The earliest known fully quadrupedal sirenian

Fossil Sirenia from the Pleistocene of Qatar: new questions about the antiquity of sea cows in the Gulf Region

One of the largest and least documented populations of dugongs (Dugong dugon) resides in the coastal waters of the United Arab Emirates, and waters surrounding Saudi Arabia, Bahrain, and Qatar. The archaeological record of dugongs in the Gulf Region is abundant, but little is known about their fossil record in the region. Here we report an isolated sirenian rib fragment from the Futaisi Member of the Fuwayrit Formation near the town of Al Ruwais, in northern Qatar. The Fuwayrit Formation is a marine Pleistocene deposit exposed onshore in Qatar and the United Arab Emirates. Based on the correlative dating of the basal Futaisi Member with other onshore platforms, the rib fragment is approximately 125 ka. We propose that this isolated rib (likely the first rib from the right side) belongs to Dugongidae, with strong similarities to extant Dugong. We cannot, however, eliminate the possibility that it belongs to an extinct taxon, especially given its similarities with other fossil dugongid material from both Qatar and elsewhere in the world. Aside from reflecting the presence of Gulf seagrass communities in the Pleistocene, this occurrence also suggests that different (and potentially multiple) lineages of sirenians inhabited the Gulf Region in the geologic past.

Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria)

Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record-including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.

The locomotion of extinct secondarily aquatic tetrapods

The colonisation of freshwater and marine ecosystems by land vertebrates has repeatedly occurred in amphibians, reptiles, birds and mammals over the course of 300 million years. Functional interpretations of the fossil record are crucial to understanding the forces shaping these evolutionary transitions. Secondarily aquatic tetrapods have acquired a suite of anatomical, physiological and behavioural adaptations to locomotion in water. However, much of this information is lost for extinct clades, with fossil evidence often restricted to osteological data and a few extraordinary specimens with soft tissue preservation. Traditionally, functional morphology in fossil secondarily aquatic tetrapods was investigated through comparative anatomy and correlation with living functional analogues. However, in the last two decades, biomechanics in palaeobiology has experienced a remarkable methodological shift. Anatomy-based approaches are increasingly rigorous, informed by quantitative techniques for analysing shape. Moreover, the incorporation of physics-based methods has enabled objective tests of functional hypotheses, revealing the importance of hydrodynamic forces as drivers of evolutionary innovation and adaptation. Here, we present an overview of the latest research on the locomotion of extinct secondarily aquatic tetrapods, with a focus on amniotes, highlighting the state-of-the-art experimental approaches used in this field. We discuss the suitability of these techniques for exploring different aspects of locomotory adaptation, analysing their advantages and limitations and laying out recommendations for their application, with the aim to inform future experimental strategies. Furthermore, we outline some unexplored research avenues that have been successfully deployed in other areas of palaeobiomechanical research, such as the use of dynamic models in feeding mechanics and terrestrial locomotion, thus providing a new methodological synthesis for the field of locomotory biomechanics in extinct secondarily aquatic vertebrates. Advances in imaging technology and three-dimensional modelling software, new developments in robotics, and increased availability and awareness of numerical methods like computational fluid dynamics make this an exciting time for analysing form and function in ancient vertebrates.

Paranasal sinus system and upper respiratory tract evolution in Mesozoic pelagic crocodylomorphs

Thalattosuchians were a predominately marine clade of Mesozoic crocodylomorphs, including semi-aquatic teleosauroid and obligately pelagic metriorhynchid subclades. Recent advances in our understanding of thalattosuchian endocranial anatomy have revealed new details of the evolutionary transition from terrestrial to marine to pelagic taxa. Paranasal sinuses, however, have received little attention. Herein, we investigate the evolution of the paranasal sinus system and part of the upper respiratory system (nasopharyngeal ducts) in Thalattosuchia, by reconstructing the nasal and paranasal anatomy in CT scans of seven thalattosuchian skulls: one teleosauroid, two basal metriorhynchoids and four metriorhynchids. Our outgroups were: three extant crocodylian species (including adult and subadult skulls) and the basal crocodyliform Protosuchus. We found thalattosuchians exhibit exceptionally reduced paranasal sinus systems, solely comprising the antorbital sinus, as has been previously proposed. The semi-aquatic basal thalattosuchians Palgiopthalmosuchus gracilirostris and Pelagosaurus typus both have an antorbital sinus partially located medial to a reduced external antorbital fenestra and broadly communicating with the dorsal alveolar canal. In pelagic metriorhynchids, the antorbital cavity is more extensive than in basal taxa and possibly had an active function associated with a hypothesized accessory suborbital diverticulum, but our reconstructions are insufficient to confirm or reject the presence of such a diverticulum. The nasopharyngeal ducts of metriorhynchids are dorsoventrally enlarged, possibly enabling stronger ventilation. The sequence of acquisition of craniofacial adaptations show a mosaic pattern and appears to predate many skeletal adaptations, suggesting these changes occurred early in the thalattosuchian marine transition.

