Charting the Course of Pinniped Evolution: insights from molecular phylogeny and fossil record integration

Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these two rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to-date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses however experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12-6 Ma, possibly due to changing sea-levels and/or competition with otariids (eared seals). Historical biogeographic analyses including fossil data allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.

The influence of the land-to-sea macroevolutionary transition on vertebral column disparification in Pinnipedia

The repeated returns of vertebrates to the marine ecosystems since the Triassic serve as an evolutionary model to understand macroevolutionary change. Here we investigate the effects of the land-to-sea transition on disparity and constraint of the vertebral column in aquatic carnivorans (Carnivora; Pinnipedia) to assess how their functional diversity and evolutionary innovations influenced major radiations of crown pinnipeds. We use three-dimensional geometric morphometrics and multivariate analysis for high-dimensional data under a phylogenetic framework to quantify vertebral size and shape in living and extinct pinnipeds. Our analysis demonstrates an important shift in vertebral column evolution by 10-12 million years ago, from an unconstrained to a constrained evolutionary scenario, a point of time that coincides with the major radiation of crown pinnipeds. Moreover, we also demonstrate that the axial skeleton of phocids and otariids followed a different path of morphological evolution that was probably driven by their specialized locomotor strategies. Despite this, we found a significant effect of habitat preference (coastal versus pelagic) on vertebral morphology of crown taxa regardless of the family they belong. In summary, our analysis provides insights into how the land-to-sea transition influenced the complex evolutionary history of pinniped vertebral morphology.

The Role of Locomotory Ancestry on Secondarily Aquatic Transitions

Land-to-sea evolutionary transitions are great transformations where terrestrial amniote clades returned to aquatic environments. These secondarily aquatic amniote clades include charismatic marine mammal and marine reptile groups, as well as countless semi-aquatic forms that modified their terrestrial locomotor anatomy to varying degrees to be suited for swimming via axial and/or appendicular propulsion. The terrestrial ancestors of secondarily aquatic groups would have started off swimming strikingly differently from one another given their evolutionary histories, as inferred by the way modern terrestrial amniotes swim. With such stark locomotor functional differences between reptiles and mammals, we ask if this impacted these transitions. Axial propulsion appears favored by aquatic descendants of terrestrially sprawling quadrupedal reptiles, with exceptions. Appendicular propulsion is more prevalent across the aquatic descendants of ancestrally parasagittal-postured mammals, particularly early transitioning forms. Ancestral terrestrial anatomical differences that precede secondarily aquatic invasions between mammals and reptiles, as well as the distribution of axial and appendicular swimming in secondarily aquatic clades, may indicate that ancestral terrestrial locomotor anatomy played a role, potentially in both constraint and facilitation, in certain aquatic locomotion styles. This perspective of the land-to-sea transition can lead to new avenues of functional, biomechanical, and developmental study of secondarily aquatic transitions.

Fossil brains provide evidence of underwater feeding in early seals

Pinnipeds (seals and related species) use their whiskers to explore their environment and locate their prey. Today they live mostly in marine habitats and are adapted for a highly specialised amphibious lifestyle with their flippers for locomotion and a hydrodynamically streamlined body. The earliest pinnipeds, however, lived on land and in freshwater habitats, much like mustelids today. Here we reconstruct the underwater foraging behaviour of one of these earliest pinnipeds (Potamotherium), focusing in particular on how it used its whiskers (vibrissae). For this purpose, we analyse the coronal gyrus of the brain of 7 fossil and 31 extant carnivorans. This region receives somatosensory input from the head. Our results show that the reliance on whiskers in modern pinnipeds is an ancestral feature that favoured survival of stem pinnipeds in marine habitats. This study provides insights into an impressive ecological transition in carnivoran evolution: from terrestrial to amphibious marine species. Adaptations for underwater foraging were crucial for this transition.

Investigating the land-to-sea transition in carnivorans from the evolution of sacrum morphology in pinnipeds

The form and function of the sacrum are of great relevance to understand the evolution of locomotion in tetrapods because it is a key piece of the vertebrate skeleton. The sacrum connects the caudal and presacral regions of the vertebral column and the hindlimbs through the pelvis. Here, we investigate sacrum shape evolution in pinnipeds (Carnivora: Pinnipedia) in relation to terrestrial mammalian carnivorans (fissipeds), and we include crown and stem taxa to quantify the morphological changes they experience in relation to the aquatic environment they inhabit. We use 3D geometric morphometric methods to explore the morphological variability and disparity of the sacrum in a set of terrestrial and aquatic carnivoran species. Our results show that the morphology of the sacrum of each pinniped family is remarkably different and that these differences may be related to the aquatic mode of locomotion (pectoral or pelvic oscillation), the use of hindlimbs to support body weight on land (otariids in contrast with phocids), and the presence or absence of a functional tail. In addition, disparity-through-time analyses indicate that the sacrum of pinnipeds is less constrained than that of fissipeds, which suggests a gravitational origin of such constraints in fissipeds. In conclusion, our results give further support to the important role played by this skeletal structure in the locomotory adaptations of mammals.

