Combining δ13C and δ15N from bone and dentine in marine mammal palaeoecological research: insights from toothed whales

Rationale Stable carbon (δ13C) and nitrogen (δ15N) isotope compositions of bone and dentine collagen extracted from subfossil specimens of extinct and extant mammalian species have been widely used to study the paleoecology of past populations. Due to possible systematic differences in stable isotope values between bone and dentine, dentine values can be transformed into bone-collagen equivalent using a correction factor. This approach has been applied to terrestrial species, but correction factors specifically for marine mammals are lacking. Here, we provide correction factors to transform dentine δ13C and δ15N values into bone-collagen equivalent for two toothed whale sister species: narwhal and beluga. Methods We sampled bone and tooth dentine from the skulls of 11 narwhals and 26 belugas. In narwhals, dentine was sampled from tusk and embedded tooth; in beluga, dentine was sampled from tooth. δ13C and δ15N were measured using an elemental analyzer coupled to a continuous flow isotope ratio mass spectrometer. Intraindividual bone and dentine isotopic compositions were used to calculate correction factors for each species, and to translate dentine isotopic values into bone-collagen equivalent. Results Our analysis revealed differences in δ13C and δ15N between bone and dentine. In narwhals, we found (i) lower average δ13C in bone compared with dentine from tusk and embedded tooth; (ii) no difference in dentine δ13C between tusk and embedded tooth; (iii) lower average δ15N in bone compared with dentine, with the highest values found in embedded tooth. For belugas, we also detected lower δ13C and δ15N in bone compared with tooth dentine. Conclusions Based on our analysis, we provide bone/dentine correction factors for narwhals (both at species and population level), and for belugas. The correction factors, when applied to dentine δ13C and δ15N values, enable the combined analysis of stable isotope data from bone and dentine.

A machine learning pipeline for classification of cetacean echolocation clicks in large underwater acoustic datasets

Machine learning algorithms, including recent advances in deep learning, are promising for tools for detection and classification of broadband high frequency signals in passive acoustic recordings. However, these methods are generally data-hungry and progress has been limited by challenges related to the lack of labeled datasets adequate for training and testing. Large quantities of known and as yet unidentified broadband signal types mingle in marine recordings, with variability introduced by acoustic propagation, source depths and orientations, and interacting signals. Manual classification of these datasets is unmanageable without an in-depth knowledge of the acoustic context of each recording location. A signal classification pipeline is presented which combines unsupervised and supervised learning phases with opportunities for expert oversight to label signals of interest. The method is illustrated with a case study using unsupervised clustering to identify five toothed whale echolocation click types and two anthropogenic signal categories. These categories are used to train a deep network to classify detected signals in either averaged time bins or as individual detections, in two independent datasets. Bin-level classification achieved higher overall precision (>99%) than click-level classification. However, click-level classification had the advantage of providing a label for every signal, and achieved higher overall recall, with overall precision from 92 to 94%. The results suggest that unsupervised learning is a viable solution for efficiently generating the large, representative training sets needed for applications of deep learning in passive acoustics.

Cetacean strandings along the Pacific and Caribbean coasts of Nicaragua from 2014 to 2021

Documenting marine mammal strandings provides important information needed to understand the occurrence and distribution patterns of species. Here, we report on strandings of cetaceans on the Pacific (n = 11) and Caribbean (n = 2) coasts of Nicaragua, documented opportunistically from 2014 to 2021. Strandings included three species of baleen whale (blue whale Balaenoptera musculus, Bryde’s whale Balaenoptera edeni, humpback whale Megaptera novaeangliae) and five species of toothed whale (dwarf sperm whale Kogia sima, Guiana dolphin Sotalia guianensis, pantropical spotted dolphin Stenella attenuata, spinner dolphin Stenella longirostris, Cuvier’s beaked whale Ziphius cavirostris). These are the first published accounts of blue whales, Bryde’s whales, dwarf sperm whales, and Cuvier’s beaked whales in Nicaraguan waters. Limited resources and the advanced decomposition of animals prevented necropsies in most cases, the identification of the causes of mortality in all cases, and the species identification of two dolphins. Information derived from these stranding events offers new insights into the occurrence of marine mammals on the Pacific and Caribbean coasts of Nicaragua and Central America.

