A heavyweight early whale pushes the boundaries of vertebrate morphology.

The fossil record of cetaceans documents how terrestrial animals acquired extreme adaptations and transitioned to a fully aquatic lifestyle1,2. In whales, this is associated with a substantial increase in maximum body size. Although an elongate body was acquired early in cetacean evolution3, the maximum body mass of baleen whales reflects a recent diversification that culminated in the blue whale4. More generally, hitherto known gigantism among aquatic tetrapods evolved within pelagic, active swimmers. Here we describe Perucetus colossus-a basilosaurid whale from the middle Eocene epoch of Peru. It displays, to our knowledge, the highest degree of bone mass increase known to date, an adaptation associated with shallow diving5. The estimated skeletal mass of P. colossus exceeds that of any known mammal or aquatic vertebrate. We show that the bone structure specializations of aquatic mammals are reflected in the scaling of skeletal fraction (skeletal mass versus whole-body mass) across the entire disparity of amniotes. We use the skeletal fraction to estimate the body mass of P. colossus, which proves to be a contender for the title of heaviest animal on record. Cetacean peak body mass had already been reached around 30 million years before previously assumed, in a coastal context in which primary productivity was particularly high.

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.

Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu.

The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic diversity and much about their natural history remain poorly understood. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous peoples of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and True's beaked whale (M. mirus) from the North Atlantic, with which it was previously subsumed. Morphometric analyses of skulls also distinguish the two species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began circa 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous peoples offers a model for broadening the cultural scope of the scientific naming process.

Microarchitecture of cetacean vertebral trabecular bone among swimming modes and diving behaviors.

Cetaceans (dolphins, whales, and porpoises) are fully aquatic mammals that are supported by water's buoyancy and swim through axial body bending. Swimming is partially mediated by variations in vertebral morphology that creates trade-offs in body flexibility and rigidity between axial regions that either enhance or reduce displacement between adjacent vertebrae. Swimming behavior is linked to foraging ecology, where deep-diving cetaceans glide a greater proportion of the time compared to their shallow-diving counterparts. In this study, we categorized 10 species of cetaceans (Families Delphinidae and Kogiidae) into functional groups determined by swimming patterns (rigid vs. flexible torso) and diving behavior (shallow vs. deep). Here, we quantify vertebral trabecular microarchitecture (a) among functional groups (rigid-torso shallow diver (RS), rigid-torso deep diver (RD), and flexible-torso deep diver (FD)), and (b) among vertebral column regions (posterior thoracic, lumbar, caudal peduncle, and fluke insertion). We microCT scanned vertebral bodies, from which 1-5 volumes of interest were selected to quantify bone volume fraction (BV/TV), specific bone surface (BS/BV), trabecular thickness (TbTh), trabecular number (TbN), trabecular separation (TbSp), and degree of anisotropy (DA). We found that BV/TV was greatest in the rigid-torso shallow-diving functional group, smallest in flexible-torso deep-diving species, and intermediate in the rigid-torso deep-diving group. DA was significantly greater in rigid-torso caudal oscillators than in their flexible-torso counterparts. We found no variation among vertebral regions for any microarchitectural variables. Despite having osteoporotic skeletons, cetacean vertebrae had greater BV/TV, TbTh, and DA than previously documented in terrestrial mammalian bone. Cetacean species are an ideal model to investigate the long-term adaptations, over an animal's lifetime and over evolutionary time, of trabecular bone in non-weight-bearing conditions.

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.

Reduction of olfactory and respiratory turbinates in the transition of whales from land to sea: the semiaquatic middle Eocene Aegyptocetus tarfa.

Ethmoturbinates, nasoturbinates, and maxilloturbinates are well developed in the narial tract of land-dwelling artiodactyls ancestral to whales, but these are greatly reduced or lost entirely in modern whales. Aegyptocetus tarfa is a semiaquatic protocetid from the middle Eocene of Egypt. Computed axial tomography scans of the skull show that A. tarfa retained all three sets of turbinates like a land mammal. It is intermediate between terrestrial artiodactyls and aquatic whales in reduction of the turbinates. Ethmoturbinates in A. tarfa have 26% of the surface area expected for an artiodactyl. These have an olfactory function and indicate that early whales retained a sense of smell in the transition from land to sea. Maxilloturbinates in A. tarfa have 6% of the surface area expected for an artiodactyl. These have a respiratory function and their markedly reduced size suggests that rapid inhalation and exhalation was already more important than warming and humidifying air, in contrast to extant land mammals. Finally, the maxilloturbinates of A. tarfa, although greatly reduced, still show some degree of similarity to those of artiodactyls, supporting the phylogenetic affinity of cetaceans and artiodactyls based on morphological and molecular evidence.