Ecophysiological steps of marine adaptation in extant and extinct non-avian tetrapods

Marine reptiles and mammals are phylogenetically so distant from each other that their marine adaptations are rarely compared directly. We reviewed ecophysiological features in extant non-avian marine tetrapods representing 31 marine colonizations to test whether there is a common pattern across higher taxonomic groups, such as mammals and reptiles. Marine adaptations in tetrapods can be roughly divided into aquatic and haline adaptations, each of which seems to follow a sequence of three steps. In combination, these six categories exhibit five steps of marine adaptation that apply across all clades except snakes: Step M1, incipient use of marine resources; Step M2, direct feeding in the saline sea; Step M3, water balance maintenance without terrestrial fresh water; Step M4, minimized terrestrial travel and loss of terrestrial feeding; and Step M5, loss of terrestrial thermoregulation and fur/plumage. Acquisition of viviparity is not included because there is no known case where viviparity evolved after a tetrapod lineage colonized the sea. A similar sequence is found in snakes but with the haline adaptation step (Step M3) lagging behind aquatic adaptation (haline adaptation is Step S5 in snakes), most likely because their unique method of water balance maintenance requires a supply of fresh water. The same constraint may limit the maximum body size of fully marine snakes. Steps M4 and M5 in all taxa except snakes are associated with skeletal adaptations that are mechanistically linked to relevant ecophysiological features, allowing assessment of marine adaptation steps in some fossil marine tetrapods. We identified four fossil clades containing members that reached Step M5 outside of stem whales, pinnipeds, sea cows and sea turtles, namely Eosauropterygia, Ichthyosauromorpha, Mosasauroidea, and Thalattosuchia, while five other clades reached Step M4: Saurosphargidae, Placodontia, Dinocephalosaurus, Desmostylia, and Odontochelys. Clades reaching Steps M4 and M5, both extant and extinct, appear to have higher species diversity than those only reaching Steps M1 to M3, while the total number of clades is higher for the earlier steps. This suggests that marine colonizers only diversified greatly after they minimized their use of terrestrial resources, with many lineages not reaching these advanced steps. Historical patterns suggest that a clade does not advance to Steps M4 and M5 unless these steps are reached early in the evolution of the clade. Intermediate forms before a clade reached Steps M4 and M5 tend to become extinct without leaving extant descendants or fossil evidence. This makes it difficult to reconstruct the evolutionary history of marine adaptation in many clades. Clades that reached Steps M4 and M5 tend to last longer than other marine tetrapod clades, sometimes for more than 100 million years.

The evolutionary history of manatees told by their mitogenomes

The manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81–10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1–4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp > 0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT = 6.06, p = 0.0069, BEB posterior probability = 0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.

Olfaction of aquatic amniotes

Amniotes originated on land, but aquatic/amphibious groups emerged multiple times independently in amniotes. On becoming aquatic, species with different phylogenetic backgrounds and body plans have to adapt themselves to handle similar problems inflicted by their new environment, and this makes aquatic adaptation of amniotes one of the greatest natural experiments. Particularly, evolution of the sense of smell upon aquatic adaptation is of great interest because receptors required for underwater olfaction differ remarkably from those for terrestrial olfaction. Here, I review the olfactory capabilities of aquatic/amphibious amniotes, especially those of cetaceans and sea snakes. Most aquatic/amphibious amniotes show reduced olfactory organs, receptor gene repertoires, and olfactory capabilities. Remarkably, cetaceans and sea snakes show extreme examples: cetaceans have lost the vomeronasal system, and furthermore, toothed whales have lost all of their olfactory nervous systems. Baleen whales can smell in the air, but their olfactory capability is limited. Fully aquatic sea snakes have lost the main olfactory system but they retain the vomeronasal system for sensing underwater. Amphibious species show an intermediate status between terrestrial and aquatic species, implying their importance on understanding the process of aquatic adaptation. The olfactory capabilities of aquatic amniotes are diverse, reflecting their diverse phylogenetic backgrounds and ecology.

