Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity

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.

Redescription of three fossil baleen whale skulls from the Miocene of Portugal reveals new cetotheriid phylogenetic insights

Cetotheriidae is a family of baleen whales that went nearly extinct during the Pleistocene (excluding Caperea marginata). For a long time, the Cetotheriidae family has been seen as a problematic clade, but in the past two decades there have been various studies trying to resolve the phylogeny of this group. In 1831, Alexandre Vandelli described three cetotheriid skulls, found during a gold exploration at Adiça beach (Portugal). These specimens constituted the first Portuguese vertebrate fossils ever published in the literature. Another skull was added to the "Vandelli skulls" by Jacinto Pedro Gomes, in 1914, during a survey of the Museu Nacional de História Natural collections without giving information on the origin of this skull. In 1941, Remington Kellogg states that one of the original "Vandelli skulls" is no longer present in the Museu Nacional de História Natural collections. Until today, there is no information on how, or exactly when, the fourth skull and one of the original three "Vandelli skulls" appeared and disappeared, respectively. Since their discovery, all the attempts to describe these specimens were not based on direct observations and no comprehensive phylogenetic analysis have included the three skulls. Here we provide a detailed anatomic description, a new phylogenetic analysis and a palaeoecological reconstruction of these specimens, clarifying their relationships within the Cetotheriidae family and fostering the importance of these historical specimens to the modern comprehension of fossil whale evolution. In addition, our results support that Cephalotropis nectus is a valid species with an emended diagnosis. We also concluded that two specimens belong to a new genus, forming two new fossil species (new combinations).

Giant baleen whales emerged from a cold southern cradle

Baleen whales (mysticetes) include the largest animals on the Earth. How they achieved such gigantic sizes remains debated, with previous research focusing primarily on when mysticetes became large, rather than where. Here, we describe an edentulous baleen whale fossil (21.12-16.39 mega annum (Ma)) from South Australia. With an estimated body length of 9 m, it is the largest mysticete from the Early Miocene. Analysing body size through time shows that ancient baleen whales from the Southern Hemisphere were larger than their northern counterparts. This pattern seemingly persists for much of the Cenozoic, even though southern specimens contribute only 19% to the global mysticete fossil record. Our findings contrast with previous ideas of a single abrupt shift towards larger size during the Plio-Pleistocene, which we here interpret as a glacially driven Northern Hemisphere phenomenon. Our results highlight the importance of incorporating Southern Hemisphere fossils into macroevolutionary patterns, especially in light of the high productivity of Southern Ocean environments.

The Deep Past of the White Shark, Carcharodon carcharias, in the Mediterranean Sea: A Synthesis of Its Palaeobiology and Palaeoecology

The white shark, Carcharodon carcharias, is the main top predator of the present-day Mediterranean Sea. The deep past of C. carcharias in the Mediterranean is witnessed by a rather conspicuous, mostly Pliocene fossil record. Here, we provide a synthesis of the palaeobiology and palaeoecology of the Mediterranean white sharks. Phenetically modern white shark teeth first appeared around the Miocene-Pliocene transition in the Pacific, and soon after in the Mediterranean. Molecular phylogenetic analyses support an origin of the Mediterranean white shark population from the dispersal of Australian/Pacific palaeopopulations, which may have occurred through the Central American Seaway. Tooth dimensions suggest that the Mediterranean white sharks could have grown up to about 7 m total length during the Pliocene. A richer-than-today marine mammal fauna was likely pivotal in supporting the Mediterranean white sharks through the Pliocene and most of the Quaternary. White sharks have seemingly become more common as other macropredators declined and disappeared, notwithstanding the concurrent demise of many potential prey items in the context of the latest Pliocene and Quaternary climatic and environmental perturbations of the Mediterranean region. The overall generalist trophic habits of C. carcharias were likely crucial for securing ecological success in the highly variable Mediterranean scenario by allowing the transition to a mostly piscivorous diet as the regional marine mammal fauna shrank.

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.

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.

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.

