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.

Persistent organic pollutants and polycyclic aromatic hydrocarbons in livers of stranded Arctocephalus australis in southern Brazilian beaches

23 livers of South American fur seal (Arctocephalus australis) found stranded in southern Brazilian beaches were evaluated for Persistent Organic Pollutants (POPs) and Polycyclic Aromatic Hydrocarbons (PAHs). POPs (DDTs, mirex, eldrin, dieldrin, aldrin, isodrin, HCHs, chlordanes and PCBs) and PAHs in livers were Soxhlet extracted, analyzed and quantified using Gas Chromatography Tandem Mass Spectrometry (GC-TQMS). The main POPs found were PCBs and DDTs, totaling 81 %. Among pesticides, mirex followed DDTs, possibly due to usage in Uruguay, followed by Σdrins, ΣCHLs and ΣHCHs. Naphthalene was the major PAH found, while heavier compounds did not significantly bioaccumulate. Concentrations of POPs resembled previous findings for A. australis. Considering only juveniles, no POPs showed significant differences between sexes. Lipidic content, weight and length did not show any correlation with POP concentration. This was the first record of PAHs and PBDEs in South American fur seals, and the levels of these pollutants were relatively low.

Vocal production learning in mammals revisited

Vocal production learning, the ability to modify the structure of vocalizations as a result of hearing those of others, has been studied extensively in birds but less attention has been given to its occurrence in mammals. We summarize the available evidence for vocal learning in mammals from the last 25 years, updating earlier reviews on the subject. The clearest evidence comes from cetaceans, pinnipeds, elephants and bats where species have been found to copy artificial or human language sounds, or match acoustic models of different sound types. Vocal convergence, in which parameter adjustments within one sound type result in similarities between individuals, occurs in a wider range of mammalian orders with additional evidence from primates, mole-rats, goats and mice. Currently, the underlying mechanisms for convergence are unclear with vocal production learning but also usage learning or matching physiological states being possible explanations. For experimental studies, we highlight the importance of quantitative comparisons of seemingly learned sounds with vocal repertoires before learning started or with species repertoires to confirm novelty. Further studies on the mammalian orders presented here as well as others are needed to explore learning skills and limitations in greater detail. This article is part of the theme issue 'Vocal learning in animals and humans'.

Nasopulmonary mites (Halarachnidae) of coastal Californian pinnipeds: Identity, prevalence, and molecular characterization

Mites from the family Halarachnidae Oudemans 1906 are obligate endoparasites that colonize the respiratory tracts of free-living and captive marine mammals. Infestations can range from mild to severe and result in respiratory tract irritation or impairment. Nasopulmonary acariasis was determined to be a contributing cause of death among several southern sea otters Enhydra lutris nereis Merriam 1904 in a longitudinal study of otter mortality, and proximity to Pacific harbor seals Phoca vitulina richardii Gray 1864 was a significant risk factor for sea otter infestation. Beyond scattered opportunistic reports, each halarachnid mite species' affinity for particular hosts and the extent of mite transmission between host species is poorly understood. We investigated the identity and prevalence of nasopulmonary mites from Pacific harbor seals, California sea lions Zalophus californianus Lesson 1828, northern elephant seals Mirounga angustirostris Gill 1866, northern fur seals Callorhinus ursinus Linnaeus 1758, and Guadalupe fur seals Arctocephalus philippii townsendi Merriam 1897 to complement published nasopulmonary mite findings from sympatric southern sea otters during a comparable timeframe. Halarachnid mite infestation was common among California sea lions (74.1%), northern fur seals (73.3%), and northern elephant seals (46.6%), but was less common among harbor seals (18.7%) and Guadalupe fur seals (8.8%). Observed host-mite relationships suggest a distinct host specificity, with genus Orthohalarachne infesting otariids, and genus Halarachne infesting phocids and lutrinids along the California coast. Harbor seals and southern sea otters were the primary hosts of H. halichoeri, but one nothern elephant seal was infested with both H. miroungae and a single H. halichoeri. We also present the first high-resolution SEM images for H. miroungae and O. attenuata and possible evidence for a new host record for H. halichoeri.

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.