Spatial genetic structure in the rock hyrax (Procavia capensis) across the Namaqualand and western Fynbos areas of South Africa — a mitochondrial and microsatellite perspective

The interplay between biotic and abiotic environments is increasingly recognized as a major determinant of spatial genetic patterns. Among spatial genetic studies, saxicolous or rock-dwelling species remain underrepresented in spite of their strict dependence on landscape structure. Here we investigated patterns and processes operating at different spatial (fine and regional scales) and time scales (using mitochondrial and microsatellite markers) in the rock hyrax (Procavia capensis (Pallas, 1766)). Our focus was on the western seaboard of South Africa and included two recognized biodiversity hotspots (Cape Floristic Region and Succulent Karoo). At fine spatial scale, significant genetic structure was present between four rocky outcrops in an isolated population, likely driven by the social system of this species. At a broader spatial scale, ecological dependence on rocky habitat and population-level processes, in conjunction with landscape structure, appeared to be the main drivers of genetic diversity and structure. Large areas devoid of suitable rocky habitat (e.g., the Knersvlakte, Sandveld, and Cape Flats, South Africa) represent barriers to gene flow in the species, although genetic clusters closely follow climatic, geological, and phytogeographic regions, possibly indicating ecological specialization or adaptation as contributing factors enforcing isolation. Taken together, our study highlights the need to consider both intrinsic and extrinsic factors when investigating spatial genetic structures within species.

Convergent evolution and possible constraint in the posterodorsal retraction of the external nares in pelagic crocodylomorphs

Amongst Mesozoic marine reptiles, metriorhynchid crocodylomorphs were unique in evolving into pelagically adapted forms with little-to-no posterodorsal retraction of the external nares. Narial retraction is a common adaptation seen in sustained swimmers, notably occurring during cetacean evolution. Mesosaurids and the basalmost known members of ichthyosauriforms, thalattosaurians, saurosphargids, sauropterygians, pleurosaurids and mosasauroids had the external nares divided by an ossified bar, bound by multiple cranial bones and were positioned back from the tip of the rostrum. However, metriorhynchids evolved from taxa with a single external naris bound solely by the premaxilla, and positioned near the tip of an elongate rostrum. We posit that metriorhynchids were uniquely disadvantaged in evolving into sustained swimmers. Herein we describe three Late Jurassic metriorhynchid cranial rostra that display differing degrees of narial retraction. In our new phylogenetic analyses, the backwards migration of the narial fossa posterior margin occurred independently at least four times in Metriorhynchidae, whereas the backwards migration of the anterior margin only occurred twice. Although Rhacheosaurini share the backwards migration of the anterior and posterior narial margins, posterodorsal retraction occurred differently along three lineages. This culminated in the Early Cretaceous, where a rhacheosaurin evolved nares bound by the premaxilla and maxilla, and significantly posterodorsally retracted.

Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes

Marine amniotes, a polyphyletic group, provide an excellent opportunity for studying convergent evolution. Their sense of smell tends to degenerate, but this process has not been explored by comparing fully aquatic species with their amphibious relatives in an evolutionary context. Here, we sequenced the genomes of fully aquatic and amphibious sea snakes and identified repertoires of chemosensory receptor genes involved in olfaction. Snakes possess large numbers of the olfactory receptor (OR) genes and the type-2 vomeronasal receptor (V2R) genes, and expression profiling in the olfactory tissues suggests that snakes use the ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal system (VNS). The number of OR genes has decreased in sea snakes, and fully aquatic species lost MOS which is responsible for detecting airborne odours. By contrast, sea snakes including fully aquatic species retain a number of V2R genes and a well-developed VNS for smelling underwater. This study suggests that the sense of smell also degenerated in sea snakes, particularly in fully aquatic species, but their residual olfactory capability is distinct from that of other fully aquatic amniotes. Amphibious species show an intermediate status between terrestrial and fully aquatic snakes, implying their importance in understanding the process of aquatic adaptation.

Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia

As limits on O₂ availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller’s sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb–O₂ affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O₂ extraction from finite lung stores and suppress tissue O₂ offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb–O₂ affinity in (sub)Arctic Steller’s sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.

