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in category paleontology

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1: Fossil calibrations for the arthropod Tree of Life
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Posted to bioRxiv 21 Mar 2016

Fossil calibrations for the arthropod Tree of Life
1,992 downloads paleontology

Joanna M. Wolfe, Allison C Daley, David A Legg, Gregory D Edgecombe

Fossil age data and molecular sequences are increasingly combined to establish a timescale for the Tree of Life. Arthropods, as the most species-rich and morphologically disparate animal phylum, have received substantial attention, particularly with regard to questions such as the timing of habitat shifts (e.g. terrestrialisation), genome evolution (e.g. gene family duplication and functional evolution), origins of novel characters and behaviours (e.g. wings and flight, venom, silk), biogeography, rate of diversification (e.g. Cambrian explosion, insect coevolution with angiosperms, evolution of crab body plans), and the evolution of arthropod microbiomes. We present herein a series of rigorously vetted calibration fossils for arthropod evolutionary history, taking into account recently published guidelines for best practice in fossil calibration. These are restricted to Palaeozoic and Mesozoic fossils, no deeper than ordinal taxonomic level, nonetheless resulting in 80 fossil calibrations for 102 clades. This work is especially timely owing to the rapid growth of molecular sequence data and the fact that many included fossils have been described within the last five years. This contribution provides a resource for systematists and other biologists interested in deep-time questions in arthropod evolution.

2: Functional Anatomy, Biomechanical Performance Capabilities and Potential Niche of StW 573: an Australopithecus Skeleton (circa 3.67 Ma) From Sterkfontein Member 2, and its significance for The Last Common Ancestor of the African Apes and for Hominin Origins
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Posted to bioRxiv 29 Nov 2018

Functional Anatomy, Biomechanical Performance Capabilities and Potential Niche of StW 573: an Australopithecus Skeleton (circa 3.67 Ma) From Sterkfontein Member 2, and its significance for The Last Common Ancestor of the African Apes and for Hominin Origins
1,913 downloads paleontology

Robin Huw Crompton, Juliet McClymont, Susannah K.S. Thorpe, William I Sellers, Jason Heaton, Travis Rayne Pickering, Todd Pataky, Dominic Stratford, Kristian Carlson, Tea Jashashvili, Amelie Beaudet, Laurent Bruxelles, Colleen Goh, Kathleen Kuman, Ronald Clarke

StW 573, from Sterkfontein Member 2, dated ca 3.67 Ma, is by far the most complete skeleton of an australopith to date. Joint morphology is in many cases closely matched in available elements of Australopithecus anamensis (eg. proximal and distal tibial and humeral joint-surfaces) and there are also close similarities to features of the scapula, in particular, of KSD-VP-1/1 A. afarensis from Woranso-Mille. The closest similarities are, however, to the partial skeleton of StW 431 from Sterkfontein Member 4. When considered together, both StW 573 and StW 431 express an hip joint morphology quite distinct from that of A. africanus Sts14, and a proximal femur of a presumed A. africanus from Jacovec Cavern at Sterkfontein, StW 598. This, and other evidence presented herein, suggests there are two pelvic girdle morphs at Sterkfontein, supporting Clarke (2013) in his recognition of a second species, A. prometheus, containing StW 573 and StW 431. StW 573 is the first hominid skeleton where limb proportions are known unequivocally. It demonstrates that some early hominins, at the time of formation of the Laetoli footprints (3.6 Ma), were large-bodied. with hindlimbs longer than forelimbs. Modelling studies on extant primates indicate that the intermembral index (IMI) of StW 573, low for a non-human great ape, would have substantially enhanced economy of bipedal walking over medium-to-long distances, but that it was still too high for effective walking while load-carrying. It would, however, have somewhat reduced the economy of horizontal climbing, but made Gorilla-like embracing of large tree-trunks less possible. Consideration of both ethnographic evidence from modern indigenous arboreal foragers and modern degeneracy theory cautions against prescriptive interpretations of hand- and foot-function, by confirming that both human-like upright bipedalism and functional capabilities of the hand and foot can be effective in short-distance arboreal locomotion.

