Assembling the ruminant tree: combining morphology, molecules, extant taxa, and fossils

A gap exists between paleontological and neontological approaches to ruminant phylogenetics, despite great increases in phylogenetic resolution through molecular work of the last three decades, and a large and growing fossil record. This gap is reflected in differing methodological approaches, with insufficient integration of the large fossil record by molecular studies on the one hand, and insufficient consideration of highly resolved genomic work by paleontological studies on the other. Both paleontological and molecular approaches seek to answer similar broad evolutionary questions, and a synthetic approach is in the interest of all. I demonstrate this by reviewing the development of each field, noting many examples in which paleontological or molecular approaches to ruminant phylogenetics are, on their own, inadequate compared to an approach which considers all sources of data together. In particular, cases such as those of Bison, Capra, and Pelea have shown that integration of genomic and anatomical data presents better resolution of relationships, and I suggest Antilocapra and Moschus may benefit from a similar approach, especially with the integration of fossil taxa into a combined (supermatrix) analysis. I present preliminary results of a new and large (in progress) morphological matrix that is intended to be used for the incorporation of anatomical data and fossil taxa into a combined analysis. The new matrix is much larger than previous morphological matrices assembled for ruminant phylogenetics, meaning it can support a larger number of fossil taxa than was previously possible. Preliminary analysis with 18 taxa recovers a highly supported tree that is mostly compatible with both traditional and molecular phylogenies, although problems of convergence remain, such as between Antilocapra and Bovidae. Finally, I propose standardization of ruminant clade names in order to limit miscommunication between paleontological and neontological workers. I propose phylogenetic definitions based on crown (extant) clades for the names Ruminantia and Pecora, and the use of Pan-Ruminantia and Pan-Pecora to accommodate each respective crown clade plus its stem group

Assembling the ruminant tree: combining morphology, molecules, extant taxa, and fossils

A gap exists between paleontological and neontological approaches to ruminant phylogenetics, despite great increases in phylogenetic resolution through molecular work of the last three decades, and a large and growing fossil record. This gap is reflected in differing methodological approaches, with insufficient integration of the large fossil record by molecular studies on the one hand, and insufficient consideration of highly resolved genomic work by paleontological studies on the other. Both paleontological and molecular approaches seek to answer similar broad evolutionary questions, and a synthetic approach is in the interest of all. I demonstrate this by reviewing the development of each field, noting many examples in which paleontological or molecular approaches to ruminant phylogenetics are, on their own, inadequate compared to an approach which considers all sources of data together. In particular, cases such as those of Bison, Capra, and Pelea have shown that integration of genomic and anatomical data presents better resolution of relationships, and I suggest Antilocapra and Moschus may benefit from a similar approach, especially with the integration of fossil taxa into a combined (supermatrix) analysis. I present preliminary results of a new and large (in progress) morphological matrix that is intended to be used for the incorporation of anatomical data and fossil taxa into a combined analysis. The new matrix is much larger than previous morphological matrices assembled for ruminant phylogenetics, meaning it can support a larger number of fossil taxa than was previously possible. Preliminary analysis with 18 taxa recovers a highly supported tree that is mostly compatible with both traditional and molecular phylogenies, although problems of convergence remain, such as between Antilocapra and Bovidae. Finally, I propose standardization of ruminant clade names in order to limit miscommunication between paleontological and neontological workers. I propose phylogenetic definitions based on crown (extant) clades for the names Ruminantia and Pecora, and the use of Pan-Ruminantia and Pan-Pecora to accommodate each respective crown clade plus its stem group

The nature of the Old World savannah palaeobiome

Non peer reviewe

The rise and fall of the Old World savannah fauna and the origins of the African savannah biome

Author correction: vol 2, pg, 402, 2018 DOI:10.1038/s41559-018-0468-8Despite much interest in the ecology and origins of the extensive grassland ecosystems of the modern world, the biogeographic relationships of savannah palaeobiomes of Africa, India and mainland Eurasia have remained unclear. Here we assemble the most recent data from the Neogene mammal fossil record in order to map the biogeographic development of Old World mammalian faunas in relation to palaeoenvironmental conditions. Using genus-level faunal similarity and mean ordinated hypsodonty in combination with palaeoclimate modelling, we show that savannah faunas developed as a spatially and temporally connected entity that we term the Old World savannah palaeobiome. The Old World savannah palaeobiome flourished under the influence of middle and late Miocene global cooling and aridification, which resulted in the spread of open habitats across vast continental areas. This extensive biome fragmented into Eurasian and African branches due to increased aridification in North Africa and Arabia during the late Miocene. Its Eurasian branches had mostly disappeared by the end of the Miocene, but the African branch survived and eventually contributed to the development of Plio-Pleistocene African savannah faunas, including their early hominins. The modern African savannah fauna is thus a continuation of the extensive Old World savannah palaeobiome.Peer reviewe

