Maureen A. O'Leary

Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution.

Background Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. Methodology/Principal Findings We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, †Creodonta, Lipotyphla, and the †raoellid artiodactylan †Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to †Indohyus, with †Mesonychia outside of Artiodactyla. The relationships of †Mesonychia and †Indohyus are highly unstable, however - in trees only two steps longer than minimum length, †Mesonychia falls inside Artiodactyla and displaces †Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. Conclusions/Significance Integration of new fossil material of †Indohyus impacts placement of another extinct clade †Mesonychia, pushing it much farther down the tree. The phylogenetic position of †Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales + hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.

The Position of Cetacea Within Mammalia: Phylogenetic Analysis of Morphological Data from Extinct and Extant Taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.

Deciphering whale origins with molecules and fossils

Recent efforts by paleontologists to find fossils that record the origin of whales have yielded an impressive collection of transitional forms from the Eocene. Simultaneously, molecular biologists have dramatically increased the genetic information relevant to whale phylogeny. Combined analyses of the available data indicate areas of congruence but also gross conflict between characters from extinct and extant organisms. The incongruence underscores key areas where data have yet to be collected or merged in a combined phylogenetic framework. Continued synthesis of molecular and paleontological evidence is the strongest test of phylogenetic hypotheses, and provides a solid foundation for scenarios of adaptation related to this remarkable macroevolutionary transformation.

Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well‐known and relatively complete fossil species. We combined data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., †entelodonts, “†anthracotheriids” and †mesonychians) are positioned. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with > 40 000 molecular characters, including new data from 10 genes. The analysis supported a topology consistent with the majority of recently published molecular studies. Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct †Mesonychia was more closely related to Cetacea than was any “artiodactylan.”“†Anthracotheriids” were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. The total evidence analysis overturned a highly nested position for Moschus supported by molecular data alone. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data. The osteological–dental data alone, however, did not support inclusion of cetaceans within crown “Artiodactyla.” Recently discovered ankle bones from fossil whales reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other “artiodactylans”.

A dyrosaurid crocodyliform braincase from Mali

Abstract A well-preserved crocodyliform specimen from the Maastrichtian or Paleocene of Mali preserves the braincase and posterior dermatocranium. It is referred to Dyrosauridae on the basis of several derived features (a prominent anterior process of the postorbital, discrete occipital processes on the exoccipitals, significant quadratojugal contribution to jaw joint) and tentatively referred to Rhabdognathus on the basis of supratemporal fenestra shape. The lacrymal and prefrontal are relatively short compared with those published for other dyrosaurids. The palatines border the internal choanae anteriorly, and the choanae are divided by a midline septum derived from the pterygoids. The prefrontal pillars are mediolaterally broad and contact the palate ventrally. One stapes is preserved in place. The basicranial pneumatic system is very unusual, in that the anterior and posterior branches of the median eustachian canal are both separate at the palatal surface, and the pterygoids form part of the border for the anterior branch. The lateral eustachian openings lie within fossae on the lateral surface of the braincase and face laterally, with a descending process of the exoccipital nearly intersecting the opening. The braincase and surrounding dermal bones are elongate anteroposteriorly, and the postorbitals posterior ramus extends along the posterodorsal margin of the infratemporal fenestra. The quadrate ramus projects ventrally. These observations clarify character optimizations in previous phylogenetic analyses of Crocodyliformes.

The time of origin of whales and the role of behavioral changes in the terrestrial-aquatic transition

Addition of the recently discovered fossil Nalacetus to a phylogenetic analysis of basicranial, cranial, dental, postcranial, and soft morphological characters reveals that it is the most basal cetacean, and that mesonychians form the monophyletic sister group to Cetacea. The molars of Nalacetus elucidate transformations in dental morphology that occurred early in the cetacean radiation and clarify certain derived differences in molar cusp position between cetaceans and the extinct clade, Mesonychia, hypothesized to be their sister taxon. Nalacetus and other archaic cetaceans share derived vertically elongate shearing facets on the lower molars. Applying the Extant Phylogenetic Bracket, we advance the hypothesis that these facets are an osteological correlate of aquatic predation. Our functional interpretation of this character and its distribution within Cetacea indicates that a behavioral change in tooth use characterized the origin of the clade. Comparison of the transformation of this dental character with that of the cetacean pelvis indicates that a change in tooth use (feeding behavior) occurred before loss of the ability to engage in terrestrial locomotion. The most parsimonious phylogenetic hypothesis presented here has a significant fit with the stratigraphic record as determined by the Manhattan Stratigraphic Measure, which is corroborated by retention indices of stratigraphic data. Ghost lineages necessitated by the phylogenetic hypothesis extend the stratigraphic range of Cetacea into the middle Paleocene (Torrejonian), ten million years earlier than the oldest cetacean fossil currently known. Primitive features of Nalacetus , the large number of synapomorphies diagnosing Cetacea, and the implied ghost lineage suggest that the early cetacean radiation was much more extensive than has been previously recognized.