Ecomorphology of toothed whales (Cetacea, Odontoceti) as revealed by 3D skull geometry

Extant odontocetes (toothed whales) exhibit differences in body size and brain mass, biosonar mode, feeding strategies, and diving and habitat adaptations. Strong selective pressures associated with these factors have likely contributed to the morphological diversification of their skull. Here, we used 3D landmark geometric morphometric data from the skulls of 60 out of ~ 72 extant odontocete species and a well-supported phylogenetic tree to test whether size and shape variation are associated with ecological adaptations at an interspecific scale. Odontocete skull morphology exhibited a significant phylogenetic signal, with skull size showing stronger signal than shape. After accounting for phylogeny, significant associations were detected between skull size and biosonar mode, body length, brain and body mass, maximum and minimum prey size, and maximum peak frequency. Brain mass was also strongly correlated with skull shape together with surface temperature and average and minimum prey size. When asymmetric and symmetric components of shape were analysed separately, a significant correlation was detected between sea surface temperature and both symmetric and asymmetric components of skull shape, and between diving ecology and the asymmetric component. Skull shape variation of odontocetes was strongly influenced by evolutionary allometry but most of the associations with ecological variables were not supported after phylogenetic correction. This suggests that ecomorphological feeding adaptations vary more between, rather than within, odontocete families, and functional anatomical patterns across odontocete clades are canalised by size constraints.

Rostrum morphology and feeding strategy of the baleen whale indicate that right whales and pygmy right whales became skimmers independently

Baleen whales have lost their functional teeth and begun to use their baleen plates to feed on small prey. Modern baleen whales exhibit different types of feeding strategies, such as lunging, skimming and so on. The evolution of feeding strategy in the Chaeomysticeti is an important step in considering niche partitioning and diversification, feeding efficiency and gigantism, and evolution and extinction. This study analyses the rostrum morphology to test the hypothesis that specific rostral morphologies facilitate special feeding strategies, using modern species and their observed feeding strategies. By this means, the convergence of rostral morphology can be recognized in the closest groups in the morphospace. As a result, the two linages (Balaenidae and Caperea marginata) are recognized to have convergent rostral morphology. In addition, an early member of the Chaeomysticeti, Yamatocetus canaliculatus, and most fossil species are plotted in or close to the cluster of lunge feeders. The original feeding strategy of the Chaeomysticeti could be more similar to lunge feeding than to skim feeding. Fossil relatives of the two linages showing transitional conditions indicate that they shifted to skim feeding independently. The evolution of the feeding strategy of the Chaeomysticeti is possibly more complex than that was thought.

Attenuated evolution of mammals through the Cenozoic

The Cenozoic diversification of placental mammals is the archetypal adaptive radiation. Yet, discrepancies between molecular divergence estimates and the fossil record fuel ongoing debate around the timing, tempo, and drivers of this radiation. Analysis of a three-dimensional skull dataset for living and extinct placental mammals demonstrates that evolutionary rates peak early and attenuate quickly. This long-term decline in tempo is punctuated by bursts of innovation that decreased in amplitude over the past 66 million years. Social, precocial, aquatic, and herbivorous species evolve fastest, especially whales, elephants, sirenians, and extinct ungulates. Slow rates in rodents and bats indicate dissociation of taxonomic and morphological diversification. Frustratingly, highly similar ancestral shape estimates for placental mammal superorders suggest that their earliest representatives may continue to elude unequivocal identification.

Trophic position of Otodus megalodon and great white sharks through time revealed by zinc isotopes

Diet is a crucial trait of an animal's lifestyle and ecology. The trophic level of an organism indicates its functional position within an ecosystem and holds significance for its ecology and evolution. Here, we demonstrate the use of zinc isotopes (δ⁶⁶Zn) to geochemically assess the trophic level in diverse extant and extinct sharks, including the Neogene megatooth shark (Otodus megalodon) and the great white shark (Carcharodon carcharias). We reveal that dietary δ⁶⁶Zn signatures are preserved in fossil shark tooth enameloid over deep geologic time and are robust recorders of each species' trophic level. We observe significant δ⁶⁶Zn differences among the Otodus and Carcharodon populations implying dietary shifts throughout the Neogene in both genera. Notably, Early Pliocene sympatric C. carcharias and O. megalodon appear to have occupied a similar mean trophic level, a finding that may hold clues to the extinction of the gigantic Neogene megatooth shark.

The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution, these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate the past number of lineages. Here, we present new methodological developments around the fossilized birth–death process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]

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

[Figure: see text].