Rorqual whale nasal plugs: protecting the respiratory tract against water entry and barotrauma.

The upper respiratory tract of rorquals, lunge-feeding baleen whales, must be protected against water incursion and the risk of barotrauma at depth, where air-filled spaces like the bony nasal cavities may experience high adverse pressure gradients. We hypothesize these two disparate tasks are accomplished by paired cylindrical nasal plugs that attach on the rostrum and deep inside the nasal cavity. Here, we present evidence that the large size and deep attachment of the plugs is a compromise, allowing them to block the nasal cavities to prevent water entry while also facilitating pressure equilibration between the nasal cavities and ambient hydrostatic pressure (Pamb) at depth. We investigated nasal plug behaviour using videos of rorquals surfacing, plug morphology from dissections, histology and MRI scans, and plug function by mathematically modelling nasal pressures at depth. We found each nasal plug has three structurally distinct regions: a muscular rostral region, a predominantly fatty mid-section and an elastic tendon that attaches the plug caudally. We propose muscle contraction while surfacing pulls the fatty sections rostrally, opening the nasal cavities to air, while the elastic tendons snap the plugs back into place, sealing the cavities after breathing. At depth, we propose Pamb pushes the fatty region deeper into the nasal cavities, decreasing air volume by about half and equilibrating nasal cavity to Pamb, preventing barotrauma. The nasal plugs are a unique innovation in rorquals, which demonstrate their importance and novelty during diving, where pressure becomes as important an issue as the danger of water entry.

A new fossil species supports an early origin for toothed whale echolocation.

Odontocetes (toothed whales, dolphins and porpoises) hunt and navigate through dark and turbid aquatic environments using echolocation; a key adaptation that relies on the same principles as sonar. Among echolocating vertebrates, odontocetes are unique in producing high-frequency vocalizations at the phonic lips, a constriction in the nasal passages just beneath the blowhole, and then using air sinuses and the melon to modulate their transmission. All extant odontocetes seem to echolocate; however, exactly when and how this complex behaviour--and its underlying anatomy--evolved is largely unknown. Here we report an odontocete fossil, Oligocene in age (approximately 28 Myr ago), from South Carolina (Cotylocara macei, gen. et sp. nov.) that has several features suggestive of echolocation: a dense, thick and downturned rostrum; air sac fossae; cranial asymmetry; and exceptionally broad maxillae. Our phylogenetic analysis places Cotylocara in a basal clade of odontocetes, leading us to infer that a rudimentary form of echolocation evolved in the early Oligocene, shortly after odontocetes diverged from the ancestors of filter-feeding whales (mysticetes). This was followed by enlargement of the facial muscles that modulate echolocation calls, which in turn led to marked, convergent changes in skull shape in the ancestors of Cotylocara, and in the lineage leading to extant odontocetes.

The First Finding of the Late Miocene Baleen Whales of the Genus Zygiocetus (Cetotheriidae, Mysticeti) in Crimea (Melek-Chesme Locality, Kerch Peninsula).

Fragments of four Zygiocetus sp. whale skeletons from the Melek-Chesme locality at the Kerch Peninsula are described. This is the first finding of the representatives of this genus in Crimea.

Convergent evolution in toothed whale cochleae.

BACKGROUND: Odontocetes (toothed whales) are the most species-rich marine mammal lineage. The catalyst for their evolutionary success is echolocation - a form of biological sonar that uses high-frequency sound, produced in the forehead and ultimately detected by the cochlea. The ubiquity of echolocation in odontocetes across a wide range of physical and acoustic environments suggests that convergent evolution of cochlear shape is likely to have occurred. To test this, we used SURFACE; a method that fits Ornstein-Uhlenbeck (OU) models with stepwise AIC (Akaike Information Criterion) to identify convergent regimes on the odontocete phylogeny, and then tested whether convergence in these regimes was significantly greater than expected by chance. RESULTS: We identified three convergent regimes: (1) True's (Mesoplodon mirus) and Cuvier's (Ziphius cavirostris) beaked whales; (2) sperm whales (Physeter macrocephalus) and all other beaked whales sampled; and (3) pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales and Dall's porpoise (Phocoenoides dalli). Interestingly the 'river dolphins', a group notorious for their convergent morphologies and riverine ecologies, do not have convergent cochlear shapes. The first two regimes were significantly convergent, with habitat type and dive type significantly correlated with membership of the sperm whale + beaked whale regime. CONCLUSIONS: The extreme acoustic environment of the deep ocean likely constrains cochlear shape, causing the cochlear morphology of sperm and beaked whales to converge. This study adds support for cochlear morphology being used to predict the ecology of extinct cetaceans.