Selection of a reference gene for studies of adipose tissues of toothed whales

Fat metabolism in toothed whales is different from other mammals. RT-qPCR is still a reliable technique for studying the relative expressions of various genes involved in metabolism. This study was done for Risso’s dolphin, a toothed whale and information produced here will be important for further transcriptomics studies focused on unrevealed marine mammal fat metabolism. In this study, we sought to identify a suitable reference gene with minimum resources. Seven candidate reference genes ZC3H10, FTL, LGALS1, RPL27A, GAPDH, FTH1 and DCN were initially tested for amplification efficiency using RT-qPCR by producing standard curves. Then, three nearly 100% efficient genes FTL, LGALS1 and GAPDH were selected for the gene stability analysis to determine one stable gene across eight different fat tissues, liver, and muscle of Risso’s dolphins based on four algorithms, provided in geNorm, NormFinder, BestKeeper and Delta Ct. Finally, a RefFinder comprehensive ranking was done based on stability values and the genes were ranked as: FTL>LGALS1>GAPDH. The FTL and LGHLS were identified as the most stable genes; however, GAPDH was third, a well-known housekeeping gene for mammals. Finally, we suggest using FTL as a reliable reference gene for functional genomics studies on toothed whales in the future.

A drastic shift in the energetic landscape of toothed whale sperm cells

Mammalia spermatozoa are a notable example of energetic compartmentalization. While mitochondrial oxidative phosphorylation is restricted to the midpiece, sperm-specific glycolysis operates in the flagellum. Consequently, these highly specialized cells exhibit a clear adaptability to fuel substrates. This plasticity is essential to ensure sperm motility, and is known to vary among species. Here we describe an extreme example of spermatozoa-energetics adaptation. We show that toothed whales exhibit impaired sperm glycolysis, due to gene and exon erosion, and demonstrate that dolphin spermatozoa motility depends uniquely on endogenous fatty acid β-oxidation, but not carbohydrates. Our findings substantiate the observation of large mitochondria in spermatozoa, possibly boosting ATP production from endogenous fatty acids. This unique energetic rewiring emphasizes the physiological body reorganisation imposed by the carbohydrate-depleted marine environment.

Speciation in the face of gene flow within the toothed whale superfamily Delphinoidea

Understanding speciation is a central aspect in Biology. The formation of new species was once thought to be a simple bifurcation process. However, recent advances in genomic resources now provide the opportunity to investigate the role of post-divergence gene flow in the speciation process. The diversification of lineages in the presence of gene flow appears almost paradoxical. However, with enough time and in the presence of incomplete physical and/or ecological barriers to gene flow, speciation can and does occur. Speciation without complete isolation seems especially likely to occur in highly mobile, wide ranging marine species, such as cetaceans, which face limited geographic barriers. The toothed whale superfamily Delphinoidea represents a good example to further explore speciation in the presence of interspecific gene flow. Delphinoidea consists of three families (Delphinidae, Phocoenidae, and Monodontidae) and within all three families, contemporary interspecific hybrids have been reported. Here, we utilise publicly available genomes from nine species, representing all three families, to investigate signs of post-divergence gene flow across their genomes, and to address the speciation processes that led to the diversity seen today within Delphinoidea. We use a multifaceted approach including: (i) phylogenetics, (ii) the distribution of shared derived alleles, and (iii) demography-based. We find that the divergence and evolution of lineages in Delphinoidea did not follow a simple bifurcating pattern, but were much more complex. Our results indicate multiple, long-lasting ancestral gene flow events both within and among families, which continued for millions of years after initial divergence.