Diphyllobothrium sprakeri n. sp. (Cestoda: Diphyllobothriidae): a hidden broad tapeworm from sea lions off North and South America

BACKGROUND

The systematic of several marine diphyllobothriid tapeworms of pinnipeds has been revised in recent years. However, 20 species of Diphyllobothrium from phocids and otariids are still recognized as incertae sedis. We describe a new species of Diphyllobothrium from the intestine of California sea lions Zalophus californianus (Lesson) (type-host) and South American sea lions Otaria flavescens (Shaw).

METHODS

Zalophus californianus from the Pacific coast of the USA and O. flavescens from Peru and Argentina were screened for parasites. Partial fragments of the large ribosomal subunit gene (lsrDNA) and the cytochrome c oxidase subunit 1 (cox1) mitochondrial gene were amplified for 22 isolates. Properly fixed material from California sea lions was examined using light and scanning electron microscopy.

RESULTS

A total of four lsrDNA and 21 cox1 sequences were generated and aligned with published sequences of other diphyllobothriid taxa. Based on cox1 sequences, four diphyllobothriid tapeworms from O. flavescens in Peru were found to be conspecific with Adenocephalus pacificus Nybelin, 1931. The other newly generated sequences fall into a well-supported clade with sequences of a putative new species previously identified as Diphyllobothrium sp. 1. from Z. californianus and O. flavescens. A new species, Diphyllobothrium sprakeri n. sp., is proposed for tapeworms of this clade.

CONCLUSIONS

Diphyllobothrium sprakeri n. sp. is the first diphyllobothriid species described from Z. californianus from the Pacific coast of North America, but O. flavescens from Argentina, Chile and Peru was confirmed as an additional host. The present study molecularly confirmed the first coinfection of two diphyllobothriid species in sea lions from the Southern Hemisphere.

The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific

The extant genera of fur seals and sea lions of the family Otariidae (Carnivora: Pinnipedia) are thought to have emerged in the Pliocene or the early Pleistocene in the North Pacific. Among them, the Steller sea lion (Eumetopias jubatus) is the largest and distributed both in the western and eastern North Pacific. In contrast to the limited distribution of the current population around the Japanese Islands that is now only along the coast of Hokkaido, their fossil records have been known from the middle and late Pleistocene of Honshu Island. One such important fossil specimen has been recorded from the upper lower Pleistocene Omma Formation (ca. 1.36–0.83 Ma) in Kanazawa, Ishikawa Prefecture, Japan, which now bears the institutional number GKZ-N 00001. Because GKZ-N 00001 is the earliest fossil having been identified as a species of the sea lion genus Eumetopias, it is of importance to elucidate the evolutionary history of that genus. The morphometric comparisons were made among 51 mandibles of fur seals and sea lions with GKZ-N 00001. As results of bivariate analyses and PCA based on 39 measurements for external morphologies with internal structures by CT scan data, there is almost no difference between GKZ-N 00001 and extant male individuals of E. jubatus. In this regard, GKZ-N 00001 is identified specifically as the Steller sea lion E. jubatus. Consequently, it is recognized as the oldest Steller sea lion in the North Pacific. About 0.8 Ma, the distribution of the Steller sea lion had been already established at least in the Japan Sea side of the western North Pacific.

Complete mitochondrial genome of the Antarctic fur seal (Arctocephalus gazella)

The Antarctic fur seal (Arctocephalus gazella) is an abundant Antarctic otariid. Here, we present the complete mitochondrial DNA sequence of this species, which includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and the control region for a total length of 16,156 bp. A phylogenetic analysis including all 25 publically available pinniped mitogenomes nested the Antarctic fur seal within the Otariid clade, which was clearly resolved from the Phocidae and Odobenidae.

A new Miocene pinniped Allodesmus (Mammalia: Carnivora) from Hokkaido, northern Japan

A nearly complete pinniped skeleton from the middle Miocene Okoppezawa Formation (ca 16.3-13.9 Ma), Hokkaido, northern Japan, is described as the holotype of Allodesmus uraiporensis sp. nov. The new species is distinguishable from other species of the genus by having the palatine fissure (incisive foramen) that is located anterior to the canine, an anteriorly located supraorbital process of the frontal, and by having the calcaneum with a developed peroneal tubercle. Our phylogenetic analysis suggests that the subfamily Allodesminae are represented by two genera, Atopotarus and Allodesmus, and the latter genus is represented by at least six species; Al. kernensis, Al. sinanoensis, Al. naorai, Al. packardi, Al. demerei and Al. uraiporensis sp. nov. Allodesmus uraiporensis sp. nov. is one of the oldest and the northernmost record of the genus in the western North Pacific, and it suggests that the diversification of the genus in the western North Pacific was synchronous to the time of their diversification in the eastern North Pacific.

