus, no general and consistent relation between group sizeand the other variables was found. It remains unknown whetherthese species-specific patterns result from a historical processor whether they are specialized adaptations.     

Pakicetus inachus and the origin of whales and dolphins (Mammalia: Cetacea)

The present paper is concerned with the comparative morphology of the archeocete and odontocete skull. Among the archeocetes, the recently described lower Eocene Pakicetus inachus obviously represents an early stage of adaptation to aquatic life. The morphology of the incomplete cranial remains, however, gives no evidence that Pakicetus was an amphibious intermediate stage. The evolution of advanced archeocetes and odontocetes is characterized by the successive acquirement of new morphological devices related to the emission and perception of ultrasound under water. The formation of a sonar system in odontocetes obviously not only helped to compensate for the loss of the peripheral olfactory system but moreover was a substantial factor in the evolution of the exceptional dolphin brain.     

A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)

Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains controversial. Using the supertree approach of matrix representation with parsimony, we present the first phylogeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However, due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus, Muntiacus, Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.     

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URL http://unite.zbi.ee     

Biometrics, identification and surveillance

Governing by identity describes the emerging regime of a globalizing, mobile world. Governance depends on identification but identification increasingly depends on biometrics. This 'solution' to difficulties of verification is described and some technical weaknesses are discussed. The role of biometrics in classification systems is also considered and is shown to contain possible prejudice in relation to racialized criteria of identity. Lastly, the culture of biometric identification is shown to be limited to abstract data, artificially separated from the lived experience of the body including the orientation to others. It is proposed that creators of national ID systems in particular address these crucial deficiencies in their attempt to provide new modes of verification.     

北部湾沙田水域中华白海豚和江豚的同域分布格局及时空变化

北部湾是中华白海豚和江豚的重要分布区,但是对该水域两物种的分布格局及时空变化的研究却比较少,也不清楚这两个物种分布区是否有重叠。2003 ～ 2004 年与2011 ～2012 年期间,我们在北部湾沙田水域进行了船只调查,总计航程4 876.8 km,收集了两个物种空间分布的数据。结果表明,2003 ～ 2004 年仅发现中华白海豚,2011 ～2012 年则同时发现了中华白海豚和江豚。与2003 ～ 2004 年4 ～ 5 月相比,中华白海豚在2011 年4 ～ 5 月份的遇见率明显增加(0.152 vs 0. 028 头次/km)。中华白海豚的MCP、95% FK 家域和50% FK 核心域面积分别为162. 6 km² 、271. 35 km² 和56.78 km² ,2011 ～ 2012 年50% FK 核心家域有所扩大且东移。江豚的MCP、95% FK家域和50% FK 核心域面积分别为97.21 km² 、318.72 km² 和38.18 km² 。江豚主要分布于中华白海豚的外围远岸水域,同时两个物种的分布区有小部分重叠。基于多种因素的分析,我们推测,江豚可能存在季节性迁移以及中华白海豚对河口区有明显的偏好,可能是造成它们分布格局不同的原因。     

cDNA-derived amino acid sequences of myoglobins from nine species of whales and dolphins

We determined the myoglobin (Mb) cDNA sequences of nine cetaceans, of which six are the first reports of Mb sequences: sei whale (Balaenoptera borealis), Bryde's whale (Balaenoptera edeni), pygmy sperm whale (Kogia breviceps), Stejneger's beaked whale (Mesoplodon stejnegeri), Longman's beaked whale (Indopacetus pacificus), and melon-headed whale (Peponocephala electra), and three confirm the previously determined chemical amino acid sequences: sperm whale (Physeter macrocephalus), common minke whale (Balaenoptera acutorostrata) and pantropical spotted dolphin (Stenella attenuata). We found two types of Mb in the skeletal muscle of pantropical spotted dolphin: Mb I with the same amino acid sequence as that deposited in the protein database, and Mb II, which differs at two amino acid residues compared with Mb I. Using an alignment of the amino acid or cDNA sequences of cetacean Mb, we constructed a phylogenetic tree by the NJ method. Clustering of cetacean Mb amino acid and cDNA sequences essentially follows the classical taxonomy of cetaceans, suggesting that Mb sequence data is valid for classification of cetaceans at least to the family level.     

