Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

Into the Blue: Exploring genetic mechanisms behind the evolution of baleen whales

Marine ecosystems are ideal for studying evolutionary adaptations involved in lineage diversification due to few physical barriers and reduced opportunities for strict allopatry compared to terrestrial ecosystems. Cetaceans (whales, dolphins, and porpoises) are a diverse group of mammals that successfully adapted to various habitats within the aquatic environment around 50 million years ago. While the overall adaptive transition from terrestrial to fully aquatic species is relatively well understood, the radiation of modern whales is still unclear. Here high-quality genomes derived from previously published data were used to identify genomic regions that potentially underpinned the diversification of baleen whales (Balaenopteridae). A robust molecular phylogeny was reconstructed based on 10,159 single copy and complete genes for eight mysticetes, seven odontocetes and two cetacean outgroups. Analysis of positive selection across 3,150 genes revealed that balaenopterids have undergone numerous idiosyncratic and convergent genomic variations that may explain their diversification. Genes associated with aging, survival and homeostasis were enriched in all species. Additionally, positive selection on genes involved in the immune system were disclosed for the two largest species, blue and fin whales. Such genes can potentially be ascribed to their morphological evolution, allowing them to attain greater length and increased cell number. Further evidence is presented about gene regions that might have contributed to the extensive anatomical changes shown by cetaceans, including adaptation to distinct environments and diets. This study contributes to our understanding of the genomic basis of diversification in baleen whales and the molecular changes linked to their adaptive radiation, thereby enhancing our understanding of cetacean evolution.

Evolution of ion channels in cetaceans: a natural experiment in the tree of life

Cetaceans represent a natural experiment within the tree of life in which a lineage changed from terrestrial to aquatic habitats. This shift involved phenotypic modifications, representing an opportunity to explore the genetic bases of phenotypic diversity. Among the different molecular systems that maintain cellular homeostasis, ion channels are crucial for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have, on average, fewer protein-coding genes and a higher percentage of annotated ion channels than non-cetacean mammals. Signals of positive selection were detected in ion channels related to the heart, locomotion, visual and neurological phenotypes. Interestingly, we predict that the NaV1.5 ion channel of most toothed whales (odontocetes) is sensitive to tetrodotoxin, similar to NaV1.7, given the presence of tyrosine instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than three times faster than that of non-cetacean mammals.

Predicting ecology and hearing sensitivities in Parapontoporia-An extinct long-snouted dolphin

Analyses of the cetacean (whale and dolphin) inner ear provide glimpses into the ecology and evolution of extinct and extant groups. The paleoecology of the long-snouted odontocete (toothed whale) group, Parapontoporia, is primarily marine with its depositional context also suggesting freshwater tolerance. As an extinct relative of the exclusively riverine Lipotes vexillifer, Parapontoporia provides insight into a transition from marine to freshwater environments. High-resolution X-ray CT scans (~3 microns or less) of three individual specimens from two species, P. sternbergi and P. pacifica, were acquired. Digital endocasts of the inner ear labyrinths were extracted non-destructively. Nine measurements of the inner ear were compared with an existing dataset covering 125 terrestrial and aquatic artiodactyls. These measurements were then subjected to a principal component analysis to interpret hearing sensitivities among other artiodactyls. Based on our analyses, Parapontoporia was likely to have been able to hear within narrow-band high frequency (NBHF) ranges. This finding indicates another convergence of NBHF-style hearing, or, more intriguingly, suggests that it may be an ancestral characteristic present among the longirostrine dolphins that dominated in the Miocene prior to the evolution of more modern lineages.

A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies

The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.

Cetaceans are the next frontier for vocal rhythm research

While rhythm can facilitate and enhance many aspects of behavior, its evolutionary trajectory in vocal communication systems remains enigmatic. We can trace evolutionary processes by investigating rhythmic abilities in different species, but research to date has largely focused on songbirds and primates. We present evidence that cetaceans-whales, dolphins, and porpoises-are a missing piece of the puzzle for understanding why rhythm evolved in vocal communication systems. Cetaceans not only produce rhythmic vocalizations but also exhibit behaviors known or thought to play a role in the evolution of different features of rhythm. These behaviors include vocal learning abilities, advanced breathing control, sexually selected vocal displays, prolonged mother-infant bonds, and behavioral synchronization. The untapped comparative potential of cetaceans is further enhanced by high interspecific diversity, which generates natural ranges of vocal and social complexity for investigating various evolutionary hypotheses. We show that rhythm (particularly isochronous rhythm, when sounds are equally spaced in time) is prevalent in cetacean vocalizations but is used in different contexts by baleen and toothed whales. We also highlight key questions and research areas that will enhance understanding of vocal rhythms across taxa. By coupling an infraorder-level taxonomic assessment of vocal rhythm production with comparisons to other species, we illustrate how broadly comparative research can contribute to a more nuanced understanding of the prevalence, evolution, and possible functions of rhythm in animal communication.