Vertebrate Palaeoecology of the Pisco Formation (Miocene, Peru): Glimpses into the Ancient Humboldt Current Ecosystem

The northward-flowing Humboldt Current hosts perpetually high levels of productivity along the western coast of South America. Here, we aim to elucidate the deep-time history of this globally important ecosystem based on a detailed palaeoecological analysis of the exceptionally preserved middle–upper Miocene vertebrate assemblages of the Pisco Formation of the East Pisco Basin, southern Peru. We summarise observations on hundreds of fossil whales, dolphins, seals, seabirds, turtles, crocodiles, sharks, rays, and bony fishes to reconstruct ecological relationships in the wake of the Middle Miocene Climatic Optimum, and the marked cooling that followed it. The lowermost, middle Miocene Pisco sequence (P0) and its vertebrate assemblage testify to a warm, semi-enclosed, near-shore palaeoenvironment. During the first part of the Tortonian (P1), high productivity within a prominent upwelling system supported a diverse assemblage of mesopredators, at least some of which permanently resided in the Pisco embayment and used it as a nursery or breeding/calving area. Younger portions of the Pisco Formation (P2) reveal a more open setting, with wide-ranging species like rorquals increasingly dominating the vertebrate assemblage, but also local differences reflecting distance from the coast. Like today, these ancient precursors of the modern Humboldt Current Ecosystem were based on sardines, but notably differed from their present-day equivalent in being dominated by extremely large-bodied apex predators like Livyatan melvillei and Carcharocles megalodon.

Revisiting the sedimentary record of the rise of diatoms

Diatoms are a major primary producer in the modern oceans and play a critical role in the marine silica cycle. Their rise to dominance is recognized as one of the largest shifts in Cenozoic marine ecosystems, but the timing of this transition is debated. Here, we use a diagenetic model to examine the effect of sedimentation rate and temperature on the burial efficiency of biogenic silica over the past 66 million years (i.e., the Cenozoic). We find that the changing preservation potential of siliceous microfossils during that time would have overprinted the primary signal of diatom and radiolarian abundance. We generate a taphonomic null hypothesis of the diatom fossil record by assuming a constant flux of diatoms to the sea floor and having diagenetic conditions driven by observed shifts in temperature and sedimentation rate. This null hypothesis produces a late Cenozoic (∼5 Ma to 20 Ma) increase in the relative abundance of fossilized diatoms that is comparable to current empirical records. This suggests that the observed increase in diatom abundance in the sedimentary record may be driven by changing preservation potential. A late Cenozoic rise in diatoms has been causally tied to the rise of grasslands and baleen whales and to declining atmospheric CO₂ levels. Here we suggest that the similarity among these records primarily arises from a common driver-the cooling climate system-that drove enhanced diatom preservation as well as the rise of grasslands and whales, rather than a causal link among them.

An early Miocene extinction in pelagic sharks

Shark populations have been decimated in recent decades because of overfishing and other anthropogenic stressors; however, the long-term impacts of such changes in marine predator abundance and diversity are poorly constrained. We present evidence for a previously unknown major extinction event in sharks that occurred in the early Miocene, ~19 million years ago. During this interval, sharks virtually disappeared from open-ocean sediments, declining in abundance by >90% and morphological diversity by >70%, an event from which they never recovered. This abrupt extinction occurred independently from any known global climate event and ~2 million to 5 million years before diversifications in the highly migratory, large-bodied predators that dominate pelagic ecosystems today, indicating that the early Miocene was a period of rapid, transformative change for open-ocean ecosystems.

Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Extant baleen whales (Mysticeti) have a deciduous foetal dentition, but are edentulous at birth. Fossils reveal that the earliest mysticetes possessed an adult dentition. Aetiocetids, a diverse clade of Oligocene toothed mysticetes, have a series of small palatal foramina and associated sulci medial to the postcanine dentition. The openings have been homologized with lateral palatal foramina that transmit neurovascular structures to baleen in extant mysticetes, thereby implying a co-occurrence of teeth and baleen in aetiocetids. However, homology of the foramina and sulci have been questioned. Using CT-imaging, we report that the lateral palatal foramina of Aetiocetus weltoni are connected internally to the superior alveolar canal, which transmits neurovascular structures to baleen in extant mysticetes and to teeth in extant odontocetes. Furthermore, the lateral palatal foramina of Aetiocetus are separate from the more medially positioned canals for the greater palatine arterial system. These results provide critical evidence to support the hypothesis that the superior alveolar neurovasculature was co-opted in aetiocetids and later diverging mysticetes to serve a new function associated with baleen. We evaluate competing hypotheses for the transition from teeth to baleen, and explore the transition from raptorial feeding in early mysticetes to filter-feeding in extant species.

Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation

Understanding the origin, expansion and loss of biodiversity is fundamental to evolutionary biology. The approximately 26 living species of crocodylomorphs (crocodiles, caimans, alligators and gharials) represent just a snapshot of the group's rich 230-million-year history, whereas the fossil record reveals a hidden past of great diversity and innovation, including ocean and land-dwelling forms, herbivores, omnivores and apex predators. In this macroevolutionary study of skull and jaw shape disparity, we show that crocodylomorph ecomorphological variation peaked in the Cretaceous, before declining in the Cenozoic, and the rise and fall of disparity was associated with great heterogeneity in evolutionary rates. Taxonomically diverse and ecologically divergent Mesozoic crocodylomorphs, like marine thalattosuchians and terrestrial notosuchians, rapidly evolved novel skull and jaw morphologies to fill specialized adaptive zones. Disparity in semi-aquatic predatory crocodylians, the only living crocodylomorph representatives, accumulated steadily, and they evolved more slowly for most of the last 80 million years, but despite their conservatism there is no evidence for long-term evolutionary stagnation. These complex evolutionary dynamics reflect ecological opportunities, that were readily exploited by some Mesozoic crocodylomorphs but more limited in Cenozoic crocodylians.

What are the limits on whale ear bone size? Non-isometric scaling of the cetacean bulla

The history of cetaceans demonstrates dramatic macroevolutionary changes that have aided their transformation from terrestrial to obligate aquatic mammals. Their fossil record shows extensive anatomical modifications that facilitate life in a marine environment. To better understand the constraints on this transition, we examined the physical dimensions of the bony auditory complex, in relation to body size, for both living and extinct cetaceans. We compared the dimensions of the tympanic bulla, a conch-shaped ear bone unique to cetaceans, with bizygomatic width—a proxy for cetacean body size. Our results demonstrate that cetacean ears scale non-isometrically with body size, with about 70% of variation explained by increases in bizygomatic width. Our results, which encompass the breadth of the whale fossil record, size diversity, and taxonomic distribution, suggest that functional auditory capacity is constrained by congruent factors related to cranial morphology, as opposed to allometrically scaling with body size.

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

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

The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]

Taxon incompleteness and discrete time bins affect character change rates in simulated data

Estimating how fast or slow morphology evolves through time (phenotypic change rate, PR) has become common in macroevolutionary studies and has been important for clarifying key evolutionary events. However, the inclusion of incompletely scored taxa (e.g. fossils) and variable lengths of discrete arbitrary time bins could affect PR estimates and potentially mask real PR patterns. Here, the impact of taxon incompleteness (unscored data) on PR estimates is assessed in simulated data. Three different time bin series were likewise evaluated: bins evenly spanning the tree length (i), a shorter middle bin and longer first and third bins (ii), and a longer middle bin and shorter first and third bins (iii). The results indicate that PR values decrease as taxon incompleteness increases. Statistically significant PR values, and the dispersion among PR values, depended on the time bins. These outcomes imply that taxon incompleteness can undermine our capacity to infer morphology evolutionary dynamics and that these estimates are also influenced by our choice of discrete time bins. More importantly, the present results stress the need for a better approach to deal with taxon incompleteness and arbitrary discrete time bins.

A new large-bodied Pliocene seal with unusual cutting teeth

Today, monachine seals display the largest body sizes in pinnipeds. However, the evolution of larger body sizes has been difficult to assess due to the murky taxonomic status of fossil seals, including fossils referred to Callophoca obscura, a species thought to be present on both sides of the North Atlantic during the Neogene. Several studies have recently called into question the taxonomic validity of these fossils, especially those from the USA, as the fragmentary lectotype specimen from Belgium is of dubious diagnostic value. We find that the lectotype isolated humerus of C. obscura is too uninformative; thus, we designate C. obscura as a nomen dubium. More complete cranial and postcranial specimens from the Pliocene Yorktown Formation are described as a new taxon, Sarcodectes magnus. The cranial specimens display adaptations towards an enhanced ability to cut or chew prey that are unique within Phocidae, and estimates indicate S. magnus to be around 2.83 m in length. A parsimony phylogenetic analysis found S. magnus is a crown monachine. An ancestral state estimation of body length indicates that monachines did not have a remarkable size increase until the evolution of the lobodontins and miroungins.

