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opencc-zeroJul 2020View details →

Supplementary material 1 from: Mayorga LFSP, Vanstreels RET, Bhering RCC, Mamede N, Costa LMB, Pinheiro FCF, Reis LWD, Trazzi A, Meirelles WLC, Ribeiro AM, Siciliano S (2020) Strandings of cetaceans on the Espírito Santo coast, southeast Brazil, 1975–2015. ZooKeys 948: 129-152. https://doi.org/10.3897/zookeys.948.50468

Historical records of cetacean strandings along the coast of Espírito Santo state, southeast Brazil, 1975–2015

opencc-zeroSep 2020View details →

Data from: Palaeobiogeography of the north pacific toothed mysticetes (Cetacea, Aetiocetidae): a key to Oligocene cetacean distributional patterns

Biogeographical distributional patterns of cetaceans reflect dispersal events and colonization of the oceans from their ancestral area in the ancient Sea of Tethys ~53 Ma. Likewise, they shows several vicariance events throughout the evolutionary history of this group. However, our understanding of how these processes took place and what biogeographical scenarios occurred among the different groups of cetaceans through time, is limited. Consequently, this work focuses on explaining the distributional patterns of the well-known North Pacific toothed mysticetes, Aetiocetidae, through the power of retrodiction offered by track analysis (panbiogeography) and cladistic biogeography, using the approach of evolutionary biogeography. Our results show that the distributional patterns of Aetiocetidae explain their endemism in the North Pacific, as well as indicate that their hypothetical ancestor probably colonized the Pacific from the Atlantic Ocean by a dispersal event (founder effect) via the Central American Seaway. Furthermore, their biogeographic history shows the adaptive radiation (cladogenesis) of Aetiocetidae as result of peripatric speciation followed by sympatric speciation within a heterogeneous environment. Finally, the biogeographic framework of Aetiocetidae further supports the relevant role that the Pacific Ocean has played in the evolution of Oligocene cetaceans as a geographic area that promoted endemism, dispersal, and colonization. While at more local scales, environmental conditions further promoted increased diversity and disparity amongst Mysticeti.

opencc-zeroDec 2011View details →

Data from: Basilotritus uheni, a new cetacean (Cetacea, Basilosauridae) from the late Middle Eocene of Eastern Europe

A new basal basilosaurid cetacean, Basilotritus uheni n. gen. n. sp., comes from the late middle Eocene (Bartonian) of Ukraine. It is the earliest dated record of a cetacean from Eastern Europe. The tympanic bulla of Basilotritus uheni shares basilosaurid synapomorphies but possesses unusual traits inherited from protocetids. Cetaceans related to Basilotritus uheni and referred to as Eocetus or "Eocetus" have been recorded from Africa, Europe, North America and South America. "Eocetus" wardii from North America is recombined as Basilotritus wardii. Platyosphys paulsonii and Platyosphys einori from Ukraine are considered as nomina dubia; specimens prior referred to as Platyosphys sp. are similar or related to Basilotritus. Other records of the Eocene cetaceans from Ukraine and south Russia are identified as Basilotritus or related genera. Early basilosaurids are demonstrated to be a paraphyletic, morphologically and geographically diverse group of the genera that colonized the world ocean as late as in Bartonian age and were probably the ancestors of Neoceti, as well as of more derived basilosaurids.

opencc-zeroDec 2017View details →

Data from: Assessing cetacean surveys throughout the Mediterranean Sea: a gap analysis in environmental space

Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolation versus extrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months.

opencc-zeroDec 2018View details →

Data from: A risk-based forecast of extreme mortality events in small cetaceans: using stranding data to inform conservation practice

Effective conservation requires monitoring and pro-active risk assessments. We studied the effects of at-sea mortality events (ASMEs) in marine mammals over two decades (1990-2012) and built a risk- based indicator for the European Union's Marine Strategy Framework Directive (MSFD). Strandings of harbour porpoises (Phocoena phocoena), short-beaked common dolphins (Delphinus delphis), and striped dolphins (Stenella coeruleoalba) along French coastlines were analysed using Extreme Value Theory (EVT). EVT operationalises what is an extreme ASME, and allows the probabilistic forecasting of the expected maximum number of dead animals assuming constant pressures. For the period 2013-2018, we forecast the strandings of 80 harbour porpoises, 860 common dolphins, and 57 striped dolphins in extreme ASMEs. Comparison of these forecasts with observed strandings informs whether pressures are increasing, decreasing or stable. Applying probabilistic methods to stranding data facilitates the building of risk-based indicators, required under the MSFD, to monitor the effect of pressures on marine mammals.

opencc-zeroDec 2017View details →

Data from: Genome-wide association study of an unusual dolphin mortality event reveals candidate genes for susceptibility and resistance to cetacean morbillivirus