3: Uneven Data Quality and the Earliest Occupation of Europe: The Case of Untermassfeld (Germany)
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Posted to bioRxiv 31 Oct 2017

Uneven Data Quality and the Earliest Occupation of Europe: The Case of Untermassfeld (Germany)
1,912 downloads paleontology

Wil Roebroeks, Sabine Gaudzinski-Windheuser, Michael Baales, Ralf-Dietrich Kahlke

The database regarding the earliest occupation of Europe has increased significantly in quantity and quality of data points over the last two decades, mainly through the addition of new sites as a result of long-term systematic excavations and large-scale prospections of Early and early Middle Pleistocene exposures. The site distribution pattern suggests an ephemeral presence of hominins in the south of Europe from around one million years ago, with occasional short northward expansions along the western coastal areas when temperate conditions permitted. From around 600,000-700,000 years ago Acheulean artefacts appear in Europe and somewhat later hominin presence seems to pick up, with more sites and now some also present in colder climatic settings. It is again only later, around 350,000 years ago, that the first sites show up in more continental, central parts of Europe, east of the Rhine. A series of recent papers on the Early Pleistocene palaeontological site of Untermassfeld (Germany) makes claims that are of great interest for studies of earliest Europe and are at odds with the described pattern: the papers suggest that Untermassfeld has yielded stone tools and humanly modified faunal remains, evidence for a one million years old hominin presence in European continental mid-latitudes, and additional evidence that hominins were well-established in Europe already around that time period. Here we evaluate these claims and demonstrate that these studies are severely flawed in terms of data on provenance of the materials studied and in the interpretation of faunal remains and lithics as testifying to a hominin presence at the site. In actual fact any reference to the Untermassfeld site as an archaeological one is unwarranted. Furthermore, it is not the only European Early Pleistocene site where inferred evidence for hominin presence is problematic. The strength of the spatiotemporal patterns of hominin presence and absence depend on the quality of the data points we work with, and data base maintenance, including critical evaluation of new sites, is crucial to advance our knowledge of the expansions and contractions of hominin ranges during the Pleistocene.

4: New Evidence of the Earliest Domestic Dogs in the Americas
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Posted to bioRxiv 11 Jun 2018

New Evidence of the Earliest Domestic Dogs in the Americas
1,883 downloads paleontology

Angela Perri, Chris Widga, Dennis Lawler, Terrance Martin, Thomas Loebel, Kenneth Farnsworth, Luci kohn, Brent Buenger

The domestication of dogs probably occurred in Eurasia by 16,000 years ago, with the initial peopling of the Americas potentially happening around the same time. Dogs were long thought to have accompanied the first migrations into the Americas, but conclusive evidence for Paleoindian dogs is lacking. The direct dating of two dogs from the Koster site (Greene Co., Illinois) and a newly-described dog from the Stilwell II site (Pike Co., Illinois) to between 10,190-9,630 cal BP represents the earliest evidence of domestic dogs in the Americas and individual dog burials in worldwide archaeological record. The over 4,500 year discrepancy between the timing of initial human migration into the Americas and the earliest evidence for domesticated dogs suggests either earlier dogs are going unseen or unidentified or dogs arrived later with a subsequent human migration.

5: The skull of StW 573, a 3.67 Ma Australopithecus skeleton from Sterkfontein Caves, South Africa
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Posted to bioRxiv 04 Dec 2018

The skull of StW 573, a 3.67 Ma Australopithecus skeleton from Sterkfontein Caves, South Africa
1,751 downloads paleontology

Ronald J Clarke, Kathleen Kuman

Here we present the first full anatomical description of the 3.67 million-year-old Australopithecus skull StW 573 that was recovered with its skeleton from the Sterkfontein Member 2 breccia in the Silberberg Grotto. Analysis demonstrates that it is most similar in multiple key morphological characters to a group of fossils from Sterkfontein Member 4 and Makapansgat that are here distinguished morphologically as A. prometheus. This taxon contrasts with another group of fossils from those sites assigned to A. africanus. The anatomical reasons for why these groupings should not be lumped together (as is frequently done for the South African fossils) are discussed in detail. In support of this classification, we also present for the first time a palate (StW 576 from Sterkfontein Member 4) newly reconstructed by RJC, which has a uniquely complete adult dentition of an A. africanus. The StW 573 skull also has certain similarities with other earlier Australopithecus fossils in East Africa, A. afarensis and A. anamensis, which are discussed. One of its most interesting features is a pattern of very heavy anterior dental wear unlike that found in A. africanus but resembling that found in A. anamensis at 4.17 Ma. While StW 573 is the only hominid fossil in Sterkfontein Member 2, we conclude that competitive exclusion probably accounts for the synchronous and sympatric presence of two species of Australopithecus in the younger deposits at Makapansgat and Sterkfontein Member 4. Because the StW 573 skull is associated with a near-complete skeleton that is also described for the first time in this special issue, we are now able to use this individual to improve our understanding of more fragmentary finds in the South African fossil record of Australopithecus.