Does evolution of echolocation calls and morphology in Molossus result from convergence or stasis?

Although many processes of diversification have been described to explain variation of morphological traits within clades that have obvious differentiation among taxa, not much is known about these patterns in complexes of cryptic species. Molossus is a genus of bats that is mainly Neotropical, occurring from the southeastern United States to southern Argentina, including the Caribbean islands. Molossus comprises some groups of species that are morphologically similar but phylogenetically divergent, and other groups of species that are genetically similar but morphologically distinct. This contrast allows investigation of unequal trait diversification and the evolution of morphological and behavioural characters. In this study, we assessed the role of phylogenetic history in a genus of bat with three cryptic species complexes, and evaluated if morphology and behavior are evolving concertedly. The Genotype by Sequence genomic approach was used to build a species-level phylogenetic tree for Molossus and to estimate the ancestral states of morphological and echolocation call characters. We measured the correlation of phylogenetic distances to morphological and echolocation distances, and tested the relationship between morphology and behavior when the effect of phylogeny is removed. Morphology evolved via a mosaic of convergence and stasis, whereas call design was influenced exclusively through local adaptation and convergent evolution. Furthermore, the frequency of echolocation calls is negatively correlated with the size of the bat, but other characters do not seem to be evolving in concert. We hypothesize that slight variation in both morphology and behaviour among species of the genus might result from niche specialization, and that traits evolve to avoid competition for resources in similar environments.

Colonization of the ancient southern oceans by small-sized Phocidae: new evidence from Australia

Most of the diversity of extant southern true seals (Phocidae: Monachinae) is present in the Southern Ocean, but a poor fossil record means that the origin of this fauna remains unknown. Australia represents a large gap in the record bordering the Southern Ocean that could possibly inform on the origins of the extant Antarctic monachines, with most known fossils remaining undescribed. Here we describe the oldest Australian fossil pinniped assemblage, from the Late Miocene to the Early Pliocene of Beaumaris. Two fossils are referrable to Pinnipedia, five (possibly six) to Phocidae and a humerus is referrable to Monachinae. The humerus is not referrable to any extant tribe, potentially representing an archaic monachine. The description of this assemblage is consistent with the Neogene pinniped fauna of Australia being exclusively monachine before the arrival of otariids (fur seals and sea lions). The Beaumaris humerus, along with other Neogene phocids from the Southern Ocean margins, were smaller than their extant Antarctic relatives, possibly driven by longer food chains with less energy efficiency between trophic levels. This suggests that small archaic phocids potentially used the Southern Ocean as a means of dispersal before the arrival of extant Antarctic monachines.

Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.].

Wonky whales: the evolution of cranial asymmetry in cetaceans

BACKGROUND

Unlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earliest diverging odontocetes. Early cetaceans (whales, dolphins, and porpoises) such as archaeocetes, namely the protocetids and basilosaurids, have asymmetric rostra, but it is unclear when nasofacial asymmetry evolved during the transition from archaeocetes to modern whales. We used three-dimensional geometric morphometrics and phylogenetic comparative methods to reconstruct the evolution of asymmetry in the skulls of 162 living and extinct cetaceans over 50 million years.

RESULTS

In archaeocetes, we found asymmetry is prevalent in the rostrum and also in the squamosal, jugal, and orbit, possibly reflecting preservational deformation. Asymmetry in odontocetes is predominant in the nasofacial region. Mysticetes (baleen whales) show symmetry similar to terrestrial artiodactyls such as bovines. The first significant shift in asymmetry occurred in the stem odontocete family Xenorophidae during the Early Oligocene. Further increases in asymmetry occur in the physeteroids in the Late Oligocene, Squalodelphinidae and Platanistidae in the Late Oligocene/Early Miocene, and in the Monodontidae in the Late Miocene/Early Pliocene. Additional episodes of rapid change in odontocete skull asymmetry were found in the Mid-Late Oligocene, a period of rapid evolution and diversification. No high-probability increases or jumps in asymmetry were found in mysticetes or archaeocetes. Unexpectedly, no increases in asymmetry were recovered within the highly asymmetric ziphiids, which may result from the extreme, asymmetric shape of premaxillary crests in these taxa not being captured by landmarks alone.