First adequately-known quadrupedal sirenian from Eurasia (Eocene, Bay of Biscay, Huesca, northeastern Spain)

Sirenians are the only extant herbivorous mammals fully adapted to an aquatic lifestyle. They originated in Africa during the Paleocene from an undetermined clade of afrotherian mammals, and by the end of the Eocene they were widely distributed across the tropical latitudes. Here we introduce Sobrarbesiren cardieli gen. et sp. nov. It is the first adequately-known quadrupedal sirenian from Eurasia and the oldest record of this clade from western Europe. Fossils have been recovered from the middle Lutetian (SBZ15) site of Castejón de Sobrarbe-41 (Huesca, Spain), and comprise many cranial and postcranial remains, including pelvic girdle and hind limb bones, from at least six sirenian individuals of different ontogenetic stages. Sobrarbesiren shows a suite of characters previously considered synapomorphies of different clades of derived sirenians, such as the presence of the processus retroversus of the squamosal and the pterygoid fossa, combined with ancestral characters such as the presence of an alisphenoid canal, a permanent P5, at least two sacral vertebrae, a primitive pelvis and functional femora and fibulae. Sobrarbesiren is recovered as the sister taxon of Dugongidae and represents a transitional stage of adaptation to aquatic life between the amphibious quadrupedal prorastomids and the aquatic quadrupedal protosirenids.

Evolution of the patellar sesamoid bone in mammals

The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four and six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition) and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function, especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats-from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds-remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.

Out of Asia: Anthropoid Origins and the Colonization of Africa

Anthropoid primates other than humans show a conspicuously disjunct geographic distribution today, inhabiting mostly tropical and subtropical parts of Asia, Africa, and Central and South America. During the latter part of the Eocene, early anthropoids showed a similarly disjunct distribution, although South America and Africa were both island continents then. Attempts to explain the historical biogeography of anthropoids as resulting from vicariance caused by tectonic rifting between South America and Africa conflict with both the chronology and the topology of anthropoid evolution. The only viable hypotheses that remain entail sweepstakes dispersal across marine barriers by early monkeys on natural rafts. Early anthropoids and certain Asian rodent clades seem to have been especially adept at accomplishing sweepstakes dispersal, particularly during the Eocene, although this process has classically been envisioned as highly random and extremely rare. This article identifies and discusses biological and geological factors that make sweepstakes dispersal by certain taxa at given times far less random than previously conceived.

Farewell to life on land - thoracic strength as a new indicator to determine paleoecology in secondary aquatic mammals

Habitat shifts from land to water have occurred independently in several mammal lineages. However, because we do not know completely about the relationship between skeletal morphology and function, both reliable life reconstructions of each extinct taxon and the timing of those shifts in locomotor strategies are yet to be fully understood. We estimated the strengths of rib cages against vertical compression in 26 extant and four extinct mammal specimens including cetartiodactyls, paenungulates, and carnivorans, representing 11 terrestrial, six semi-aquatic, and nine obligate aquatic taxa. Our analyses of extant taxa showed that strengths were high among terrestrial/semi-aquatic mammals, whose rib cages are subjected to vertical compression during the support on land, whereas strengths were low among obligate aquatic mammals, whose rib cages are not subjected to antigravity force in the water. We therefore propose rib strength as a new index to estimate the ability of an animal to be supported on land while being supported by either the forelimbs or thoracic region. According to our analyses of extinct taxa, this ability to be supported on land was rejected for a basal cetacean (Cetartiodactyla: Ambulocetus) and two desmostylians (Paenungulata: Paleoparadoxia and Neoparadoxia). However, this ability was not rejected for one desmostylian species (Desmostylus). Further study of the ribs of extant/extinct semi-aquatic taxa may help in understanding the ecological shifts in these groups.

Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia

The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.

Distinct patterns of desynchronized limb regression in malagasy scincine lizards (squamata, scincidae)

Scincine lizards in Madagascar form an endemic clade of about 60 species exhibiting a variety of ecomorphological adaptations. Several subclades have adapted to burrowing and convergently regressed their limbs and eyes, resulting in a variety of partial and completely limbless morphologies among extant taxa. However, patterns of limb regression in these taxa have not been studied in detail. Here we fill this gap in knowledge by providing a phylogenetic analysis of DNA sequences of three mitochondrial and four nuclear gene fragments in an extended sampling of Malagasy skinks, and microtomographic analyses of osteology of various burrowing taxa adapted to sand substrate. Based on our data we propose to (i) consider Sirenoscincus Sakata & Hikida, 2003, as junior synonym of Voeltzkowia Boettger, 1893; (ii) resurrect the genus name Grandidierina Mocquard, 1894, for four species previously included in Voeltzkowia; and (iii) consider Androngo Brygoo, 1982, as junior synonym of Pygomeles Grandidier, 1867. By supporting the clade consisting of the limbless Voeltzkowia mira and the forelimb-only taxa V. mobydick and V. yamagishii, our data indicate that full regression of limbs and eyes occurred in parallel twice in the genus Voeltzkowia (as hitherto defined) that we consider as a sand-swimming ecomorph: in the Voeltzkowia clade sensu stricto the regression first affected the hindlimbs and subsequently the forelimbs, whereas the Grandidierina clade first regressed the forelimbs and subsequently the hindlimbs following the pattern prevalent in squamates. Timetree reconstructions for the Malagasy Scincidae contain a substantial amount of uncertainty due to the absence of suitable primary fossil calibrations. However, our preliminary reconstructions suggest rapid limb regression in Malagasy scincids with an estimated maximal duration of 6 MYr for a complete regression in Paracontias, and 4 and 8 MYr respectively for complete regression of forelimbs in Grandidierina and hindlimbs in Voeltzkowia.