Infectious diseases are significant demographic and evolutionary drivers of populations, but studies about the genetic basis of disease resistance and susceptibility are scarce in wildlife populations. Cetacean morbillivirus (CeMV) is a highly contagious disease that is increasing in both geographic distribution and incidence, causing unusual mortality events (UME) and killing tens of thousands of individuals across multiple cetacean species worldwide since the late 1980's. The largest CeMV outbreak in the Southern Hemisphere reported to date occurred in Australia in 2013, where it was a major factor in a UME, killing mainly young Indo-Pacific bottlenose dolphins (Tursiops aduncus). Using cases (non-survivors) and controls (putative survivors) from the most affected population, we carried out a genome-wide association study to identify candidate genes for resistance and susceptibility to CeMV. The genomic dataset consisted of 278,147,988 sequence reads and 35,493 high quality SNPs genotyped across 38 individuals. Association analyses found highly significant differences in allele and genotype frequencies amongst cases and controls at 65 SNPs, and Random Forests conservatively identified eight as candidates. Annotation of these SNPs identified five candidate genes (MAPK8, FBXW11, INADL, ANK3, and ACOX3) with functions associated with stress, pain and immune responses. Our findings provide the first insights into the genetic basis of host defence to this highly contagious disease, enabling the development of an applied evolutionary framework to monitor CeMV resistance across cetacean species. Biomarkers could now be established to assess potential risk factors associated with these genes in other CeMV affected cetacean populations and species. These results could also possibly aid in the advancement of vaccines against morbilliviruses.

opencc-zeroDec 2013View details →

Data from: Sexual selection targets cetacean pelvic bones

Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline to analyze the size and shape evolution of pelvic bones from 130 individuals (29 species) in the context of inferred mating system. We present two main findings: 1) males from species with relatively intense sexual selection (inferred by relative testes size) have evolved relatively large penises and pelvic bones compared to their body size, and 2) pelvic bone shape diverges more quickly in species pairs that have diverged in inferred mating system. Neither pattern was observed in the anterior-most pair of vertebral ribs, which served as a negative control. This study provides evidence that sexual selection can affect internal anatomy that controls male genitalia. These important functions may explain why cetacean pelvic bones have not been lost through evolutionary time.

opencc-zeroDec 2014View details →

Data from: Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933–0.987, π=0.763–0.996% and Rs=4.22–4.37, He=0.624–0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.

opencc-zeroDec 2012View details →

Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans

Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions.

Fig. 7 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 7. Energy-flux model and food web stability. We tested whether the food web as preserved is functional and stable over ecological time. All shelled invertebrates (specifically ammonoids), fish, and amniote taxa discovered in the Fossil Hill Fauna are modeled as members of a food web. The member "shelled invertebrates" is basal to the food web and comprises primarily ammonoids but also halobiid bivalves and crustaceans. The member "nonshelled invertebrates plus fishes" ("fish") pools coleoid cephalopods such as squid and small- to medium-sized fish. See Methods and table S11 for food web members and their body masses, total biomasses, and energetic demands. (A) Trophic interaction matrix used for modeling energy-flux across members. Stacked bars represent the diet of predatory taxa. Filled squares within bars indicate that a taxon is taken by the predator, whereas white indicates that it is not. (B) Stability values calculated by the model for different combinations of total biomass of the two food web members "shelled invertebrates" and "fish." More negative stability values indicate a more stable food web. Error bars for blue dots represent model results assuming maximum and minimum body mass estimates for ichthyosaur taxa (table S11). Greater body masses result in less-stable food webs than smaller body masses. Stability values of extant food webs range between −10 and 0 (41). Note that we multiplied stability values by −1 for plotting. TB, total biomass (kg); red circles, the total biomass of "shelled invertebrates" equals that of "fish."

Fig. 6 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 6. The adaptive landscape of body-size evolution. (A and B) Ichthyosaurs (A) feature two early adaptive shifts toward larger skull length, whereas cetaceans (B) entered selective regimes that promoted larger skull width much later in their evolution.

Fig. 5 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 5. Exploration of the rate heterogeneity of body-size evolution. (A and B) Ichthyosaurs (A) feature the fastest rates of body evolution early in their history, whereas cetaceans (B) show a more complex pattern, with fastest rates occurring in later stages of their history. C, Cymbospondylidae; M, Merriamosauria.

Fig. 4 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 4. Body-size evolution in ichthyosaurs and cetaceans compared. Traitgram of body size, normalized such that 0 corresponds to the smallest body size in each group and 1 to the largest for ichthyosaurs (lilac; based on an early-burst model) and cetaceans (ochre; based on a Brownian motion model) (see Methods). Lilac dots indicate Cymbospondylus species from the Fossil Hill Fauna. B., Balaenoptera musculus, blue whale; C., C. youngorum sp. nov.; L., Llanocetus denticrenatus, early giant baleen whale; S., S. sikanniensis, the largest named ichthyosaur. The inset shows model-fitting results expressed as Akaike weights for five different evolutionary models from 1000 iterations. Boxes represent the interquartile ranges (IQRs), with whiskers extending 1.5 times the IQR outside the boxes. Vertical lines inside the boxes show the median. BM, Brownian motion; EB, early burst; OU, Ornstein-Uhlenbeck.