Complete mitochondrial genome of the South American fur seal (Arctocephalus australis)

The complete mitochondrial DNA sequence of the South America fur seal (Arctocephalus australis) was obtained by a shotgun sequencing approach. The mitogenome is 16,372 bp in length and includes the genes coding for the two rRNA species (12S and 16S), 13 protein-coding genes, 22 transfer RNA genes, and a control region. The base composition is 33.0% for A, 26.7% for C, 26.1 for T and 14.2% for G, with an overall GC content of 40.9%. The description of this mitogenome will be useful for further phylogeny and genetic studies on Pinnipeds.

Eotaria citrica, sp. nov., a new stem otariid from the "Topanga" formation of Southern California

A new taxon of stem otariid, Eotaria citrica sp. nov., is described from the upper Burdigalian to lower Langhian “Topanga” formation of Orange County, California. The new species is described from mandibular and dental remains that show a unique combination of plesiomorphic and derived characters. Specifically, it is characterized by having trenchant and prominent paraconid cusps in p3–m1, lingual cingula of p2–4 with faint crenulations, premolars and molars with vestigial metaconid, bilobed root of m2 and a genial tuberosity located under p3. Furthermore, additional material of the contemporaneous Eotaria crypta is described, providing new information on the morphology of this taxon. Both species of Eotaria represent the earliest stem otariids, reinforcing the hypothesis that the group originated in the north Eastern Pacific Region. At present, the “Topanga” Fm. pinniped fauna includes Eotaria citrica, Eotaria crypta, the desmatophocid Allodesmus sp., the odobenids Neotherium sp., Pelagiarctos sp. and includes the oldest records of crown pinnipeds in California. Overall this pinniped fauna is similar to the nearly contemporaneous Sharktooth Hill bonebed. However, unambiguous records of Eotaria are still missing from Sharktooth Hill. This absence may be due to taphonomic or paleoenvironmental factors. The new “Topanga” record presented here was integrated into an overview of the late Oligocene through early Pleistocene pinniped faunas of Southern California. The results show an overall increase in body size over time until the Pleistocene. Furthermore, desmatophocids were the largest pinnipeds during the middle Miocene, but were extinct by the beginning of the late Miocene. Odobenids diversified and became the dominant pinnipeds in late Miocene through Pleistocene assemblages, usually approaching or exceeding 3 m in body length, while otariids remained as the smallest taxa. This pattern contrasts with modern assemblages, in which the phocid Mirounga angustirostris is the largest pinniped taxon in the region, odobenids are extinct and medium and small size ranges are occupied by otariids or other phocids.

The better to eat you with: the comparative feeding morphology of phocid seals (Pinnipedia, Phocidae)

One adaptation crucial to the survival of mammalian lineages that secondarily transitioned from land to water environments was the ability to capture and consume prey underwater. Phocid seals have evolved diverse feeding strategies to feed in the marine environment, and the objectives of this study were to document the specialized feeding morphologies and identify feeding strategies used by extant phocids. This study used principal component analysis (PCA) to determine the major axes of diversification in the skull for all extant phocid taxa and the recently extinct Caribbean monk seal (n = 19). Prey data gathered from the literature and musculoskeletal data from dissections were included to provide a comprehensive description of each feeding strategy. Random Forest analysis was used to determine the morphological, ecological and phylogenetic variables that best described each feeding strategy. There is morphological evidence for four feeding strategies in phocids: filter; grip and tear; suction; and pierce feeding. These feeding strategies are supported by quantitative cranial and mandibular characters, dietary information, musculoskeletal data and, for some species, behavioral observations. Most phocid species are pierce feeders, using a combination of biting and suction to opportunistically catch prey. Grip and tear and filter feeding are specialized strategies with specific morphological adaptations. These unique adaptations have allowed leopard seals (Hydrurga leptonyx) and crabeater seals (Lobodon carcinophaga) to exploit novel ecological niches and prey types. This study provides the first cranial and mandibular morphological evidence for the use of specialized suction feeding in hooded seals (Cystophora cristata), northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The most important variables in determining the feeding strategy of a given phocid species were cranial and mandibular shape, diet, and phylogeny. These results provide a framework for understanding the evolution and adaptability of feeding strategies employed by extant phocid species, and these findings can be applied to other pinniped lineages and extinct taxa.