Vocal activity of tropical dolphins is inhibited by the presence of killer whales,Orcinus orca

Research has suggested killer whale (Orcinus orca) predation may affect cetacean vocal behavior; however, few data exist to test this hypothesis. Data collected during 40,976 km of visual and acoustic shipboard surveys in the tropical Pacific Ocean, including 1,232 detections of 13 species, were examined to determine if changes in dolphin vocal activity could be attributed to the presence of killer whales. Generalized linear models and Random Forest analyses were used to test the hypothesis that dolphin vocal activity was related to the distance and time to the nearest killer whale sighting. Both results show that dolphin vocalizations were inversely correlated with the temporal proximity of killer whales (P < 0.05). Despite the relative rarity of killer whales in the tropics, they appear to influence vocal behavior of nearby dolphin schools. This disruption in communication may not significantly impact interactions necessary for survival in tropical waters where killer whale density is low. However, in temperate climates, where increased productivity supports a greater abundance of killer whales, this interruption in communication may have a greater impact. The lower incidence of whistling dolphins in temperate waters may be related to the greater abundance of killer whales in these areas.     

Parallel influence of climate on the behaviour of Pacific killer whales and Atlantic bottlenose dolphins

The grouping behaviour of animals is governed by intrinsic and extrinsic factors which play an important role in shaping their social organization. We investigated the influence of ocean climate variation on the grouping behaviour of two widely separated populations of cetaceans, inhabiting north Atlantic and north Pacific coastal waters. The group size of both bottlenose dolphins in the Moray Firth, UK, and killer whales in Johnstone Strait, Canada, varied from year to year in relation to large‐scale ocean climate variation. Local indices of prey abundance were also related both to climate indices and predator group sizes. The cetaceans tended to live in smaller groups when there was less salmon available in both areas which seem to occur 2 years after a lower phase of the North Atlantic and Pacific Decadal Oscillations. These findings suggest that, even in highly social mammals, climate variation may influence social organization through changes in prey availability.     

Phylogenetic identification and population differentiation of bottlenose dolphins (Tursiops spp.) in Melanesia,as revealed by mitochondrial DNA

The taxonomic status of many dolphin populations remains uncertain in poorly studied regions of the world's ocean. Here we attempt to clarify the phylogenetic identity of two distinct forms of bottlenose dolphins (Tursiops spp.) described in the Melanesian region of the Pacific Ocean. Mitochondrial DNA control region sequences from samples collected in New Caledonia (n = 88) and the Solomon Islands (n = 19) were compared to previously published sequences of Tursiops spp., representing four phylogenetic units currently recognized within the genus. Phylogenetic reconstructions confirm that the smaller coastal form in Melanesia belongs to the same phylogenetic unit as T. aduncus populations in the Pacific, but differs from T. aduncus in Africa, and that the larger more oceanic form belongs to the species T. truncatus. Analyses of population diversity reveal high levels of regional population structuring among the two forms, with contrasting levels of diversity. From a conservation perspective, genetic isolation of T. aduncus in the Solomon Islands raises further concern about recent impacts of the commercial, live‐capture export industry. Furthermore, the low level of mtDNA diversity in T. aduncus of New Caledonia suggests a recent population bottleneck or founder effect and isolation. This raises concerns for the conservation status of these local populations.     

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. The backend of this interface is a relational database storing the conformational details of DNA obtained in 39 different MD simulation trajectories comprising all the 136 unique tetranucleotide steps. Examples of the use of this data to predict DNA structures are included. Availability: http://humphry.chem.wesleyan.edu:8080/MDDNA. Supplementary information: Supplementary data including color figures are available at Bioinformatics online.     

A comprehensive and validated molecular taxonomy of beaked whales, family Ziphiidae

DNA sequences from orthologous loci can provide universal characters for taxonomic identification. Molecular taxonomy is of particular value for groups in which distinctive morphological features are difficult to observe or compare. To assist in species identification for the little known family Ziphiidae (beaked whales), we compiled a reference database of mitochondrial DNA (mtDNA) control region (437 bp) and cytochrome b (384 bp) sequences for all 21 described species in this group. This mtDNA database is complemented by a nuclear database of actin intron sequences (925 bp) for 17 of the 21 species. All reference sequences were derived from specimens validated by diagnostic skeletal material or other documentation, and included four holotypes. Phylogenetic analyses of mtDNA sequences confirmed the genetic distinctiveness of all beaked whale species currently recognized. Both mitochondrial loci were well suited for species identification, with reference sequences for all known ziphiids forming robust species-specific clades in phylogenetic reconstructions. The majority of species were also distinguished by nuclear alleles. Phylogenetic comparison of sequence data from "test" specimens to these reference databases resulted in three major taxonomic discoveries involving animals previously misclassified from morphology. Based on our experience with this family and the order Cetacea as a whole, we suggest that a molecular taxonomy should consider the following components: comprehensiveness, validation, locus sensitivity, genetic distinctiveness and exclusivity, concordance, and universal accessibility and curation.     

DNA barcode-based molecular identification system for fish species

In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at .