Common dolphin whistle responses to experimental mid-frequency sonar

Oceanic delphinids that occur in and around Navy operational areas are regularly exposed to intense military sonar broadcast within the frequency range of their hearing. However, empirically measuring the impact of sonar on the behavior of highly social, free-ranging dolphins is challenging. Additionally, baseline variability or the frequency of vocal state-switching among social oceanic dolphins during undisturbed conditions is lacking, making it difficult to attribute changes in vocal behavior to anthropogenic disturbance. Using a network of drifting acoustic buoys in controlled exposure experiments, we investigated the effects of mid-frequency (3-4 kHz) active sonar (MFAS) on whistle production in short-beaked (Delphinus delphis delphis) and long-beaked common dolphins (Delphinus delphis bairdii) in southern California. Given the complexity of acoustic behavior exhibited by these group-living animals, we conducted our response analysis over varying temporal windows (10 min- 5 s) to describe both longer-term and instantaneous changes in sound production. We found that common dolphins exhibited acute and pronounced changes in whistle rate in the 5 s following exposure to simulated Navy MFAS. This response was sustained throughout sequential MFAS exposures within experiments simulating operational conditions, suggesting that dolphins may not habituate to this disturbance. These results indicate that common dolphins exhibit brief yet clearly detectable acoustic responses to MFAS. They also highlight how variable temporal analysis windows-tuned to key aspects of baseline vocal behavior as well as experimental parameters related to MFAS exposure-enable the detection of behavioral responses. We suggest future work with oceanic delphinids explore baseline vocal rates a-priori and use information on the rate of change in vocal behavior to inform the analysis time window over which behavioral responses are measured.

Organisation and evolution of the major histocompatibility complex class I genes in cetaceans

A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.

Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis)

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.

Localization of peptide hormones in the placentas of Bryde's (Balaenoptera brydei), sei (B. borealis), and common minke (B. acutorostrata) whales

In this study, we examined the morphological features of the placentas from 3 species of rorqual whales (Balaenopteridae), namely Bryde's (Balaenoptera brydei), sei (B. borealis), and common minke (B. acutorostrata) whales, and verified the secretion of 2 placental-specific peptide hormones, placental lactogen (PL) and chorionic gonadotropin (CG). The placentas were collected in the second phase of the Japanese Whale Research Program under a special permit in the North Pacific (JARPN II) between 2009 and 2010. For all three species of rorqual whales, as the fetus grew, the interdigitation between the maternal endometrial folds and chorionic villi became more complicated, and many blood capillaries of chorionic villi and endometrium became larger and infiltrated the trophoblast cells and endometrial epithelial cells, respectively. In the immunohistochemical examination, the trophoblast cells (except for areolar trophoblast cells) showed immunoreactivities for the PL and luteinizing hormone (LH) antibodies, and this phenomenon was similar in the placentas of all 3 rorqual whale species. Our results suggest that PL and LH-like CG play roles in regulating pregnancy in the placenta of cetacean.

Revised taxonomy of eastern North Pacific killer whales (Orcinus orca): Bigg's and resident ecotypes deserve species status

Killer whales (Orcinus orca) are currently recognized as a single ecologically and morphologically diverse, globally distributed species. Multiple morphotypes or ecotypes have been described, often associated with feeding specialization, and several studies have suggested taxonomic revision to include multiple subspecies or species in the genus. We review the ecological, morphological and genetic data for the well-studied 'resident' and Bigg's (aka 'transient') ecotypes in the eastern North Pacific and use quantitative taxonomic guidelines and standards to determine whether the taxonomic status of these killer whale ecotypes should be revised. Our review and new analyses indicate that species-level status is justified in both cases, and we conclude that eastern North Pacific Bigg's killer whales should be recognized as Orcinus rectipinnus (Cope in Scammon, 1869) and resident killer whales should be recognized as Orcinus ater (Cope in Scammon, 1869).

Evolutionary novelties underlie sound production in baleen whales

Baleen whales (mysticetes) use vocalizations to mediate their complex social and reproductive behaviours in vast, opaque marine environments1. Adapting to an obligate aquatic lifestyle demanded fundamental physiological changes to efficiently produce sound, including laryngeal specializations2-4. Whereas toothed whales (odontocetes) evolved a nasal vocal organ5, mysticetes have been thought to use the larynx for sound production1,6-8. However, there has been no direct demonstration that the mysticete larynx can phonate, or if it does, how it produces the great diversity of mysticete sounds9. Here we combine experiments on the excised larynx of three mysticete species with detailed anatomy and computational models to show that mysticetes evolved unique laryngeal structures for sound production. These structures allow some of the largest animals that ever lived to efficiently produce frequency-modulated, low-frequency calls. Furthermore, we show that this phonation mechanism is likely to be ancestral to all mysticetes and shares its fundamental physical basis with most terrestrial mammals, including humans10, birds11, and their closest relatives, odontocetes5. However, these laryngeal structures set insurmountable physiological limits to the frequency range and depth of their vocalizations, preventing them from escaping anthropogenic vessel noise12,13 and communicating at great depths14, thereby greatly reducing their active communication range.