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.

Sexual dimorphism in the walrus mandible: comparative description and geometric morphometrics

The modern walrus Odobenus rosmarus is characterized by marked sexual dimorphism, related to its polygynous behavior and the aggressive competition between males during the breeding season. Previous studies treated skeletal sexual dimorphism in walruses either qualitatively or with basic quantitative measurements. The present study combines a detailed qualitative comparison of male and female walrus mandibles with quantitative two-dimensional geometric morphometrics analysis (principal component analysis, Procrustes ANOVA and a linear discriminant analysis). In addition to identifying previously recognized sexually dimorphic features (e.g., convexity of the anterior margin of the mandible in adult males), our study finds new morphological differences between males and females, such as a relative dorsal expansion of the anterior part of the mandible and an accentuated concavity between the dorsal margin and the coronoid process in adult males. Both our qualitative comparisons and quantitative analyses demonstrate that sexual dimorphism as expressed in the mandible of extant walruses is statistically significant and that (variation in) mandibular morphology can be used as tool to attribute sex with a good degree of accuracy to isolated mandibles or skeletons lacking the cranium. Sexual dimorphism in walruses is directly related to their sexual behavior, characterized as aggressive in males and linked to a polygynous reproduction system. Indeed, the difference in size of the tusks between males and females but also the use of these during intraspecific fights, can reasonably account for this great mandibular morphological disparity between adult males and females, but also among different ontogenetic stages. Finally, the results obtained in the present study may serve as a starting point for assessing sexual dimorphism more in-depth and studying inter- and intraspecific variation in the mandibles of fossil walruses by identifying quantified size and shape mandibular features.

Comparative examination of pinniped craniofacial musculature and its role in aquatic feeding

Secondarily aquatic tetrapods have many unique morphologic adaptations for life underwater compared with their terrestrial counterparts. A key innovation during the land-to-water transition was feeding. Pinnipeds, a clade of air-breathing marine carnivorans that include seals, sea lions, and walruses, have evolved multiple strategies for aquatic feeding (e.g., biting, suction feeding). Numerous studies have examined the pinniped skull and dental specializations for underwater feeding. However, data on the pinniped craniofacial musculoskeletal system and its role in aquatic feeding are rare. Therefore, the objectives of this study were to conduct a comparative analysis of pinniped craniofacial musculature and examine the function of the craniofacial musculature in facilitating different aquatic feeding strategies. We performed anatomic dissections of 35 specimens across six pinniped species. We describe 32 pinniped craniofacial muscles-including facial expression, mastication, tongue, hyoid, and soft palate muscles. Pinnipeds broadly conform to mammalian patterns of craniofacial muscle morphology. Pinnipeds also exhibit unique musculoskeletal morphologies-in muscle position, attachments, and size-that likely represent adaptations for different aquatic feeding strategies. Suction feeding specialists (bearded and northern elephant seals) have a significantly larger masseter than biters. Further, northern elephant seals have large and unique tongue and hyoid muscle morphologies compared with other pinniped species. These morphologic changes likely help generate and withstand suction pressures necessary for drawing water and prey into the mouth. In contrast, biting taxa (California sea lions, harbor, ringed, and Weddell seals) do not exhibit consistent craniofacial musculoskeletal adaptations that differentiate them from suction feeders. Generally, we discover that all pinnipeds have well-developed and robust craniofacial musculature. Pinniped head musculature plays an important role in facilitating different aquatic feeding strategies. Together with behavioral and kinematic studies, our data suggest that pinnipeds' robust facial morphology allows animals to switch feeding strategies depending on the environmental context-a critical skill in a heterogeneous and rapidly changing underwater habitat.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

The largest hoplophonine and a complex new hypothesis of nimravid evolution

Nimravids were the first carnivorans to evolve saberteeth, but previously portrayed as having a narrow evolutionary trajectory of increasing degrees of sabertooth specialization. Here I present a novel hypothesis about the evolution of this group, including a description of Eusmilus adelos, the largest known hoplophonine, which forces a re-evaluation of not only their relationships, but perceived paleoecology. Using a tip-dated Bayesian analysis with sophisticated evolutionary models, nimravids can now be viewed as following two paths of evolution: one led to numerous early dirk-tooth forms, including E. adelos, while the other converged on living feline morphology, tens of millions of years before its appearance in felids.

The influence of movement on negative and positive emotional responses to animals

Two studies were conducted to explore whether the addition of animal movement would influence the intensity of emotional reactions towards that animal. Both studies compared self-reported emotional reactions with still images and videos for six animal categories (snakes, spiders, rodents, hoofed animals, animals with flippers, and turtles). In Study 1, participants reported fear and disgust to the animal stimuli, which were averaged into a single negative emotion rating. In Study 2, participants reported either fear and disgust or joy and affection to the animal stimuli, which were averaged into either a single negative or positive emotion rating. Upon combining the reported emotions from the two studies, movement was found to increase negative emotion reported to snakes and spiders and decrease negative emotion reported to rodents, hoofed animals, and animals with flippers. Results from Study 2 indicated that movement increased reported positive emotions to all six animal categories. Our findings suggest that animal movement is an important component of emotional reactions to animals.