Vascularization of the gray whale palate (Cetacea, Mysticeti, Eschrichtius robustus): soft tissue evidence for an alveolar source of blood to baleen

The origin of baleen in mysticetes heralded a major transition during cetacean evolution. Extant mysticetes are edentulous in adulthood, but rudimentary teeth develop in utero within open maxillary and mandibular alveolar grooves. The teeth are resorbed prenatally and the alveolar grooves close as baleen germ develops. Arteries supplying blood to highly vascularized epithelial tissue from which baleen develops pass through lateral nutrient foramina in the area of the embryonic alveolar grooves and rudimentary teeth. Those vessels are hypothesized to be branches of the superior alveolar artery, but branches of the greater palatine arteries may play a role in the baleen vascularization. Through a combination of latex injection, CT, and traditional dissection of the palate of a neonatal gray whale (Eschrichtius robustus), we confirm that the baleen receives blood from vessels within the superior alveolar canal via the lateral foramina. The greater palatine artery is restricted to its own passage with no connections to the baleen. This study has implications for the presence of baleen in extinct taxa by identifying the vessels and bony canals that supply blood to the epithelium from which baleen develops. The results indicate that the lateral foramina in edentulous mysticete fossils are bony correlates for the presence of baleen, and the results can be used to help identify bony canals and foramina that have been used to reconstruct baleen in extinct mysticetes that retained teeth in adulthood. Further comparisons are made with mammals that also possess oral keratin structures, including ruminants, ornithorhynchid monotremes, and sirenians.

Convergent evolution of the genomes of marine mammals

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Early Triassic marine biotic recovery: the predators' perspective

Examining the geological past of our planet allows us to study periods of severe climatic and biological crises and recoveries, biotic and abiotic ecosystem fluctuations, and faunal and floral turnovers through time. Furthermore, the recovery dynamics of large predators provide a key for evaluation of the pattern and tempo of ecosystem recovery because predators are interpreted to react most sensitively to environmental turbulences. The end-Permian mass extinction was the most severe crisis experienced by life on Earth, and the common paradigm persists that the biotic recovery from the extinction event was unusually slow and occurred in a step-wise manner, lasting up to eight to nine million years well into the early Middle Triassic (Anisian) in the oceans, and even longer in the terrestrial realm. Here we survey the global distribution and size spectra of Early Triassic and Anisian marine predatory vertebrates (fishes, amphibians and reptiles) to elucidate the height of trophic pyramids in the aftermath of the end-Permian event. The survey of body size was done by compiling maximum standard lengths for the bony fishes and some cartilaginous fishes, and total size (estimates) for the tetrapods. The distribution and size spectra of the latter are difficult to assess because of preservation artifacts and are thus mostly discussed qualitatively. The data nevertheless demonstrate that no significant size increase of predators is observable from the Early Triassic to the Anisian, as would be expected from the prolonged and stepwise trophic recovery model. The data further indicate that marine ecosystems characterized by multiple trophic levels existed from the earliest Early Triassic onwards. However, a major change in the taxonomic composition of predatory guilds occurred less than two million years after the end-Permian extinction event, in which a transition from fish/amphibian to fish/reptile-dominated higher trophic levels within ecosystems became apparent.