The evolution of menopause in toothed whales

Understanding how and why menopause has evolved is a long-standing challenge across disciplines. Females can typically maximize their reproductive success by reproducing for the whole of their adult life. In humans, however, women cease reproduction several decades before the end of their natural lifespan1,2. Although progress has been made in understanding the adaptive value of menopause in humans3,4, the generality of these findings remains unclear. Toothed whales are the only mammal taxon in which menopause has evolved several times5, providing a unique opportunity to test the theories of how and why menopause evolves in a comparative context. Here, we assemble and analyse a comparative database to test competing evolutionary hypotheses. We find that menopause evolved in toothed whales by females extending their lifespan without increasing their reproductive lifespan, as predicted by the 'live-long' hypotheses. We further show that menopause results in females increasing their opportunity for intergenerational help by increasing their lifespan overlap with their grandoffspring and offspring without increasing their reproductive overlap with their daughters. Our results provide an informative comparison for the evolution of human life history and demonstrate that the same pathway that led to menopause in humans can also explain the evolution of menopause in toothed whales.

Downsizing a heavyweight: factors and methods that revise weight estimates of the giant fossil whale Perucetus colossus

Extremes in organismal size have broad interest in ecology and evolution because organismal size dictates many traits of an organism's biology. There is particular fascination with identifying upper size extremes in the largest vertebrates, given the challenges and difficulties of measuring extant and extinct candidates for the largest animal of all time, such as whales, terrestrial non-avian dinosaurs, and extinct marine reptiles. The discovery of Perucetus colossus, a giant basilosaurid whale from the Eocene of Peru, challenged many assumptions about organismal extremes based on reconstructions of its body weight that exceeded reported values for blue whales (Balaenoptera musculus). Here we present an examination of a series of factors and methodological approaches to assess reconstructing body weight in Perucetus, including: data sources from large extant cetaceans; fitting published body mass estimates to body outlines; testing the assumption of isometry between skeletal and body masses, even with extrapolation; examining the role of pachyostosis in body mass reconstructions; addressing method-dependent error rates; and comparing Perucetus with known physiological and ecological limits for living whales, and Eocene oceanic productivity. We conclude that Perucetus did not exceed the body mass of today's blue whales. Depending on assumptions and methods, we estimate that Perucetus weighed 60-70 tons assuming a length 17 m. We calculated larger estimates potentially as much as 98-114 tons at 20 m in length, which is far less than the direct records of blue whale weights, or the 270 ton estimates that we calculated for body weights of the largest blue whales measured by length.

Biology and Cultural Importance of the Narwhal

Though narwhal have survived multiple ice ages, including 2.5 Ma and the last interglacial period with warming temperatures, Arctic climate change during the Anthropocene introduces new challenges. Despite their evolutionary connection to Arctic Pleistocene fossils, narwhal archeocete ancestors from the Pliocene (Bohaskaia monodontoides) and Miocene (Denebola and Odobenocetopsidae) inhabited warm waters. Narwhal Arctic adaptation holds valuable insights into unique traits, including thin skin; extreme diving capacity; and a unique straight, spiraled, and sensory tooth organ system. Inaccessible weather, ice conditions, and darkness limit scientific studies, though Inuit knowledge adds valuable observations of narwhal ecology, biology, and behavior. Existing and future studies in myriad fields of physical, chemical, biological, and genetic science, combined and integrated with remote sensing and imaging technologies, will help elucidate narwhal evolution, biology, and adaptation. When integrated with Qaujimajatuqangit, "the Inuit way of knowing," these studies help describe interesting biologic expressions of the narwhal.

Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes

Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.

Drivers of morphological evolution in the toothed whale jaw

Toothed whales (odontocetes) emit high-frequency underwater sounds (echolocate)-an extreme and unique innovation allowing them to sense their prey and environment. Their highly specialized mandible (lower jaw) allows high-frequency sounds to be transmitted back to the inner ear. Echolocation is evident in the earliest toothed whales, but little research has focused on the evolution of mandibular form regarding this unique adaptation. Here, we use a high-density, three-dimensional geometric morphometric analysis of 100 living and extinct cetacean species spanning their ∼50-million-year evolutionary history. Our analyses demonstrate that most shape variation is found in the relative length of the jaw and the mandibular symphysis. The greatest morphological diversity was obtained during two periods of rapid evolution: the initial evolution of archaeocetes (stem whales) in the early to mid-Eocene as they adapted to an aquatic lifestyle, representing one of the most extreme adaptive transitions known, and later on in the mid-Oligocene odontocetes as they became increasingly specialized for a range of diets facilitated by increasingly refined echolocation. Low disparity in the posterior mandible suggests the shape of the acoustic window, which receives sound, has remained conservative since the advent of directional hearing in the aquatic archaeocetes, even as the earliest odontocetes began to receive sounds from echolocation. Diet, echolocation, feeding method, and dentition type strongly influence mandible shape. Unlike in the toothed whale cranium, we found no significant asymmetry in the mandible. We suggest that a combination of refined echolocation and associated dietary specializations have driven morphology and disparity in the toothed whale mandible.

