Delphinus delphis isolate:G181
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PROVIDER: PRJNA577923 | ENA |
REPOSITORIES: ENA
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Project description:Delphinus delphis Genome sequencing and assembly
| PRJNA901261 | ENA
Project description:Delphinus delphis genome sequencing and assembly and multi-tissue transcriptome
| PRJNA902134 | ENA
Project description:Delphinus delphis Genome sequencing and assembly and multi-tissue Transcriptome
| PRJNA903213 | ENA
Project description:Marine mammals are regularly reported as bycatch in commercial and artisanal fisheries, but data are often insufficient to allow assessment of these incidental mortalities. Observer coverage of the mackerel trawl fishery in New Zealand waters between 1995 and 2011 allowed evaluation of common dolphin Delphinus delphis bycatch on the North Island west coast, where this species is the most frequently caught cetacean. Observer data were used to develop a statistical model to estimate total captures and explore covariates related to captures. A two-stage Bayesian hurdle model was used, with a logistic generalised linear model predicting whether any common dolphin captures occurred on a given tow of the net, and a zero-truncated Poisson distribution to estimate the number of dolphin captures, given that there was a capture event. Over the 16-year study period, there were 119 common dolphin captures reported on 4299 observed tows. Capture events frequently involved more than one individual, with a maximum of nine common dolphin observed caught in a single tow. There was a peak of 141 estimated common dolphin captures (95% c.i.: 56 to 276; 6.27 captures per 100 tows) in 2002-03, following the marked expansion in annual effort in this fishery to over 2000 tows. Subsequently, the number of captures fluctuated although fishing effort remained relatively high. Of the observed capture events, 60% were during trawls where the top of the net (headline) was <40 m below the surface, and the model determined that this covariate best explained common dolphin captures. Increasing headline depth by 21 m would halve the probability of a dolphin capture event on a tow. While lack of abundance data prevents assessment of the impact of these mortalities on the local common dolphin population, a clear recommendation from this study is the increasing of headline depth to reduce common dolphin captures.
| S-EPMC3661492 | biostudies-literature
Project description:Reproductive biology was assessed in 106 female common dolphins (Delphinus delphis) examined post-mortem from stranding and bycatch events along the New Zealand coastline between 1997 and 2019. The average age (ASM) and length (LSM) at sexual maturity was estimated at 7.5 years and 183.5 cm, respectively. The total number of corpora in mature individuals increased with age and appeared to persist throughout life. Ovarian asymmetry was apparent, with the left ovary displaying higher rates of ovulation, and a maximum of 19 corpora recorded for a 24-year-old female. The estimated ovulation and annual pregnancy rates for mature females were 0.39 year−1 and 30%, respectively. Conception and calving occurred year-round, with a weak seasonal increase observed in late austral spring and early austral summer. As these data did not clearly show whether seasonality was present, the gestation, lactation, and resting periods were calculated as either 12.6 or 12.8 months based on the presence/absence of seasonality, respectively. Similarly, calving interval ranged from 3.15 to 3.2 years, depending upon whether seasonality was considered. The estimated LSM of the New Zealand population aligns with other populations globally, although the estimated ASM is younger by approximately 6 months. Other reproductive parameters align with Northern Hemisphere populations, although demonstrate variation, which may reflect adaptations to local conditions such as water temperature and prey availability. As the species is subject to anthropogenic impacts including pollution and bycatch, we suggest our findings be used as a baseline with which to monitor trends in population parameters. Supplementary Information The online version contains supplementary material available at 10.1007/s00227-022-04139-3.
| S-EPMC9705467 | biostudies-literature
Project description:A female short-beaked common dolphin calf was found stranded in San Diego, California in October 2010, presenting with multifocal ulcerative lesions in the trachea and bronchi. Viral particles suggestive of polyomavirus were detected by EM, and subsequently confirmed by PCR and sequencing. Full genome sequencing (Ion Torrent) revealed a circular dsDNA genome of 5,159 bp that was shown to form a distinct lineage within the genus Polyomavirus based on phylogenetic analysis of the early and late transcriptomes. Viral infection and distribution in laryngeal mucosa was characterised using in-situ hybridisation, and apoptosis observed in the virus-infected region. These results demonstrate that polyomaviruses can be associated with respiratory disease in cetaceans, and expand our knowledge of their diversity and clinical significance in marine mammals.
| S-EPMC3707911 | biostudies-literature
Project description:Reproductive parameters were assessed in 64 male common dolphins (Delphinus delphis) examined post-mortem from strandings and bycatch in New Zealand between 1999 and 2020. The stages of male sexual maturation were assessed using morphological measurements and histological examination of testicular tissue. Age was determined via growth layer groups (GLGs) in teeth. The average age (ASM) and length (LSM) at attainment of sexual maturity were estimated to be 8.8 years and 198.3 cm, respectively. Individual variation in ASM (7.5-10 years) and LSM (190-220 cm) was observed in New Zealand common dolphins. However, on average, sexual maturity was attained at a similar length but at a marginally younger age (< 1 year) in New Zealand compared to populations in the Northern Hemisphere. All testicular variables proved better predictors of sexual maturity compared to demographic variables (age and total body length), with combined testes weight the best outright predictor of sexual maturity. Reproductive seasonality was observed in male common dolphins, with a significant increase in combined testes weight in austral summer. This aligns with most other studied populations, where seasonality in reproduction is typically observed. Given the known anthropogenic impacts on New Zealand common dolphins, we recommend that these findings be used as a baseline from which to monitor population-level changes as part of conservation management efforts.Supplementary informationThe online version contains supplementary material available at 10.1007/s00227-023-04266-5.
| S-EPMC10558376 | biostudies-literature
Project description:BackgroundHigh levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia.ResultsWe identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits.ConclusionTo the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.
| S-EPMC9275043 | biostudies-literature
Project description:The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.
| S-EPMC11022445 | biostudies-literature