Gradual adaptation of bone structure to aquatic lifestyle in extinct sloths from Peru

Non-pathological densification (osteosclerosis) and swelling (pachyostosis) of bones are the main modifications affecting the skeleton of land vertebrates (tetrapods) that returned to water. However, a precise temporal calibration of the acquisition of such adaptations is still wanting. Here, we assess the timing of such acquisition using the aquatic sloth Thalassocnus, from the Neogene of the Pisco Formation, Peru. This genus is represented by five species occurring in successive vertebrate-bearing horizons of distinct ages. It yields the most detailed data about the gradual acquisition of aquatic adaptations among tetrapods, in displaying increasing osteosclerosis and pachyostosis through time. Such modifications, reflecting a shift in the habitat from terrestrial to aquatic, occurred over a short geological time span (ca 4 Myr). Otherwise, the bones of terrestrial pilosans (sloths and anteaters) are much more compact than the mean mammalian condition, which suggests that the osteosclerosis of Thalassocnus may represent an exaptation.

Evolution of mammalian diving capacity traced by myoglobin net surface charge

Extended breath-hold endurance enables the exploitation of the aquatic niche by numerous mammalian lineages and is accomplished by elevated body oxygen stores and adaptations that promote their economical use. However, little is known regarding the molecular and evolutionary underpinnings of the high muscle myoglobin concentration phenotype of divers. We used ancestral sequence reconstruction to trace the evolution of this oxygen-storing protein across a 130-species mammalian phylogeny and reveal an adaptive molecular signature of elevated myoglobin net surface charge in diving species that is mechanistically linked with maximal myoglobin concentration. This observation provides insights into the tempo and routes to enhanced dive capacity evolution within the ancestors of each major mammalian aquatic lineage and infers amphibious ancestries of echidnas, moles, hyraxes, and elephants, offering a fresh perspective on the evolution of this iconic respiratory pigment.

Cranial remain from Tunisia provides new clues for the origin and evolution of Sirenia (Mammalia, Afrotheria) in Africa

Sea cows (manatees, dugongs) are the only living marine mammals to feed solely on aquatic plants. Unlike whales or dolphins (Cetacea), the earliest evolutionary history of sirenians is poorly documented, and limited to a few fossils including skulls and skeletons of two genera composing the stem family of Prorastomidae (Prorastomus and Pezosiren). Surprisingly, these fossils come from the Eocene of Jamaica, while stem Hyracoidea and Proboscidea - the putative sister-groups to Sirenia - are recorded in Africa as early as the Late Paleocene. So far, the historical biogeography of early Sirenia has remained obscure given this paradox between phylogeny and fossil record. Here we use X-ray microtomography to investigate a newly discovered sirenian petrosal from the Eocene of Tunisia. This fossil represents the oldest occurrence of sirenians in Africa. The morphology of this petrosal is more primitive than the Jamaican prorastomids’ one, which emphasizes the basal position of this new African taxon within the Sirenia clade. This discovery testifies to the great antiquity of Sirenia in Africa, and therefore supports their African origin. While isotopic analyses previously suggested sirenians had adapted directly to the marine environment, new paleoenvironmental evidence suggests that basal-most sea cows were likely restricted to fresh waters.

Iterative evolution of sympatric seacow (Dugongidae, Sirenia) assemblages during the past ~26 million years

Extant sirenians show allopatric distributions throughout most of their range. However, their fossil record shows evidence of multispecies communities throughout most of the past ∼26 million years, in different oceanic basins. Morphological differences among co-occurring sirenian taxa suggest that resource partitioning played a role in structuring these communities. We examined body size and ecomorphological differences (e.g., rostral deflection and tusk morphology) among sirenian assemblages from the late Oligocene of Florida, early Miocene of India and early Pliocene of Mexico; each with three species of the family Dugongidae. Although overlapping in several ecomorphological traits, each assemblage showed at least one dominant trait in which coexisting species differed. Fossil sirenian occurrences occasionally are monotypic, but the assemblages analyzed herein show iterative evolution of multispecies communities, a phenomenon unparalleled in extant sirenian ecology. As primary consumers of seagrasses, these communities likely had a strong impact on past seagrass ecology and diversity, although the sparse fossil record of seagrasses limits direct comparisons. Nonetheless, our results provide robust support for previous suggestions that some sirenians in these extinct assemblages served as keystone species, controlling the dominance of climax seagrass species, permitting more taxonomically diverse seagrass beds (and sirenian communities) than many of those observed today.