Recent selection created distinctive variability patterns on MHC class II loci in three dolphin species from the Mediterranean Sea

The major histocompatibility complex (MHC) includes highly polymorphic genes involved in antigen presentation, which is crucial for adaptive immune response. They represent fitness related genetic markers particularly informative for populations exposed to environmental challenges. Here we analyse the diversity and evolutionary traits of MHC class II DQA and DQB genes in the dolphins Stenella coeruleoalba and Grampus griseus from the Mediterranean Sea. We found substantial nucleotide and functional diversity, as well as strong evidence of balancing selection indicated by allele and supertype frequencies, Tajima's D statistics and dN/dS tests. The Risso's dolphin, considered the least abundant in the region, showed the effect of divergent allele advantage at the nucleotide and functional-peptide levels. An outstanding polymorphism was found in the striped dolphin, particularly intriguing in the DQA gene where the Ewens-Watterson test detected a selection sweep that occurred in recent history. We hypothesize that morbillivirus, which has recurrently invaded Mediterranean populations over the last decades, exerted the detected selective pressure.

Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians

The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals.

Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials

The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.

Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.

Patterns of enrichment and acceleration in evolutionary rates of promoters suggest a role of regulatory regions in cetacean gigantism

BACKGROUND

Cetaceans (whales, porpoises, and dolphins) are a lineage of aquatic mammals from which some species became giants. Only recently, gigantism has been investigated from the molecular point of view. Studies focused mainly on coding regions, and no data on the influence of regulatory regions on gigantism in this group was available. Accordingly, we investigated the molecular evolution of non-coding regulatory regions of genes already described in the literature for association with size in mammals, focusing mainly on the promoter regions. For this, we used Ciiider and phyloP tools. Ciiider identifies significantly enriched transcription factor binding sites, and phyloP estimates the molecular evolution rate of the promoter.

RESULTS

We found evidence of enrichment of transcription binding factors related to large body size, with distinct patterns between giant and non-giant cetaceans in the IGFBP7 and NCAPG promoters, in which repressive agents are present in small cetaceans and those that stimulate transcription, in giant cetaceans. In addition, we found evidence of acceleration in the IGF2, IGFBP2, IGFBP7, and ZFAT promoters.

CONCLUSION

Our results indicate that regulatory regions may also influence cetaceans' body size, providing candidate genes for future research to understand the molecular basis of the largest living animals.

Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes

Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.

The better to eat you with: morphological disparity and enamel ultrastructure in odontocetes

Variations in the shape and size of teeth have been associated with changes in enamel ultrastructure across odontocetes. Characterizing these features in extinct taxa can elucidate their functional morphology and feeding strategy, while also shedding light into macroevolutionary patterns during the evolutionary history of cetaceans. This study aimed to (1) describe the enamel and dentine ultrastructure of the Early Miocene odontocetes Notocetus vanbenedeni and Phoberodon arctirostris from Patagonia (Argentina) and (2) quantify tooth and enamel ultrastructure morphological disparity among odontocetes. Enamel was predominantly prismatic, thin in the anterior tooth of N. vanbenedeni and P. arctirostris; whilst thick on the posterior tooth of N. vanbenedeni. Together with skull morphology, data suggests a raptorial feeding strategy for P. arctirostris and a combination suction feeding method for N. vanbenedeni. Statistical analyses supported these inferences, indicating that enamel characters are useful for paleoecological research. Morphological disparity analyses showed that extant odontocetes occupy a larger morphospace and have more disparate morphologies, whilst extinct odontocetes were more similar among each other than with the extant group. There was no clear phylogenetic-based grouping, suggesting that tooth and enamel ultrastructure disparity were mainly driven by ecological pressures. These results highlight enamel ultrastructure as a source for broader-scale paleoecological studies in cetaceans.

Cranial asymmetry in odontocetes: a facilitator of sonic exploration?

Directional cranial asymmetry is an intriguing condition that has evolved in all odontocetes which has mostly been associated with sound production for echolocation. In this study, we investigated how cranial asymmetry varies across odontocete species both in terms of quality (i.e., shape), and quantity (magnitude of deviation from symmetry). We investigated 72 species across all ten families of Odontoceti using two-dimensional geometric morphometrics. The average asymmetric shape was largely consistent across odontocetes - the rostral tip, maxillae, antorbital notches and braincase, as well as the suture crest between the frontal and interparietal bones were displaced to the right, whereas the nasal septum and premaxillae showed leftward shifts, in concert with an enlargement of the right premaxilla and maxilla. A clear phylogenetic signal related to asymmetric shape variation was identified across odontocetes using squared-change parsimony. The magnitude of asymmetry was widely variable across Odontoceti, with greatest asymmetry in Kogiidae, Monodontidae and Globicephalinae, followed by Physeteridae, Platanistidae and Lipotidae, while the asymmetry was lowest in Lissodelphininae, Phocoenidae, Iniidae and Pontoporiidae. Ziphiidae presented a wide spectrum of asymmetry. Generalized linear models explaining magnitude of asymmetry found associations with click source level while accounting for cranial size. Using phylogenetic generalized least squares, we reconfirm that source level and centroid size significantly predict the level of cranial asymmetry, with more asymmetric marine taxa generally consisting of bigger species emitting higher output sonar signal, i.e. louder sounds. Both characteristics theoretically support foraging at depth, the former by allowing extended diving and the latter being adaptive for prey detection at longer distances. Thus, cranial asymmetry seems to be an evolutionary pathway that allows odontocetes to devote more space for sound-generating structures associated with echolocation and thus increases biosonar search range and foraging efficiency beyond simple phylogenetic scaling predictions.