CONCLUSIONS

Early ancestors of living whales had little cranial asymmetry and likely were not able to echolocate. Archaeocetes display high levels of asymmetry in the rostrum, potentially related to directional hearing, which is lost in early neocetes-the taxon including the most recent common ancestor of living cetaceans. Nasofacial asymmetry becomes a significant feature of Odontoceti skulls in the Early Oligocene, reaching its highest levels in extant taxa. Separate evolutionary regimes are reconstructed for odontocetes living in acoustically complex environments, suggesting that these niches impose strong selective pressure on echolocation ability and thus increased cranial asymmetry.

Was the Devonian placoderm Titanichthys a suspension feeder?

Large nektonic suspension feeders have evolved multiple times. The apparent trend among apex predators for some evolving into feeding on small zooplankton is of interest for understanding the associated shifts in anatomy and behaviour, while the spatial and temporal distribution gives clues to an inherent relationship with ocean primary productivity and how past and future perturbations to these may impact on the different tiers of the food web. The evolution of large nektonic suspension feeders-'gentle giants'-occurred four times among chondrichthyan fishes (e.g. whale sharks, basking sharks and manta rays), as well as in baleen whales (mysticetes), the Mesozoic pachycormid fishes and at least twice in radiodontan stem group arthropods (Anomalocaridids) during the Cambrian explosion. The Late Devonian placoderm Titanichthys has tentatively been considered to have been a megaplanktivore, primarily due to its gigantic size and narrow, edentulous jaws while no suspension-feeding apparatus have ever been reported. Here, the potential for microphagy and other feeding behaviours in Titanichthys is assessed via a comparative study of jaw mechanics in Titanichthys and other placoderms with presumably differing feeding habits (macrophagy and durophagy). Finite-element models of the lower jaws of Titanichthys termieri in comparison to Dunkleosteus terrelli and Tafilalichthys lavocati reveal considerably less resistance to von Mises stress in this taxon. Comparisons with a selection of large-bodied extant taxa of similar ecological diversity reveal similar disparities in jaw stress resistance. Our results, therefore, conform to the hypothesis that Titanichthys was a suspension feeder with jaws ill-suited for biting and crushing but well suited for gaping ram feeding.

A new member of fossil balaenid (Mysticeti, Cetacea) from the early Pliocene of Hokkaido, Japan

The family Balaenidae includes two genus and four extant species. Extinct balaenids are known for at least four genus and 10 species. The oldest known record of members of the Balaenidae is known from the early Miocene, but still need more early members of the family to provide better phylogenetic hypotheses. FCCP 1049 from the lower part of the Chippubetsu Formation, Fukagawa Group (3.5-5.2 Ma, Zanclean, early Pliocene) was preliminary described and identified as Balaenula sp. by Furusawa and Kimura in 1982. Later works discussed that FCCP 1049 is different from the genus, and is placed in different clade from Balaenula astensis. The result of our phylogenetic analysis places FCCP 1049 basal to Balaenella brachyrhynus, and is again separated from B. astensis. In this study, FCCP 1049 is re-described and named as Archaeobalaena dosanko gen. et sp. nov. Archaeobalaena dosanko is distinguishable from other balaenids by having a deep promontorial groove of the pars cochlearis of the periotic. Archaeobalaena dosanko can be differentiated from other balaenids, except Morenocetus parvus by having a slender zygomatic process, and posteriorly oriented postorbital process in dorsal view. Archaeobalaena dosanko adds detailed skull, periotic and bulla morphologies for the earlier balaenids.

Extensive Diversity and Disparity of the Early Miocene Platanistoids (Cetacea, Odontoceti) in the Southeastern Pacific (Chilcatay Formation, Peru)

Several aspects of the fascinating evolutionary history of toothed and baleen whales (Cetacea) are still to be clarified due to the fragmentation and discontinuity (in space and time) of the fossil record. Here we open a window on the past, describing a part of the extraordinary cetacean fossil assemblage deposited in a restricted interval of time (19–18 Ma) in the Chilcatay Formation (Peru). All the fossils here examined belong to the Platanistoidea clade as here redefined, a toothed whale group nowadays represented only by the Asian river dolphin Platanista gangetica. Two new genera and species, the hyper-longirostrine Ensidelphis riveroi and the squalodelphinid Furcacetus flexirostrum, are described together with new material referred to the squalodelphinid Notocetus vanbenedeni and fragmentary remains showing affinities with the platanistid Araeodelphis. Our cladistic analysis defines the new clade Platanidelphidi, sister-group to Allodelphinidae and including E. riveroi and the clade Squalodelphinidae + Platanistidae. The fossils here examined further confirm the high diversity and disparity of platanistoids during the early Miocene. Finally, morphofunctional considerations on the entire platanistoid assemblage of the Chilcatay Formation suggest a high trophic partitioning of this peculiar cetacean paleocommunity.