Shifting sources of productivity in the coastal marine tropics during the Cenozoic era

Changes in the rates and sources of marine primary production over time are difficult to document owing to the absence of direct estimates of past productivity. Here, I use the maximum body sizes of the largest species in each of 23 tropical shallow-water marine molluscan guilds (groups of species with similar habits and trophic roles) to trace the relative importance of planktonic and benthic primary productivity from the Eocene (55 Ma) onwards. The largest members of guilds are least constrained in exploiting resources and therefore reflect the availability and accessibility of those resources most accurately. Maximum sizes of suspension-feeders and predators increased by a factor of 2.3 and 4.0, respectively, whereas those in four out of five herbivorous guilds declined. I interpret these patterns, which are discernible throughout the coastal tropics, to mean that primary production in the Eocene marine tropics was concentrated on the seafloor, as is the case today on offshore reefs and islands, and that the Miocene to the recent interval witnessed a dramatic increase in planktonic productivity along continental margins. The rise in planktonic fertility is best explained by an increase in nutrient supply from the land associated with intense global tectonic activity and more vigorous ocean mixing owing to cooling.

The new framework for understanding placental mammal evolution

An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of dermopterans within euarchontoglires. A variety of names for sub-clades within the new placental mammal tree have been proposed, not all of which follow conventions regarding priority and stability. More importantly, the new phylogenetic framework enables the formulation of new hypotheses and testing thereof, for example regarding the possible developmental dichotomy that seems to distinguish members of the newly identified southern and northern radiations of living placental mammals.

A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence

BACKGROUND

The placental mammalian clade Afrotheria is now supported by diverse forms of genomic data, but interordinal relationships within, and morphological support for, the group remains elusive. As a means for addressing these outstanding problems, competing hypotheses of afrotherian interordinal relationships were tested through simultaneous parsimony analysis of a large data set (> 4,590 parsimony informative characters) containing genomic data (> 17 kb of nucleotide data, chromosomal associations, and retroposons) and 400 morphological characters scored across 16 extant and 35 extinct afrotherians.

RESULTS

Parsimony analysis of extant taxa alone recovered the interordinal topology (Afrosoricida, ((Macroscelidea, Tubulidentata), (Hyracoidea, (Proboscidea, Sirenia)))). Analysis following addition of extinct taxa instead supported Afroinsectivora (Afrosoricida + Macroscelidea) and Pseudoungulata (Tubulidentata + Paenungulata), as well as Tethytheria (Proboscidea + Sirenia). This latter topology is, however, sensitive to taxon deletion and different placements of the placental root, and numerous alternative interordinal arrangements within Afrotheria could not be statistically rejected. Relationships among extinct stem members of each afrotherian clade were more stable, but one alleged stem macroscelidean (Herodotius) never grouped with that clade and instead consistently joined pseudoungulates or paenungulates. When character transformations were optimized onto a less resolved afrotherian tree that reflects uncertainty about the group's interordinal phylogeny, a total of 21 morphological features were identified as possible synapomorphies of crown Afrotheria, 9 of which optimized unambiguously across all character treatments and optimization methods.

CONCLUSION

Instability in afrotherian interordinal phylogeny presumably reflects rapid divergences during two pulses of cladogenesis - the first in the Late Cretaceous, at and just after the origin of crown Afrotheria, and the second in the early Cenozoic, with the origin of crown Paenungulata. Morphological evidence for divergences during these two pulses either never existed or has largely been "erased" by subsequent evolution along long ordinal branches. There may, nevertheless, be more morphological character support for crown Afrotheria than is currently assumed; the features identified here as possible afrotherian synapomorphies can be further scrutinized through future phylogenetic analyses with broader taxon sampling, as well as recovery of primitive fossil afrotherians from the Afro-Arabian landmass, where the group is likely to have first diversified.

Swimming kinematics of the Florida manatee (Trichechus manatus latirostris): hydrodynamic analysis of an undulatory mammalian swimmer

The submerged swimming of the Florida manatee (Trichechus manatus latirostris), a subspecies of the West Indian manatee, was studied by filming individuals as they swam rectilinearly in a large pool at several rehabilitation centers. The swimming was analyzed using videography to detail the kinematics in conjunction with a hydromechanical model to determine the power output (P(t)) and propulsive efficiency (eta(p)). Manatees swam at velocities of 0.06-1.14 m s(-1). Locomotion was accomplished by undulation of the body and caudal fluke. Undulatory locomotion is a rapid and relatively high-powered propulsive mode involved in cruising and migrating by a variety of swimmers. Manatees displayed an undulatory swimming mode by passing a dorso-ventrally oriented traveling wave posteriorly along the body. The propulsive wave traveled at a higher velocity than the forward velocity of the animal. The frequency of the propulsive cycle (f) increased linearly with increasing swimming velocity (U). Amplitude at the tip of the caudal fluke (A) remained constant with respect to U and was 22% of body length. P(t) increased curvilinearly with U. The mean eta(p), expressing the relationship of the thrust power generated by the paddle-shaped caudal fluke to the total mechanical power, was 0.73. The maximum eta(p) was 0.82 at 0.95 m s(-1). Despite use of a primitive undulatory swimming mode and paddle-like fluke for propulsion, the manatee is capable of swimming with a high efficiency but lower power outputs compared with the oscillatory movements of the high-aspect ratio flukes of cetaceans. The swimming performance of the manatee is in accordance with its habits as an aquatic grazer that seasonally migrates over extended distances.

Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade

The phylogenetic pattern and timing of the radiation of mammals, especially the geographical origins of major crown clades, are areas of controversy among molecular biologists, morphologists and palaeontologists. Molecular phylogeneticists have identified an Afrotheria clade, which includes several taxa as different as tenrecs (Tenrecidae), golden moles (Chrysochloridae), elephant-shrews (Macroscelididae), aardvarks (Tubulidentata) and paenungulates (elephants, sea cows and hyracoids). Molecular data also suggest a Cretaceous African origin for Afrotheria within Placentalia followed by a long period of endemic evolution on the Afro-Arabian continent after the mid-Cretaceous Gondwanan breakup (approx. 105-25 Myr ago). However, there was no morphological support for such a natural grouping so far. Here, we report new dental and postcranial evidence of Eocene stem hyrax and macroscelidid from North Africa that, for the first time, provides a congruent phylogenetic view with the molecular Afrotheria clade. These new fossils imply, however, substantial changes regarding the historical biogeography of afrotheres. Their long period of isolation in Africa, as assumed by molecular inferences, is now to be reconsidered inasmuch as Eocene paenungulates and elephant-shrews are here found to be related to some Early Tertiary Euramerican 'hyopsodontid condylarths' (archaic hoofed mammals). As a result, stem members of afrotherian clades are not strictly African but also include some Early Paleogene Holarctic mammals.

Vertebral anatomy in the Florida manatee, Trichechus manatus latirostris: a developmental and evolutionary analysis

The vertebral column of the Florida manatee presents an unusual suite of morphological traits. Key among these are a small precaudal count, elongate thoracic vertebrae, extremely short neural spines, lack of a sacral series, high lumbar variability, and the presence of six instead of seven cervical vertebrae. This study documents vertebral morphology, size, and lumbar variation in 71 skeletons of Trichechus manatus latirostris (Florida manatee) and uses the skeletons of Trichechus senegalensis (west African manatee) and Dugong dugon (dugong) in comparative analysis. Vertebral traits are used to define morphological, and by inference developmental, column modules and to propose their hierarchical relationships. A sequence of evolutionary innovations in column morphology is proposed. Results suggest that the origin of the fluke and low rates of cervical growth originated before separation of trichechids (manatees) and dugongids (dugongs). Meristic reduction in count is a later, trichechid innovation and is expressed across the entire precaudal column. Elongation of thoracic vertebrae may be an innovative strategy to generate an elongate column in an animal with a small precaudal count. Elimination of the lumbus through both meristic and homeotic reduction is currently in progress.

Evolution of marine mammals: Back to the sea after 300 million years

The fossil record demonstrates that mammals re-entered the marine realm on at least seven separate occasions. Five of these clades are still extant, whereas two are extinct. This review presents a brief introduction to the phylogeny of each group of marine mammals, based on the latest studies using both morphological and molecular data. Evolutionary highlights are presented, focusing on changes affecting the sensory systems, locomotion, breathing, feeding, and reproduction in Cetacea, Sirenia, Desmostylia, and Pinnipedia. Aquatic adaptations are specifically cited, supported by data from morphological and geochemical studies. For example, analysis of oxygen isotopes incorporated into fossil tooth enamel indicates whether these mammals foraged in (and, therefore, ingested) fresh water or sea water. Comparisons between groups are made to see if there are any common patterns, particularly relating to adaptations to aquatic life. Results show that aquatic characteristics evolved in mosaic patterns and that different morphological solutions to aquatic conditions were achieved separately in each of these groups. Changes in the axial and appendicular skeleton assist with locomotion for aquatic foraging. Nostril and eye placement modifications accommodate wading versus underwater foraging needs. All groups exhibit aquatic adaptations directly related to feeding, particularly changes in the dentition and rostrum. The earliest representatives of these clades all show morphological features that indicate they were feeding while in the water, suggesting that feeding ecology is a key factor in the evolution of marine mammals.