Homoplasy of Retrotransposon Insertions in Toothed Whales

Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18-0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal.

A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea

The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.

A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales

Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent- and identity-by-descent-based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne ) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome-wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome-wide datasets to help resolve long-standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long-term small Ne , low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps.

Evolution and development of the cetacean skull roof: a case study in novelty and homology

Skulls of living whales and dolphins (cetaceans) are telescoped-bones of the skull roof are overlapped by expanded facial bones and/or anteriorly extended occipital bones. Evolution of the underlying skull roof (calvarium), which lies between the telescoped regions, is relatively unstudied. We explore the evolution and development of the calvarium of toothed whales (odontocetes) by integrating fetal data with Oligocene odontocete fossils from North America, including eight neonatal and juvenile skulls of Olympicetus†. We identified two potential synapomorphies of crown Cetacea: contact of interparietals with frontals, and a single anterior median interparietal (AMI) element. Within Odontoceti, loss of contact between the parietals diagnoses the clade including Delphinida, Ziphiidae and Platanistidae (=Synrhina). Delphinida is characterized by a greatly enlarged interparietal. New fetal series of delphinoids reveal a consistent developmental pattern with three elements: the AMI and bilateral posterior interparietals (PIs). The PIs most resemble the medial interparietal elements of terrestrial artiodactyls, suggesting that the AMI of cetaceans could be a unique ossification. More broadly, the paucity of conserved anatomical relationships of the interparietals, as well as the fact that the elements often do not coalesce into a single bone, demonstrates that assessing homology of the interparietals across mammals remains challenging. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Testing heterochrony: Connecting skull shape ontogeny and evolution of feeding adaptations in baleen whales

Ontogeny plays a key role in the evolution of organisms, as changes during the complex processes of development can allow for new traits to arise. Identifying changes in ontogenetic allometry-the relationship between skull shape and size during growth-can reveal the processes underlying major evolutionary transformations. Baleen whales (Mysticeti, Cetacea) underwent major morphological changes in transitioning from their ancestral raptorial feeding mode to the three specialized filter-feeding modes observed in extant taxa. Heterochronic processes have been implicated in the evolution of these feeding modes, and their associated specialized cranial morphologies, but their role has never been tested with quantitative data. Here, we quantified skull shapes ontogeny and reconstructed ancestral allometric trajectories using 3D geometric morphometrics and phylogenetic comparative methods on sample representing modern mysticetes diversity. Our results demonstrate that Mysticeti, while having a common developmental trajectory, present distinct cranial shapes from early in their ontogeny corresponding to their different feeding ecologies. Size is the main driver of shape disparity across mysticetes. Disparate heterochronic processes are evident in the evolution of the group: skim feeders present accelerated growth relative to the ancestral nodes, while Balaenopteridae have overall slower growth, or pedomorphosis. Gray whales are the only taxon with a relatively faster rate of growth in this group, which might be connected to its unique benthic feeding strategy. Reconstructed ancestral allometries and related skull shapes indicate that extinct taxa used less specialized filter-feeding modes, a finding broadly in line with the available fossil evidence.

New heterodont odontocetes from the Oligocene Pysht Formation in Washington State, U.S.A., and a reevaluation of Simocetidae (Cetacea, Odontoceti)

Odontocetes first appeared in the fossil record by the early Oligocene, and their early evolutionary history can provide clues as to how some of their unique adaptations, such as echolocation, evolved. Here, three new specimens from the early to late Oligocene Pysht Formation are described further increasing our understanding of the richness and diversity of early odontocetes, particularly for the North Pacific. Phylogenetic analysis shows that the new specimens are part of a more inclusive, redefined Simocetidae, which now includes Simocetus rayi, Olympicetus sp. 1, Olympicetus avitus, O. thalassodon sp. nov., and a large unnamed taxon (Simocetidae gen. et sp. A), all part of a North Pacific clade that represents one of the earliest diverging groups of odontocetes. Amongst these, Olympicetus thalassodon sp. nov. represents one of the best known simocetids, offering new information on the cranial and dental morphology of early odontocetes. Furthermore, the inclusion of CCNHM 1000, here considered to represent a neonate of Olympicetus sp., as part of the Simocetidae, suggests that members of this group may not have had the capability of ultrasonic hearing, at least during their early ontogenetic stages. Based on the new specimens, the dentition of simocetids is interpreted as being plesiomorphic, with a tooth count more akin to that of basilosaurids and early toothed mysticetes, while other features of the skull and hyoid suggest various forms of prey acquisition, including raptorial or combined feeding in Olympicetus spp., and suction feeding in Simocetus. Finally, body size estimates show that small to moderately large taxa are present in Simocetidae, with the largest taxon represented by Simocetidae gen. et sp. A with an estimated body length of 3 m, which places it as the largest known simocetid, and amongst the largest Oligocene odontocetes. The new specimens described here add to a growing list of Oligocene marine tetrapods from the North Pacific, further promoting faunistic comparisons across other contemporaneous and younger assemblages, that will allow for an improved understanding of the evolution of marine faunas in the region.