Bivalve Borings in Phosphatic Coprolites and Bone, Cretaceous–Paleogene, Northeastern Mali

Abstract Bivalve borings are described for the first time in coprolites. They occur along with bored bone from Cretaceous through Eocene phosphatic conglomerates in the Taoudeni and Iullemmeden Basins of northeastern Mali. Coprolites are extensively penetrated by flask-shaped borings (Gastrochaenolites): the oldest known occurrence of the ichnospecies G. ornatus preserves mechanical scratch traces at the base of some early Eocene coprolite borings. The alleged tracemaker, a pholad bivalve of the Subfamily Martesiinae, is preserved as an external mold in one of the early Eocene coprolites. It is the first occurrence of rock-borers in this subfamily from the Paleocene of West Africa. Bored coprolites were very firm to fully lithified (paleocoprolites) when bored by the pholads, indicating early-diagenetic phosphogenesis of the clasts. The intense and repeated bioerosion of coprolites and bone by pholads suggests a long residence time in shallow-marine waters for the clasts. Therefore, the vertebrate fossil assemblages in these Mali conglomerates are considered highly time-averaged. Recognition of Gastrochaenolites borings in vertebrate remains provides useful taphonomic and paleoenvironmental information, despite their destructive impact on the fossils.

Next-generation phenomics for the Tree of Life

The phenotype represents a critical interface between the genome and the environment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree building, and they enable scientists to reconstruct the evolutionary history of organisms, including most fossil taxa, for which genetic data are unavailable. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life. In contrast to recent advances in molecular sequencing, which has become faster and cheaper through recent technological advances, phenotypic data collection remains often prohibitively slow and expensive. The next-generation phenomics project is a collaborative, multidisciplinary effort to leverage advances in image analysis, crowdsourcing, and natural language processing to develop and implement novel approaches for discovering and scoring the phenome, the collection of phentotypic characters for a species. This research represents a new approach to data collection that has the potential to transform phylogenetics research and to enable rapid advances in constructing the Tree of Life. Our goal is to assemble large phenomic datasets built using new methods and to provide the public and scientific community with tools for phenomic data assembly that will enable rapid and automated study of phenotypes across the Tree of Life.

Titanosaurian (Dinosauria: Sauropoda) remains from the “Continental Intercalaire” of Mali

Abstract We describe fragmentary new postcranial remains of a sauropod from “Continental Intercalaire” rocks of the Tilemsi Valley in northeastern Mali. Addition of this taxon to recently published cladistic analyses indicates that it is nested within Titanosauria and it is among the oldest members of this clade. “Continental Intercalaire” rocks have been poorly understood and, until now, few vertebrate fossils from these rocks have been tied to stratigraphic sections. We present a preliminary description of the dinosaurian locality and tie it to a synthetic stratigraphic section of the Tilemsi Valley. Preliminary analysis of the geology and sedimentology of the locality suggests that the bones fossilized in fluvial deposits of Early Cretaceous (pre-Cenomanian) age.

First Mesozoic Record of the Stingray Myliobatis wurnoensis from Mali and a Phylogenetic Analysis of Myliobatidae Incorporating Dental Characters

New specimens, including the first record of lower dental plates, of the extinct myliobatid Myliubatis wurnoensis were recovered from the Maastrichtian (Late Cretaceous) of the Iullemmeden Basin, Mali, and are the oldest record of the taxon. We evaluated the phylogenetic position of this taxon with reference to other myliobatids (extinct and extant) using osteology and dentition. Our results indicate that Myliobatinae and Myliobatis are each paraphyletic, and that Aetobatus and Rhinoptera are monophyletic. We also found that taxa known only from the Cretaceous, Brachyrhizodus and Igdabatis, are highly nested within Myliobatidae. The phylogenetic position of these taxa unambiguously extends the origin of Myliobatidae and most of its representative taxa into the Mesozoic.