Axial allometry in a neutrally buoyant environment: effects of the terrestrial-aquatic transition on vertebral scaling

Ecological diversification into new environments presents new mechanical challenges for locomotion. An extreme example of this is the transition from a terrestrial to an aquatic lifestyle. Here, we examine the implications of life in a neutrally buoyant environment on adaptations of the axial skeleton to evolutionary increases in body size. On land, mammals must use their thoracolumbar vertebral column for body support against gravity and thus exhibit increasing stabilization of the trunk as body size increases. Conversely, in water, the role of the axial skeleton in body support is reduced, and, in aquatic mammals, the vertebral column functions primarily in locomotion. Therefore, we hypothesize that the allometric stabilization associated with increasing body size in terrestrial mammals will be minimized in secondarily aquatic mammals. We test this by comparing the scaling exponent (slope) of vertebral measures from 57 terrestrial species (23 felids, 34 bovids) to 23 semi-aquatic species (pinnipeds), using phylogenetically corrected regressions. Terrestrial taxa meet predictions of allometric stabilization, with posterior vertebral column (lumbar region) shortening, increased vertebral height compared to width, and shorter, more disc-shaped centra. In contrast, pinniped vertebral proportions (e.g. length, width, height) scale with isometry, and in some cases, centra even become more spool-shaped with increasing size, suggesting increased flexibility. Our results demonstrate that evolution of a secondarily aquatic lifestyle has modified the mechanical constraints associated with evolutionary increases in body size, relative to terrestrial taxa.

Evolutionary relationships between digeneans of the family Brachycladiidae Odhner, 1905 and their marine mammal hosts: A cophylogenetic study

Cophylogenetic studies examine the congruence between host and parasite phylogenies. There are few studies that quantify the relative contribution of coevolutionary events, i.e. duplication, loss, failure-to-diverge, host-switching and spreading in trophically-transmitted parasites at the marine realm. We addressed this issue in the Brachycladiidae, a cosmopolitan digenean family specific to marine mammals. We used, for the first time, distance-based and event-based methods to explicitly test the coevolutionary events that have shaped the current brachycladiid-marine mammal associations. Parasite phylogeny was constructed using mtDNA ND3 sequences of nine brachycladiid species, and host phylogeny using cytochrome b sequences of 104 mammalian species. A total of 50 host-parasite links were identified. Distance-based methods supported the hypothesis of a global non-random association of host and parasite phylogenies. Significant individual links (i.e., 24 out of 50) were those related to Campula oblonga, Nasitrema delphini, N. globicephalae and Brachycladium atlanticum and their associated taxa from the Delphinoidea. Regarding event-based methods, we explored 54 schemes using different combinations of costs for each potential coevolutionary event. Three coevolutionary scenarios were identified across all schemes and in all cases the number of loss events (87-156) was the most numerous, followed by failure-to-diverge (40), duplication (3-6), host-switching (0-3) and cospeciation (0-2). We developed a framework to interpret the evolution of this host-parasite system and confirmed that failure-to-diverge and colonization with or without subsequent diversification could have been decisive in the establishment of the associations between brachycladiids and marine mammals.

The oldest known fur seal

The poorly known fossil record of fur seals and sea lions (Otariidae) does not reflect their current diversity and widespread abundance. This limited fossil record contrasts with the more complete fossil records of other pinnipeds such as walruses (Odobenidae). The oldest known otariids appear 5-6 Ma after the earliest odobenids, and the remarkably derived craniodental morphology of otariids offers few clues to their early evolutionary history and phylogenetic affinities among pinnipeds. We report a new otariid, Eotaria crypta, from the lower middle Miocene 'Topanga' Formation (15-17.1 Ma) of southern California, represented by a partial mandible with well-preserved dentition. Eotaria crypta is geochronologically intermediate between 'enaliarctine' stem pinnipedimorphs (16.6-27 Ma) and previously described otariid fossils (7.3-12.5 Ma), as well as morphologically intermediate by retaining an M2 and a reduced M1 metaconid cusp and lacking P2-4 metaconid cusps. Eotaria crypta eliminates the otariid ghost lineage and confirms that otariids evolved from an 'enaliarctine'-like ancestor.