Scaling of swimming performance in baleen whales.

The scale dependence of locomotor factors has long been studied in comparative biomechanics, but remains poorly understood for animals at the upper extremes of body size. Rorqual baleen whales include the largest animals, but we lack basic kinematic data about their movements and behavior below the ocean surface. Here, we combined morphometrics from aerial drone photogrammetry, whale-borne inertial sensing tag data and hydrodynamic modeling to study the locomotion of five rorqual species. We quantified changes in tail oscillatory frequency and cruising speed for individual whales spanning a threefold variation in body length, corresponding to an order of magnitude variation in estimated body mass. Our results showed that oscillatory frequency decreases with body length (∝length-0.53) while cruising speed remains roughly invariant (∝length0.08) at 2 m s-1 We compared these measured results for oscillatory frequency against simplified models of an oscillating cantilever beam (∝length-1) and an optimized oscillating Strouhal vortex generator (∝length-1). The difference between our length-scaling exponent and the simplified models suggests that animals are often swimming non-optimally in order to feed or perform other routine behaviors. Cruising speed aligned more closely with an estimate of the optimal speed required to minimize the energetic cost of swimming (∝length0.07). Our results are among the first to elucidate the relationships between both oscillatory frequency and cruising speed and body size for free-swimming animals at the largest scale.

Neuroanatomy and inner ear labyrinths of the narwhal, Monodon monoceros, and beluga, Delphinapterus leucas (Cetacea: Monodontidae).

Narwhals (Monodon monoceros) and belugas (Delphinapterus leucas) are the only extant members of the Monodontidae, and are charismatic Arctic-endemic cetaceans that are at risk from global change. Investigating the anatomy and sensory apparatuses of these animals is essential to understanding their ecology and evolution, and informs efforts for their conservation. Here, we use X-ray CT scans to compare aspects of the endocranial and inner ear labyrinth anatomy of extant monodontids and use the overall morphology to draw larger inferences about the relationship between morphology and ecology. We show that differences in the shape of the brain, vasculature, and neural canals of both species may relate to differences in diving and other behaviors. The cochleae are similar in morphology in the two species, signifying similar hearing ranges and a close evolutionary relationship. Lastly, we compare two different methods for calculating 90var - a calculation independent of body size that is increasingly being used as a proxy for habitat preference. We show that a 'direct' angular measurement method shows significant differences between Arctic and other habitat preferences, but angle measurements based on planes through the semicircular canals do not, emphasizing the need for more detailed study and standardization of this measurement. This work represents the first comparative internal anatomical study of the endocranium and inner ear labyrinths of this small clade of toothed whales.

How do baleen whales stow their filter? A comparative biomechanical analysis of baleen bending.

Bowhead and right whale (balaenid) baleen filtering plates, longer in vertical dimension (≥3-4 m) than the closed mouth, presumably bend during gape closure. This has not been observed in live whales, even with scrutiny of video-recorded feeding sequences. To determine what happens to the baleen during gape closure, we conducted an integrative, multifactorial study including materials testing, functional (flow tank and kinematic) testing and histological examination. We measured baleen bending properties along the dorsoventral length of plates and anteroposterior location within a rack of plates via mechanical (axial bending, composite flexure, compression and tension) tests of hydrated and air-dried tissue samples from balaenid and other whale baleen. Balaenid baleen is remarkably strong yet pliable, with ductile fringes, and low stiffness and high elasticity when wet; it likely bends in the closed mouth when not used for filtration. Calculation of flexural modulus from stress/strain experiments shows that the balaenid baleen is slightly more flexible where it emerges from the gums and at its ventral terminus, but kinematic analysis indicates plates bend evenly along their whole length. Fin and humpback whale baleen has similar material properties but less flexibility, with no dorsoventral variation. The internal horn tubes have greater external and hollow luminal diameter but lower density in the lateral relative to medial baleen of bowhead and fin whales, suggesting a greater capacity for lateral bending. Baleen bending has major consequences not only for feeding morphology and energetics but also for conservation given that entanglement in fishing gear is a leading cause of whale mortality.