A right whale (Mysticeti, Balaenidae) from the Pleistocene of Taiwan

Current patterns of biological distribution result from the deep past. Of particular interest, some closely related species appear at high latitudes of both hemispheres, but not in between, a pattern known as antitropical distribution. However, the timing, pathway, and drivers of antitropical distributions remain mostly unknown. Here we describe a new fossil, a left tympanic bulla (part of the ear bones), from the Middle/Late Pleistocene (0.78-0.01 mya, but not excluding the possibility of Holocene in age, as the specimen was dredged from the sea bottom and the geological horizon remains uncertain) of Taiwan. The tympanic bulla is diagnostic in baleen whales, and this specimen shows morphological features that are identical to extant Eubalaena, including: relatively large size (the anteroposterior length is 117 mm); rectangular outline in medial view; short anterior lobe, judging from the remaining of the lateral furrow; squared anterior margin; prominent transverse crease on the involucrum; transversely compressed in anterior view; well-developed and rounded outer lip; and parallel involucral and main ridges. Although incomplete, the morphological characters and overall similarity to extant Eubalaena allow a reliable taxonomic assignment to Eubalaena sp. The occurrence of a Pleistocene Eubalaena on the southern margin of the western North Pacific is the first balaenid fossil evidence indicative of the biotic interchange between two hemispheres leading to the origin of antitropical distribution in the Pleistocene; alternatively, this specimen might merely represent an extra-limital record of the North Pacific Eubalaena. Furthermore, this find suggests that the Eubalaena interchange, being one of the largest species displaying antitropical distribution pairs in the history of life, likely took place along the western Pacific. Notably, this does not preclude the Eubalaena interchange from other routes, such as the eastern Pacific or the Atlantic Ocean, and future finds should test the scenario for the biotic interchange between Northern and Southern Hemispheres of Eubalaena.

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets

DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the “no intralocus-recombination” assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets.

Rise of the titans: baleen whales became giants earlier than thought

Baleen whales (Mysticeti) are major ecosystem engineers, thanks to their enormous size and bulk filter feeding strategy. Their signature gigantism is thought to be a relatively recent phenomenon, resulting from a Plio-Pleistocene mode shift in their body size evolution. Here, we report the largest whale fossil ever described: an Early Pleistocene (1.5-1.25 Ma) blue whale from Italy with an estimated body length of up to 26 m. Macroevolutionary modelling taking into account this specimen, as well as additional material from the Miocene of Peru, reveals that the proposed mode shift occurred either somewhat earlier, or perhaps not at all. Large-sized mysticetes comparable to most extant species have existed since at least the Late Miocene, suggesting a long-term impact on global marine ecosystems.

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.

Norrisanima miocaena, a new generic name and redescription of a stem balaenopteroid mysticete (Mammalia, Cetacea) from the Miocene of California

Rorqual whales are among the most species rich group of baleen whales (or mysticetes) alive today, yet the monophyly of the traditional grouping (i.e., Balaenopteridae) remains unclear. Additionally, many fossil mysticetes putatively assigned to either Balaenopteridae or Balaenopteroidea may actually belong to stem lineages, although many of these fossil taxa suffer from inadequate descriptions of fragmentary skeletal material. Here we provide a redescription of the holotype of Megaptera miocaena, a fossil balaenopteroid from the Monterey Formation of California, which consists of a partial cranium, a fragment of the rostrum, a single vertebra, and both tympanoperiotics. Kellogg (1922) assigned the type specimen to the genus MegapteraGray (1846), on the basis of its broad similarities to distinctive traits in the cranium of extant humpback whales (Megaptera novaeangliae (Borowski, 1781)). Subsequent phylogenetic analyses have found these two species as sister taxa in morphological datasets alone; the most recent systematic analyses using both molecular and morphological data sets place Megaptera miocaena as a stem balaenopteroid unrelated to humpback whales. Here, we redescribe the type specimen of Megaptera miocaena in the context of other fossil balaenopteroids discovered nearly a century since Kellogg’s original description and provide a morphological basis for discriminating it from Megaptera novaeangliae. We also provide a new generic name and recombine the taxon as Norrisanima miocaena, gen. nov., to reflect its phylogenetic position outside of crown Balaenopteroidea, unrelated to extant Megaptera. Lastly, we refine the stratigraphic age of Norrisanima miocaena, based on associated microfossils to a Tortonian age (7.6–7.3 Ma), which carries implications for understanding the origin of key features associated with feeding and body size evolution in this group of whales.