A new species of hippopotamine (Cetartiodactyla, Hippopotamidae) from the late Miocene Baynunah Formation, Abu Dhabi, United Arab Emirates

The discovery of new hippopotamid material from the late Miocene Baynunah Formation (Abu Dhabi, United Arab Emirates) has prompted the revision of the existing material of this as yet unnamed fossil taxon. The Baynunah hippopotamid appears to be distinct from all other contemporary and later species in having a relatively more elongate symphysis, a feature similar to the earlier (and more primitive) Kenyapotamus. Yet, the Baynunah hippopotamid presents a dentition typical of the Hippopotaminae. It is therefore a distinct species attributed to the later subfamily, described and named in this contribution. This species provides further evidence for a ca. 8 Ma evolutionary event (termed “Hippopotamine Event”) that initiated the spread and ecological significance of the Hippopotaminae into wet habitats across Africa and Eurasia. The morphological affinities of the new species from Abu Dhabi suggest that the Arabian Peninsula was not a dispersal route from Africa toward southern Asia for the Hippopotamidae at ca. 7.5 Ma to 6.5 Ma

An ecometric analysis of the fossil mammal record of the Turkana Basin

Peer reviewe

Unraveling bovin phylogeny: accomplishments and challenges

The phylogenetic systematics of bovin species forms a common basis for studies at multiple scales, from the level of domestication in populations to major cladogenesis. The main big-picture accomplishments of this productive field, including two recent works, one in BMC Genomics, are reviewed with an eye for some of the limitations and challenges impeding progress. See Research article http://www.biomedcentral.com/1471-2164/10/17

Paleoecology of the Serengeti during the Oldowan-Acheulean transition at Olduvai Gorge, Tanzania : The mammal and fish evidence

Eight years of excavation work by the Olduvai Geochronology and Archaeology Project (OGAP) has produced a rich vertebrate fauna from several sites within Bed II, Olduvai Gorge, Tanzania. Study of these as well as recently re-organized collections from Mary Leakey's 1972 HWK EE excavations here provides a synthetic view of the faunal community of Olduvai during Middle Bed II at similar to 1.7-1.4 Ma, an interval that captures the local transition from Oldowan to Acheulean technology. We expand the faunal list for this interval, name a new bovid species, clarify the evolution of several mammalian lineages, and record new local first and last appearances. Compositions of the fish and large mammal assemblages support previous indications for the dominance of open and seasonal grassland habitats at the margins of an alkaline lake. Fish diversity is low and dominated by cichlids, which indicates strongly saline conditions. The taphonomy of the fish assemblages supports reconstructions of fluctuating lake levels with mass die-offs in evaporating pools. The mammals are dominated by grazing bovids and equids. Habitats remained consistently dry and open throughout the entire Bed II sequence, with no major turnover or paleoecological changes taking place. Rather, wooded and wet habitats had already given way to drier and more open habitats by the top of Bed I, at 1.85-1.80 Ma. This ecological change is close to the age of the Oldowan-Acheulean transition in Kenya and Ethiopia, but precedes the local transition in Middle Bed II. The Middle Bed II large mammal community is much richer in species and includes a much larger number of large-bodied species (>300 kg) than the modern Serengeti. This reflects the severity of Pleistocene extinctions on African large mammals, with the loss of large species fitting a pattern typical of defaunation or 'downsizing' by human disturbance. However, trophic network (food web) analyses show that the Middle Bed II community was robust, and comparisons with the Serengeti community indicate that the fundamental structure of food webs remained intact despite Pleistocene extinctions. The presence of a generalized meateating hominin in the Middle Bed II community would have increased competition among carnivores and vulnerability among herbivores, but the high generality and interconnectedness of the Middle Bed II food web suggests this community was buffered against extinctions caused by trophic interactions. (C) 2017 Published by Elsevier Ltd.Peer reviewe

Magnetostratigraphy and paleoecology of the hominid-bearing locality Çorakyerler, Tuglu Formation (Çankiri Basin, Central Anatolia)

Peer reviewe