Convergent evolution of forelimb-propelled swimming in seals

Modern pinnipeds (true and eared seals) employ two radically different swimming styles, with true seals (phocids) propelling themselves primarily with their hindlimbs, whereas eared seals (otariids) rely on their wing-like foreflippers.^1,2 Current explanations of this functional dichotomy invoke either pinniped diphyly^3-5 or independent colonizations of the ocean by related but still largely terrestrial ancestors.^6-8 Here, we show that pinniped swimming styles form an anatomical, functional, and behavioral continuum, within which adaptations for forelimb swimming can arise directly from a hindlimb-propelled bauplan. Within phocids, southern seals (monachines) show a convergent trend toward wing-like, hydrodynamically efficient forelimbs used for propulsion during slow swimming, turning, bursts of speed, or when initiating movement. This condition is most evident in leopard seals, which have well-integrated foreflippers with little digit mobility, reduced claws, and hydrodynamic characteristics comparable to those of forelimb-propelled otariids. Using monachines as a model, we suggest that the last common ancestor of modern seals may have been hindlimb-propelled and aquatically adapted, thus resolving the apparent contradiction at the root of pinniped evolution.

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea (whales, dolphins, and porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each other's closest living relatives. Ancestral reconstructions suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea + Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified eight skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ∼16 Ma earlier in cetaceans (∼46.5 Ma) than in hippos (∼30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids ("anthracotheres"), support the hypothesis that aquatic skin adaptations evolved independently in hippos and cetaceans.

The Role of the Tail or Lack Thereof in the Evolution of Tetrapod Aquatic Propulsion

Synopsis Secondary aquatic vertebrates exhibit a diversity of swimming modes that use paired limbs and/or the tail. Various secondarily aquatic tetrapod clades, including amphibians, reptiles, and mammals employ transverse undulations or oscillations of the tail for swimming. These movements have often been classified according to a kinematic gradient that was established for fishes, but may not be appropriate to describe the swimming motions of tetrapods. To understand the evolution of movements and design of the tail in aquatic tetrapods, we categorize the types of tails used for swimming and examine swimming kinematics and hydrodynamics. From a foundation of a narrow, elongate ancestral tail, the tails used for swimming by aquatic tetrapods are classified as tapered, keeled, paddle, and lunate. Tail undulations are associated with tapered, keeled, and paddle tails for a diversity of taxa. Propulsive undulatory waves move down the tail with increasing amplitude toward the tail tip, while moving posteriorly at a velocity faster than the anterior motion of the body indicating that the tail is used for thrust generation. Aquatic propulsion is associated with the transfer of momentum to the water from the swimming movements of the tail, particularly at the trailing edge. The addition of transverse extensions and flattening of the tail increases the mass of water accelerated posteriorly and affects vorticity shed into the wake for more aquatically adapted animals. DPIV (Digital Particle Image Velocimetry) reveals differences were exhibited in the vortex wake between the morphological and kinematic extremes of the alligator with a tapering undulating tail and the dolphin with oscillating wing-like flukes that generate thrust. In addition to exploring the relationship between shape of undulating tails and swimming performance across aquatic tetrapods, the role of tail reduction or loss of a tail in aquatic-tetrapod swimming was also explored. For aquatic tetrapods, reduction would have been due to factors including locomotor and defensive specializations and phylogenetic and physiological constraints. Possession of a thrust-generating tail for swimming, or lack thereof, guided various lineages of secondarily aquatic vertebrates into different evolutionary trajectories for effective aquatic propulsion (i.e., speed, efficiency, acceleration).

First monk seal from the Southern Hemisphere rewrites the evolutionary history of true seals

Living true seals (phocids) are the most widely dispersed semi-aquatic marine mammals, and comprise geographically separate northern (phocine) and southern (monachine) groups. Both are thought to have evolved in the North Atlantic, with only two monachine lineages-elephant seals and lobodontins-subsequently crossing the equator. The third and most basal monachine tribe, the monk seals, have hitherto been interpreted as exclusively northern and (sub)tropical throughout their entire history. Here, we describe a new species of extinct monk seal from the Pliocene of New Zealand, the first of its kind from the Southern Hemisphere, based on one of the best-preserved and richest samples of seal fossils worldwide. This unanticipated discovery reveals that all three monachine tribes once coexisted south of the equator, and forces a profound revision of their evolutionary history: rather than primarily diversifying in the North Atlantic, monachines largely evolved in the Southern Hemisphere, and from this southern cradle later reinvaded the north. Our results suggest that true seals crossed the equator over eight times in their history. Overall, they more than double the age of the north-south dichotomy characterizing living true seals and confirms a surprisingly recent major change in southern phocid diversity.

Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: “bare-branch attraction,” namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.]