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

Investigating the Relationship Between Body Shape and Life History Traits in Toothed Whales: Can Body Shape Predict Fast-Slow Life Histories?

A widespread pattern in vertebrate life-history evolution is for species to evolve towards either fast or slow life histories; however, the underlying causes of this pattern remain unclear. Toothed whales (Odontoceti) are a diverse group with a range of body sizes and life histories, making them an ideal model to investigate potential drivers of this dichotomy. Using ancestral reconstruction, we identified that certain groups of odontocetes evolved more-streamlined, presumably faster, body shapes around the same time that killer whales (Orcinus orca) evolved into whale predators approximately 1 Mya during the Pleistocene. This suggests that the evolution of a streamlined body shape may have been an adaptation to escape killer whale predation, leading to longer life-history events. To test this hypothesis, we performed a cluster analysis of odontocete whales and confirmed the dual pattern of life-history traits, with one group referred to as 'reproducers' characterized by early age of maturity, short gestation, short interbirth interval, and short lifespan, and the other group referred to as 'bet-hedgers' exhibiting the opposite pattern. However, we found that life history grouping was relatively unrelated to whale shape (i.e., more streamlined or less streamlined). Therefore, we incorporated principal component results into mixed effects models, and the model results indicated that body shape was positively related to neonate length (a measure of investment in progeny), but not significantly related to the temporal life-history traits. Thus, whale body shape is not a sufficient explanation for the evolution of fast-slow life histories in odontocete whales.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11692-023-09605-4.

Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

Potential new species of pseudaliid lung nematode (Metastrongyloidea) from two stranded neonatal orcas (Orcinus orca) characterized by ITS-2 and COI sequences

Knowledge about parasite species of orcas, their prevalence, and impact on the health status is scarce. Only two records of lungworm infections in orca exist from male neonatal orcas stranded in Germany and Norway. The nematodes were identified as Halocercus sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but morphological identification to species level remained impossible due to the fragile structure and ambiguous morphological features. Pseudaliid nematodes (Metastrongyloidea) are specific to the respiratory tract of toothed whales and are hypothesized to have become almost extinct in terrestrial mammals. Severe lungworm infections can cause secondary bacterial infections and bronchopneumonia and are a common cause of mortality in odontocetes. DNA isolations and subsequent sequencing of the rDNA ITS-2 and mtDNA COI revealed nucleotide differences between previously described Halocercus species from common dolphin (H. delphini) and harbor porpoises (H. invaginatus) that were comparatively analyzed, pointing toward a potentially new species of pseudaliid lungworm in orcas. New COI sequences of six additional metastrongyloid lungworms of seals and porpoises were derived to elucidate phylogenetic relationships and differences between nine species of Metastrongyloidea.

A genomic timescale for placental mammal evolution

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Anthropogenic litter in terrestrial flora and fauna: Is the situation as bad as in the ocean? A field study in Southern Germany on five meadows and 150 ruminants in comparison with marine debris

In contrast to the abundance of research on marine debris, terrestrial anthropogenic litter and its impacts are largely lacking scientific attention. Therefore, the main objective of the present study is to find out whether ingested litter produces pathological consequences to the health of domestic ruminants, as it does in their relatives in the ocean, the cetaceans. For this purpose, five meadows (49°18'N, 10°24'E) with a total survey area of 139,050 m² as well as the gastric content of 100 slaughtered cattle and 50 slaughtered sheep have been examined for persistent man-made debris in Northern Bavaria, Germany. All the five meadows contained garbage, and plastics were always part of it. Including glass and metal, 521 persistent anthropogenic objects were detected altogether, equalling a litter density of 3747 items per km². Of the examined animals, 30.0% of the cattle and 6.0% of the sheep harboured anthropogenic foreign bodies in their gastric tract. As in the case of cetaceans, plastics were the most dominant litter material. Bezoars had formed around plastic fibres of agricultural origin in two young bulls, whereas pointed metal objects were associated in cattle with traumatic lesions in the reticulum and the tongue. Of all the ingested anthropogenic debris, 24 items (26.4%) had direct equivalents in the studied meadows. Comparing with marine litter, 28 items (30.8%) were also present in marine environments and 27 items (29.7%) were previously reported as foreign bodies in marine animals. At least in this study region, waste pollution affected terrestrial environments and domestic animals, with clear equivalents in the marine world. Ingested foreign bodies produced lesions that may have reduced the animals' welfare and, regarding commercial purposes, their productivity.

The genome of the pygmy right whale illuminates the evolution of rorquals

BACKGROUND

Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales.

RESULTS

Here, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance.

CONCLUSIONS

Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.

