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opencc-zeroOct 2019View details →

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.

opencc-zeroAug 2022View details →

Geographic range size, water temperature and extrinsic threats predict the extinction risk in global cetaceans

Despite that cetaceans provide significant ecological contributions to the health and stability of aquatic ecosystems, they are highly endangered with nearly one-third of species assessed as threatened with extinction. Nevertheless, to date, few studies have explicitly examined the patterns and processes of extinction risk and threats for this taxon, and even less between the two subclades (Mysticeti and Odontoceti). To fill this gap, we compiled a dataset of six intrinsic traits (active region, geographic range size, body weight, diving depth, school size and reproductive cycle), six environmental factors relating to sea surface temperature and chlorophyll concentration, and two human-related threat indices that are commonly recognized for cetaceans. We then employed phylogenetic generalized least square (PGLS) models and model selection to identify the key predictors of extinction risk in all cetaceans, as well as in the two subclades. We found that geographic range size, sea surface temperature and human threat index were the most important predictors of extinction risk in all cetaceans and in odontocetes. Interestingly, maximum body weight was positively associated with the extinction risk in mysticetes, but negatively related to that for odontocetes. By linking seven major threat types to extinction risk, we further revealed that fisheries bycatch was the most common threat, yet the impacts of certain threats could be overestimated when considering all species rather than just threatened ones. Overall, we suggest that conservation efforts should focus on small-ranged cetaceans and species living in warmer waters or under strong anthropogenic pressures. Moreover, further studies should consider the extinction risk of species when superimposing risk maps and quantifying risk severity. Finally, we emphasize that mysticetes and odontocetes should be conserved with different strategies, because their extinction risk patterns and major threat types are considerably different. For instance, large-bodied mysticetes and small-ranged odontocetes require special conservation priority.

opencc-zeroSep 2022View details →

Ecological impacts of unsustainable sand mining: Urgent lessons learned from a critically endangered freshwater cetacean

Sand production, tripled in the last two decades, is an emerging concern for global biodiversity. However, the paucity of sand mining data worldwide prevents understanding the extent of sand mining impacts and how it affects wildlife populations and ecosystems, which is critical for timely mitigation and conservation actions. Integrating remote sensing and field surveys over fourteen years, we investigated mining impacts on the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) in Dongting Lake, China. We found that sand mining presented a consistent, widespread disturbance in Dongting Lake. The porpoise strongly avoided mining sites, especially the areas subjected to higher mining intensity. The extensive sand mining significantly contracted the porpoise's range and restricted their habitat use in the lake. Water traffic for sand transportation further blocked the species' river-lake movements, affecting the population connectivity. In addition, mining-induced loss of nearshore habitats, a critical foraging and nursery ground for the porpoise, occurred in nearly 70% of the water channels of our study region. Our findings provide the first empirical evidence on the impacts of unregulated sand extractions on species distribution. Our spatiotemporally explicit approach and findings can support regulation and conservation, yielding broader implications for sustainable sand mining worldwide. This dataset contains (1) sand mining information from 2006–2019 in Dongting Lake, (2) data of porpoise distributions from nine range-wide surveys from 2006–2019, (3) water traffic information at the outlet channel of Dongting Lake from 2001–2019, (4) data of the lake morphology from 2006–2019, (5) codes for all data analyses.

opencc-by-4.0Jul 2024View details →

Distance sampling visual observation sightings data for cetaceans from Antarctic Tourist vesssels

The following is two summer sampling seasons of distance sampling data collected by trained observer teams of two from Antarctic tourist vessels. The data set contains 5 key dataframes. This data has be cleaned and quality controlled.  Effort - details the type of visual observation effort, the observer on effort and other information  Environment - details the environmental conditions under which the data were collected.  Sightings - details the observations made, and distance estiamtes (relative to the ship) for cetceans.  Resightings - used in select cases, see protocols. gpsData - automated collection of location data at 5 sec intervals, some gaps exists, which were interpolated later for analysis Work is ongoing with the dataset, please contact authors about its use.

opennotspecifiedMar 2016View details →

Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker

Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.

Fig. 5 in Accumulations of Fossils of the Whale Barnacle Coronula bifida Bronn, 1831 (Thoracica: Coronulidae) Provides Evidence of a Late Pliocene Cetacean Migration Route through the Straits of Taiwan

Fig. 5. (A-F) Amphibalanus? sp. collected from the Liuchungchi Formation, Niupu, Chiayi, Western Central Taiwan, (Plio-Pleistocene age). Note that the shell compartment are tubiferous and possess interlaminate figures.

Fig. 2 in Accumulations of Fossils of the Whale Barnacle Coronula bifida Bronn, 1831 (Thoracica: Coronulidae) Provides Evidence of a Late Pliocene Cetacean Migration Route through the Straits of Taiwan

Fig. 2. Trace fossils from the Liuchungchi Formation,Chukou Niupu at Chaiyi City, Taiwan. (A) Asterosoma isp. (#2267); (B) Bifasiculus? isp. (#2265); (C) Asterosoma isp. (#2263); (D) Asterosoma isp. (#2264). These ichnofossils were likely formed by annelids, and give evidence for low-energy sea bottom conditions. Specimens held in the Chia-Yi Municipal Museum, Chaiyi City. (The diameter of the coin is 26 mm).

Fig. 4 in Accumulations of Fossils of the Whale Barnacle Coronula bifida Bronn, 1831 (Thoracica: Coronulidae) Provides Evidence of a Late Pliocene Cetacean Migration Route through the Straits of Taiwan

Fig. 4. (A-F) Striatobalanus sp. collected from the Liuchungchi Formation, Niupu, Chiayi, Western Central Taiwan, during the Plio- Pleistocene. Note that the shell walls, radii and bases are solid (i.e. non-tubiferous).

Fig. 1 in Accumulations of Fossils of the Whale Barnacle Coronula bifida Bronn, 1831 (Thoracica: Coronulidae) Provides Evidence of a Late Pliocene Cetacean Migration Route through the Straits of Taiwan

Fig. 1. Location of the Coronula bifida Lagerstätte site near Niupu, Zhongpu Township, Chiayi, Western Central Taiwan. Insert showing the site on the Bazhang riverbed near the Chukou Niupu in Chaiyi City.

Fig. 3. Coronula bifida Bronn, 1831 in Accumulations of Fossils of the Whale Barnacle Coronula bifida Bronn, 1831 (Thoracica: Coronulidae) Provides Evidence of a Late Pliocene Cetacean Migration Route through the Straits of Taiwan

Fig. 3. Coronula bifida Bronn, 1831 from Niupu, Chiayi, Western Central Taiwan, Liuchungchi Formation (Plio-Pleistocene). Specimens (#0860-0869) held by the Chia-Yi Municipal Museum, Chaiyi City, Taiwan.

Fig. 6. A in Accumulations of Fossils of the Whale Barnacle Coronula bifida Bronn, 1831 (Thoracica: Coronulidae) Provides Evidence of a Late Pliocene Cetacean Migration Route through the Straits of Taiwan

Fig. 6. A large fossil baleen whale mandible, currently attributed to the humpback whale, Megaptera novaeangliae Gray, 1846. Recovered from the Liuchungchi Formation, Zhongpu Township, Chiayi, Western Central Taiwan. On display in the Chia-Yi Municipal Museum, Chaiyi City, Taiwan.