Fig. 3 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 3. Time-calibrated phylogenies and body-size illustrations of Ichthyosauria and Cetacea and the relationships of the new giant ichthyosaur C. youngorum sp. nov. Ichthyosaurs originated in the late Early Triassic shortly after the end-Permian mass extinction (EPME), survived the end-Triassic mass extinction (ETME), and went extinct in the early Late Cretaceous. Lilac stratigraphic ranges denote taxa from the Fossil Hill Fauna. Cetaceans originated in the late Paleocene after the Cretaceous-Paleogene mass extinction (CPME). See (10) for sources of phylogenies and table S6 for image credits. mya, million years ago.

Fig. 2 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 2. Skull of the holotype of C. youngorum sp. nov. LACM DI 157871. (A) Skull in right dorso-lateral view. (B) Skull sutures. (C) Skull in left ventrolateral view. (D) Skull sutures. (E) Snout in left ventrolateral view. (F) Middle part of dentary tooth row in right dorsolateral view. Note the bone of attachment. (G to K) Right humerus in proximal (G), dorsal (H), posterior (I), ventral (J), and anterior view (K). a, angular; ar, articular; at, anterior terrace; d, dentary; en, external nares; f, frontal; j, jugal; l, lacrimal; lte, lower temporal embayment; mx, maxilla; n, nasal; o, orbita; pa, parietal; pf, parietal foramen; pmx, premaxilla; po, postorbital; pra, prearticular; prf, prefrontal; q, quadrate; qj, quadratojugal; sa, surangular; sc, scleral ring; sq, squamosal; st, supratemporal; uto, upper temporal opening; v, cervical vertebra.

Fig. 1 in Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans

Fig. 1. Conceptual approach of our integrated study. We combine traditional paleontology with computational trait evolution and energy-flux modeling to study macroevolutionary patterns of body size evolution in marine amniotes.

opencc-zeroFeb 2022View details →

Spy in the sky: a method to identify pregnant small cetaceans

Data on sex ratios, age classes, reproductive success and health status are key metrics to manage populations yet can be difficult to collect in wild cetacean populations. Long-term individual-based studies provide a unique opportunity to apply unoccupied aerial system (UAS) photogrammetry to non-invasively measure body morphometrics of individuals with known life history information. The aims of this study were 1) to compare length measurements from UAS photogrammetry with laser photogrammetry and 2) to explore whether UAS measurements of body width could be used to remotely determine pregnancy status, sex or age class in a well-studied bottlenose dolphin population in Scotland. We carried out five boat-based surveys in July and August 2017, with concurrent photo-identification, UAS, and laser photogrammetry. Photographs were measured using bespoke programmes, MorphMetriX for UAS photos and a Zooniverse project for laser photos. In total 64 dolphins were identified using photo-ID, 54 of which had concurrent UAS body length and 47 with laser body length measurements. We also measured body widths at 10% increments from 10-90% of body length for 48 individuals of known sex, age class and/or pregnancy status. There was no significant difference in the length of individuals measured with UAS and laser photogrammetry. Discriminant analyses of the body width-length ratios expected to change during pregnancy, correctly assigned pregnancy status for 14 of the 15 females of known pregnancy status. Only one pregnant female was incorrectly assigned as not pregnant. However, our results showed that length and body width cannot accurately allocate these bottlenose dolphins to sex or age class using photogrammetry techniques alone. The present study illustrates that UAS and laser photogrammetry measurements are comparable for small cetaceans and demonstrates that UAS measurements of body width-length ratio can accurately assign pregnancy status in bottlenose dolphins.

opencc-zeroFeb 2022View details →

Novel genomic insights into body size evolution in cetaceans and a resolution of Peto's Paradox

Cetaceans (whales, dolphins, and porpoises) have undergone a radical transformation from the typical terrestrial mammalian body plan to a streamlined one while exhibited dramatic inter-specific size ranges. However, the molecular mechanisms underlying the diversifying evolution of cetacean body size are largely unknown. Here, by using genome and phenotypic data from 22 cetaceans, we seek to investigate the genome-wide gene-phenotype correlation and to explore the genetic basis under the high diversity of body size in cetaceans. Results of the functional enrichment showed that body size-related genes in cetaceans were enriched in pathways associated with immunity, cell growth, and metabolism, suggesting their potential roles in the diversifying evolution of body size in cetaceans. A series of genes was also found coevolution with body size that are mainly involved in immune surveillance, tumor suppression function, and development of 'cheater' tumors. This in turn suggests that the genes play a role in tumor control and thus resolve Peto's paradox, a finding that the expansion in body size and thereby cell number does not correlate with increases in cancer incidence in larger whales. The present study could provide novel insights into the evolution of great body size variation in cetaceans.