Formation of a fringe: A look inside baleen morphology using a multimodal visual approach

Filter-feeding has been present for hundreds of millions of years, independently evolving in aquatic vertebrates' numerous times. Mysticete whales are a group of gigantic, marine filter-feeders that are defined by their fringed baleen and are divided into two groups: balaenids and rorquals. Recent studies have shown that balaenids likely feed using a self-cleaning, cross-flow filtration mechanism where food particles are collected and then swept to the esophagus for swallowing. However, it is unclear how filtering is achieved in the rorquals (Balaenopteridae). Lunging rorqual whales engulf enormous masses of both prey and water; the prey is then separated from the water through baleen plates lining the length of their upper jaw and positioned perpendicular to flow. Rorqual baleen is composed of both major (larger) and minor (smaller) keratin plates containing embedded fringe that extends into the whale's mouth, forming a filtering fringe. We used a multimodal approach, including microcomputed tomography (µCT) and scanning electron microscopy (SEM), to visualize and describe the variability in baleen anatomy across five species of rorqual whales, spanning two orders of magnitude in body length. For most morphological measurements, larger whales exhibited hypoallometry relative to body length. µCT and SEM revealed that the major and minor plates break away from the mineralized fringes at variable distances from the gums. We proposed a model for estimating the effective pore size to determine whether flow scales with body length or prey size across species. We found that pore size is likely not a proxy for prey size but instead, may reflect changes in resistance through the filter that affect fluid flow.

Molecular phylogeny of the Pseudaliidae (Nematoda) and the origin of associations between lungworms and marine mammals

Metastrongyloid lungworms from the family Pseudaliidae infect the lungs and cranial sinuses of cetaceans worldwide, except Stenuroides herpestis, which exhibits a striking terrestrial association with the Egyptian mongoose, Herpestes ichneumon. Previous phylogenies of the Metastrongyloidea that included some (2-7) marine species of the Pseudaliidae confirmed that these species are closely related, but also grouped species of Parafilaroides (family Filaroididae) between the members of the Pseudaliidae. In this study we extracted DNA from representatives of all six genera of the Pseudaliidae and amplified the second internal transcribed spacer (ITS2) and cytochrome c oxidase subunit I (cox1) genes in order to investigate the concept of the Pseudaliidae as a monophyletic unit. Three species of Parafilaroides were also included in the analysis. Maximum Likelihood and Bayesian Inference analyses of the concatenated genes resulted in a well-supported clade including the marine pseudaliids, S. herpestis and Parafilaroides spp. These findings validate the status of S. herpestis as a pseudaliid species and support the inclusion of Parafilaroides in the Pseudaliidae. Although males of Parafilaroides spp. lack a copulatory bursa, this trait itself is highly variable in the Pseudaliidae, which include abursate species. Furthermore, life cycles seem to be closely similar between both taxa. When all the available phylogenetic data on the Metastrongyloidea were mapped of onto a phylogeny of the Laurasiatheria, there was a strong suggestion that the Pseudaliidae may have descended from ancestors infecting terrestrial carnivores, with odontocetes being colonized in the marine realm as a result of a host-switching event from pinnipeds through shared fish prey. The origin of the association between S. herpestis and mongooses remains uncertain.

An Early Miocene kentriodontoid (Cetacea: Odontoceti) from the western North Pacific, and its implications for their phylogeny and paleobiogeography

So-called 'kentriodontids' are extinct dolphin-like odontocetes known from the Early to Late Miocene worldwide. Although recent studies have proposed that they were monophyletic, their taxonomic relationships still remain controversial. Such a controversy exists partly because of the predominance of primitive morphologies in this taxon, but the fact is that quite a few 'kentriodontids' are known only from fragmentary skulls and/or isolated periotics. A new 'kentriodontid' Platysvercus ugonis gen. et sp. nov. is described based on a nearly complete skull from the upper Lower Miocene Sugota Formation, Akita Prefecture, northern Japan. Based on the phylogenetic analysis of P. ugonis described here, the monophyly of the 'kentriodontids' is confirmed, and it is recognized as the superfamily Kentriodontoidea. This new superfamily is subdivided into two families as new ranks: Kentriodontidae and Lophocetidae. Based on the paleobiogeographic analysis of the Kentriodontoidea, their common ancestor emerged in the North Pacific Ocean and spread over the Northern Hemisphere. Initial diversification of the Kentriodontidae in the North Pacific Ocean and the Lophocetidae in the North Atlantic Ocean was recognized as a vicariance event. The diversification and extinction of the Kentriodontoidea could have been synchronously influenced by climate events during the Middle Miocene.