Retinal Topography in Two Species of Baleen Whale (Cetacea: Mysticeti).

Little is known about the visual systems of large baleen whales (Mysticeti: Cetacea). In this study, we investigate eye morphology and the topographic distribution of retinal ganglion cells (RGCs) in two species of mysticete, Bryde's whale (Balaenoptera edeni) and the humpback whale (Megaptera novaeanglia). Both species have large eyes characterised by a thickened cornea, a heavily thickened sclera, a highly vascularised fibro-adipose bundle surrounding the optic nerve at the back of the eye, and a reflective blue-green tapetum fibrosum. Using stereology and retinal whole mounts, we estimate a total of 274,268 and 161,371 RGCs in the Bryde's whale and humpback whale retinas, respectively. Both species have a similar retinal topography, consisting of nasal and temporal areas of high RGC density, suggesting that having higher visual acuity in the anterior and latero-caudal visual fields is particularly important in these animals. The temporal area is larger in both species and contains the peak RGC densities (160 cells mm-2 in the humpback whale and 200 cells mm-2 in Bryde's whale). In the Bryde's whale retina, the two high-density areas are connected by a weak centro-ventral visual streak, but such a specialisation is not evident in the humpback whale. Measurements of RGC soma area reveal that although the RGCs in both species vary substantially in size, RGC soma area is inversely proportional to RGC density, with cells in the nasal and temporal high-density areas being relatively more homogeneous in size compared to the RGCs in the central retina and the dorsal and ventral retinal periphery. Some of the RGCs were very large, with soma areas of over 2,000 µm2. Using peak RGC density and eye axial diameter (Bryde's whale: 63.5 mm; humpback whale: 48.5 mm), we estimated the peak anatomical spatial resolving power in water to be 4.8 cycles/degree and 3.3 cycles/degree in the Bryde's whale and the humpback whale, respectively. Overall, our findings for these two species are very similar to those reported for other species of cetaceans. This indicates that, irrespective of the significant differences in body size and shape, behavioural ecology and feeding strategy between mysticetes and odontocetes (toothed whales), cetacean eyes are adapted to vision in dim light and adhere to a common "bauplan" that evolved prior to the divergence of the two cetacean parvorders (Odontoceti and Mysticeti) over 30 million years ago.

Investigation of Whalebone from the Miocene Kovran Locality (Kamchatka Krai, Russia).

New information on the microstructures, general morphology, and features of preservation of plates of a whalebone from the Miocene Kovran locality in the Kamchatka Peninsula are provided. The plates have a chevron-like bend which is absent in extant Balaenopteridae, Balaenidae, and Eschrichtiidae. This shape is possibly related to the filtration mechanism characteristic of these whales.

The remarkable convergence of skull shape in crocodilians and toothed whales.

The striking resemblance of long-snouted aquatic mammals and reptiles has long been considered an example of morphological convergence, yet the true cause of this similarity remains untested. We addressed this deficit through three-dimensional morphometric analysis of the full diversity of crocodilian and toothed whale (Odontoceti) skull shapes. Our focus on biomechanically important aspects of shape allowed us to overcome difficulties involved in comparing mammals and reptiles, which have fundamental differences in the number and position of skull bones. We examined whether diet, habitat and prey size correlated with skull shape using phylogenetically informed statistical procedures. Crocodilians and toothed whales have a similar range of skull shapes, varying from extremely short and broad to extremely elongate. This spectrum of shapes represented more of the total variation in our dataset than between phylogenetic groups. The most elongate species (river dolphins and gharials) are extremely convergent in skull shape, clustering outside of the range of the other taxa. Our results suggest the remarkable convergence between long-snouted river dolphins and gharials is driven by diet rather than physical factors intrinsic to riverine environments. Despite diverging approximately 288 million years ago, crocodilians and odontocetes have evolved a remarkably similar morphological solution to feeding on similar prey.

How whales used to filter: exceptionally preserved baleen in a Miocene cetotheriid.