Borealodon osedax, a new stem mysticete (Mammalia, Cetacea) from the Oligocene of Washington State and its implications for fossil whale-fall communities

Baleen whales (mysticetes) lack teeth as adults and instead filter feed using keratinous baleen plates. They do not echolocate with ultrasonic frequencies like toothed whales but are instead known for infrasonic acoustics. Both baleen and infrasonic hearing are separately considered key innovations linked to their gigantism, evolutionary success and ecological diversity. The earliest mysticetes had teeth, and the phylogenetic position of many so-called toothed mysticetes remains debated, including those belonging to the nominal taxonomic groups Llanocetidae, Mammalodontidae and Aetiocetidae. Here, we report a new stem mysticete, Borealodon osedax gen. et sp. nov., from the Oligocene of Washington State, USA. Borealodon preserves multi-cusped teeth with apical wear; microCT scans of the inner ear indicate that the minimum frequency hearing limit of Borealodon was similar to mammalodontids. Borealodon is not recovered within a monophyletic Mammalodontidae nor a monophyletic Aetiocetidae; instead, it represents an unnamed lineage of stem Mysticeti, adding to the diversity of stem mysticetes, especially across the Rupelian-Chattian boundary. Furthermore, the presence of a putative chemosynthetic bivalve along with Osedax, a bone-boring annelid, found in association with the type specimen of Borealodon, offer more insights into the evolution of deep-sea whale-fall communities.

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

Fossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

Isotopes from fossil coronulid barnacle shells record evidence of migration in multiple Pleistocene whale populations

Migration is an integral feature of modern mysticete whale ecology, and the demands of migration may have played a key role in shaping mysticete evolutionary history. Constraining when migration became established and assessing how it has changed through time may yield valuable insight into the evolution of mysticete whales and the oceans in which they lived. However, there are currently few data which directly assess prehistoric mysticete migrations. Here we show that calcite δ¹⁸O profiles of two species of modern whale barnacles (coronulids) accurately reflect the known migration routes of their host whales. We then analyze well-preserved fossil coronulids from three different locations along the eastern Pacific coast, finding that δ¹⁸O profiles from these fossils exhibit trends and ranges similar to modern specimens. Our results demonstrate that migration is an ancient behavior within the humpback and gray whale lineages and that multiple Pleistocene populations were undertaking migrations of an extent similar to those of the present day.

A large Late Miocene cetotheriid (Cetacea, Mysticeti) from the Netherlands clarifies the status of Tranatocetidae

Cetotheriidae are a group of small baleen whales (Mysticeti) that evolved alongside modern rorquals. They once enjoyed a nearly global distribution, but then largely went extinct during the Plio-Pleistocene. After languishing as a wastebasket taxon for more than a century, the concept of Cetotheriidae is now well established. Nevertheless, the clade remains notable for its variability, and its scope remains in flux. In particular, the recent referral of several traditional cetotheriids to a new and seemingly unrelated family, Tranatocetidae, has created major phylogenetic uncertainty. Here, we describe a new species of Tranatocetus, the type of Tranatocetidae, from the Late Miocene of the Netherlands. Tranatocetus maregermanicum sp. nov. clarifies several of the traits previously ascribed to this genus, and reveals distinctive auditory and mandibular morphologies suggesting cetotheriid affinities. This interpretation is supported by a large phylogenetic analysis, which mingles cetotheriids and tranatocetids within a unified clade. As a result, we suggest that both groups should be reintegrated into the single family Cetotheriidae.

Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

Background

Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes.

Results

In eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions.

Conclusions

Whole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species.

Electronic supplementary material

The online version of this article (10.1186/s13100-018-0143-2) contains supplementary material, which is available to authorized users.