The prevalence of vestigial teeth in two beaked whale species from the North Atlantic

Beaked whales, Family Ziphiidae, occur in deep offshore and oceanic seas, where they are very difficult to study, so that much of our knowledge about them is derived from stranded animals. Most beaked whales (e.g., genera Mesoplodon and Ziphius) have only one pair of mandibular teeth. A reduced dentition is widely regarded as an adaptation to suction feeding, primarily on squid. However, vestigial maxillary and mandibular teeth have been recorded in some species. Here, we describe new records of vestigial teeth in 12 Sowerby’s beaked whales, Mesoplodon bidens, and one Cuvier’s beaked whale, Ziphius cavirostris, from a total 14 animals of these species, which stranded in 2019–2021 in Scotland. In nine M. bidens some tooth crowns were erupted and mild occlusal wear was visible, whereas pathological teeth were seen in ten individuals. The occurrence of vestigial teeth in Sowerby’s beaked whale appears to be significantly under-recorded, suggesting that vestigial teeth form as part of the normal development of the dentition. The reasons for the under-recording of the occurrence and the possible functionality of vestigial teeth in ziphiids are discussed.

The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism

Cetaceans are a group of aquatic mammals with the largest body sizes among living animals, including giant representatives such as blue and fin whales. To understand the genetic bases of gigantism in cetaceans, we performed molecular evolutionary analyses on five genes (GHSR, IGF2, IGFBP2, IGFBP7, and EGF) from the growth hormone/insulin-like growth factor axis, and four genes (ZFAT, EGF, LCORL, and PLAG1) previously described as related to the size of species evolutionarily close to cetaceans, such as pigs, cows, and sheep. Our dataset comprised 19 species of cetaceans, seven of which are classified as giants because they exceed 10 m in length. Our results revealed signs of positive selection in genes from the growth hormone/insulin-like growth factor axis and also in those related to body increase in cetacean-related species. In addition, pseudogenization of the EGF gene was detected in the lineage of toothless cetaceans, Mysticeti. Our results suggest the action of positive selection on gigantism in genes that act both in body augmentation and in mitigating its consequences, such as cancer suppression when involved in processes such as division, migration, and cell development control.

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

Despite the fact that cetaceans provide significant ecological contributions to the health and stability of aquatic ecosystems, many 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 squares 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 threatened status 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.

Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling

Computing distance between two genomes without alignments or even access to assemblies has many downstream analyses. However, alignment-free methods, including in the fast-growing field of genome skimming, are hampered by a significant methodological gap. While accurate methods (many k-mer-based) for assembly-free distance calculation exist, measuring the uncertainty of estimated distances has not been sufficiently studied. In this paper, we show that bootstrapping, the standard non-parametric method of measuring estimator uncertainty, is not accurate for k-mer-based methods that rely on k-mer frequency profiles. Instead, we propose using subsampling (with no replacement) in combination with a correction step to reduce the variance of the inferred distribution. We show that the distribution of distances using our procedure matches the true uncertainty of the estimator. The resulting phylogenetic support values effectively differentiate between correct and incorrect branches and identify controversial branches that change across alignment-free and alignment-based phylogenies reported in the literature.

Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees

Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive to hard-to-avoid errors introduced in the gene tree estimation step. This dilemma has created much debate on the merits of concatenation versus summary methods and practical obstacles to using summary methods more widely and to the exclusion of concatenation. The most successful attempt at making summary methods resilient to noisy gene trees has been contracting low support branches from the gene trees. Unfortunately, this approach requires arbitrary thresholds and poses new challenges. Here, we introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the unweighted ASTRAL. Our simulations show that weighting improves accuracy across many conditions and reduces the gap with concatenation in conditions with low gene tree discordance and high noise. On empirical data, weighting improves congruence with concatenation and increases support. Together, our results show that weighting, enabled by a new optimization algorithm we introduce, improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines.

The ontogeny of asymmetry in echolocating whales

Extreme asymmetry of the skull is one of the most distinctive traits that characterizes toothed whales (Odontoceti, Cetacea). The origin and function of cranial asymmetry are connected to the evolution of echolocation, the ability to use high-frequency sounds to navigate the surrounding environment. Although this novel phenotype must arise through changes in cranial development, the ontogeny of cetacean asymmetry has never been investigated. Here we use three-dimensional geometric morphometrics to quantify the changes in degree of asymmetry and skull shape during prenatal and postnatal ontogeny for five genera spanning odontocete diversity (oceanic dolphins, porpoises and beluga). Asymmetry in early ontogeny starts low and tracks phylogenetic relatedness of taxa. Distantly related taxa that share aspects of their ecology overwrite these initial differences via heterochronic shifts, ultimately converging on comparable high levels of skull asymmetry. Porpoises maintain low levels of asymmetry into maturity and present a decelerated rate of growth, probably retained from the ancestral condition. Ancestral state reconstruction of allometric trajectories demonstrates that both paedomorphism and peramorphism contribute to cranial shape diversity across odontocetes. This study provides a striking example of how divergent developmental pathways can produce convergent ecological adaptations, even for some of the most unusual phenotypes exhibited among vertebrates.

How low can you go? Introducing SeXY: sex identification from low-quantity sequencing data despite lacking assembled sex chromosomes

Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex‐identification pipeline, for very low‐coverage shotgun sequencing data from a single individual. SeXY was designed to utilize low‐effort screening data for sex identification and does not require a conspecific sex‐chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1000 mapped reads and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high‐quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1000 mapped reads. For lower‐quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1000 mapped reads in many cases.

Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean

The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.