Baleen is a comb-like structure that enables mysticete whales to bulk feed on vast quantities of small prey, and ultimately allowed them to become the largest animals on Earth. Because baleen rarely fossilises, extremely little is known about its evolution, structure and function outside the living families. Here we describe, for the first time, the exceptionally preserved baleen apparatus of an entirely extinct mysticete morphotype: the Late Miocene cetotheriid, Piscobalaena nana, from the Pisco Formation of Peru. The baleen plates of P. nana are closely spaced and built around relatively dense, fine tubules, as in the enigmatic pygmy right whale, Caperea marginata. Phosphatisation of the intertubular horn, but not the tubules themselves, suggests in vivo intertubular calcification. The size of the rack matches the distribution of nutrient foramina on the palate, and implies the presence of an unusually large subrostral gap. Overall, the baleen morphology of Piscobalaena likely reflects the interacting effects of size, function and phylogeny, and reveals a previously unknown degree of complexity in modern mysticete feeding evolution.

Multi-year longitudinal profiles of cortisol and corticosterone recovered from baleen of North Atlantic right whales (Eubalaena glacialis).

Research into stress physiology of mysticete whales has been hampered by difficulty in obtaining repeated physiological samples from individuals over time. We investigated whether multi-year longitudinal records of glucocorticoids can be reconstructed from serial sampling along full-length baleen plates (representing ∼10years of baleen growth), using baleen recovered from two female North Atlantic right whales (Eubalaena glacialis) of known reproductive history. Cortisol and corticosterone were quantified with immunoassay of subsamples taken every 4cm (representing ∼60d time intervals) along a full-length baleen plate from each female. In both whales, corticosterone was significantly elevated during known pregnancies (inferred from calf sightings and necropsy data) as compared to intercalving intervals; cortisol was significantly elevated during pregnancies in one female but not the other. Within intercalving intervals, corticosterone was significantly elevated during the first year (lactation year) and/or the second year (post-lactation year) as compared to later years of the intercalving interval, while cortisol showed more variable patterns. Cortisol occasionally showed brief high elevations ("spikes") not paralleled by corticosterone, suggesting that the two glucocorticoids might be differentially responsive to certain stressors. Generally, immunoreactive corticosterone was present in higher concentration in baleen than immunoreactive cortisol; corticosterone:cortisol ratio was usually >4 and was highly variable in both individuals. Further investigation of baleen cortisol and corticosterone profiles could prove fruitful for elucidating long-term, multi-year patterns in stress physiology of large whales, determined retrospectively from stranded or archived specimens.

The influence of air-filled structures on wave propagation and beam formation of a pygmy sperm whale (Kogia breviceps) in horizontal and vertical planes.

The wave propagation, sound field, and transmission beam pattern of a pygmy sperm whale (Kogia breviceps) were investigated in both the horizontal and vertical planes. Results suggested that the signals obtained at both planes were similarly characterized with a high peak frequency and a relatively narrow bandwidth, close to the ones recorded from live animals. The sound beam measured outside the head in the vertical plane was narrower than that of the horizontal one. Cases with different combinations of air-filled structures in both planes were used to study the respective roles in controlling wave propagation and beam formation. The wave propagations and beam patterns in the horizontal and vertical planes elucidated the important reflection effect of the spermaceti and vocal chambers on sound waves, which was highly significant in forming intensive forward sound beams. The air-filled structures, the forehead soft tissues and skull structures formed wave guides in these two planes for emitted sounds to propagate forward.

Model inadequacy and mistaken inferences of trait-dependent speciation.

Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models-have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are inferred to have statistically significant associations with speciation rate. We first demonstrate this unfortunate effect for a known model assumption violation: shifts in speciation rate associated with a character not included in the model. We further show that for many empirical phylogenies, characters simulated in the absence of state-dependent diversification exhibit an even higher Type I error rate, indicating that the method is susceptible to additional, unknown model inadequacies. For traits that evolve slowly, the root cause appears to be a statistical framework that does not require replicated shifts in character state and diversification. However, spurious associations between character state and speciation rate arise even for traits that lack phylogenetic signal, suggesting that phylogenetic pseudoreplication alone cannot fully explain the problem. The surprising severity of this phenomenon suggests that many trait-diversification relationships reported in the literature may not be real. More generally, we highlight the need for diagnosing and understanding the consequences of model inadequacy in phylogenetic comparative methods.