6: How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model (TRiPS)
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Posted to bioRxiv 02 Sep 2015

How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model (TRiPS)
1,623 downloads paleontology

Jostein Starrfelt

The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that utilizes the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson Sampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543-2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades; the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic-Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic.

7: Osmunda pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae
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Posted to bioRxiv 04 Jun 2014

Osmunda pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae
1,330 downloads paleontology

Benjamin Bomfleur, Guido W. Grimm, Stephen McLoughlin

The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae—based solely on molecular data—likely results from un- or misinformative out-group signals.

8: Life Inside A Dinosaur Bone: A Thriving Microbiome
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Posted to bioRxiv 07 Sep 2018

Life Inside A Dinosaur Bone: A Thriving Microbiome
1,312 downloads paleontology

Evan Thomas Saitta, Renxing Liang, Chui Y Lau, Caleb M Brown, Nicholas R Longrich, Thomas G Kaye, Ben J. Novak, Steven Salzberg, Paul Donohoe, Marc Dickinson, Jakob Vinther, Ian D Bull, Richard A Brooker, Peter Martin, Geoffrey D Abbott, Timothy DJ Knowles, Kirsty Penkman, Tullis C. Onstott

Fossils were long thought to lack original organic material, but the discovery of organic molecules in fossils and sub-fossils, thousands to millions of years old, has demonstrated the potential of fossil organics to provide radical new insights into the fossil record. How long different organics can persist remains unclear, however. Non-avian dinosaur bone has been hypothesised to preserve endogenous organics including collagen, osteocytes, and blood vessels, but proteins and labile lipids are unstable during diagenesis or over long periods of time. Furthermore, bone is porous and an open system, allowing microbial and organic flux. Some of these organics within fossil bone have therefore been identified as either contamination or microbial biofilm, rather than original organics. Here, we use biological and chemical analyses of Late Cretaceous dinosaur bones and sediment matrix to show that dinosaur bone hosts a diverse microbiome. Fossils and matrix were freshly-excavated, aseptically-acquired, and then analysed using microscopy, spectroscopy, chromatography, spectrometry, DNA extraction, and 16S rRNA amplicon sequencing. The fossil organics differ from modern bone collagen chemically and structurally. A key finding is that 16S rRNA amplicon sequencing reveals that the subterranean fossil bones host a unique, living microbiome distinct from that of the surrounding sediment. Even in the subsurface, dinosaur bone is biologically active and behaves as an open system, attracting microbes that might alter original organics or complicate the identification of original organics. These results suggest caution regarding claims of dinosaur bone soft tissue preservation and illustrate a potential role for microbial communities in post-burial taphonomy.

9: A multiscale stratigraphic investigation of the context of StW 573 Little Foot and Member 2, Sterkfontein Caves, South Africa
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Posted to bioRxiv 29 Nov 2018

A multiscale stratigraphic investigation of the context of StW 573 Little Foot and Member 2, Sterkfontein Caves, South Africa
1,213 downloads paleontology

Laurent Bruxelles, Dominic J Stratford, Richard Maire, Travis R Pickering, Jason L Heaton, Amelie Beaudet, Kathleen Kuman, Robin Crompton, Kris J Carlson, Tea Jashashvili, Juliet McClymont, George Leader, Ronald J Clarke

The Sterkfontein Caves has an 80 year history of yielding remarkable evidence of hominin evolution and is currently the world's richest Australopithecus-bearing site. Included in Sterkfontein's hominin assemblage is StW 573 (Little Foot). Discovered in the Member 2 deposit in the Silberberg Grotto, StW 573 represents the most complete Australopithecus skeleton yet found. Because of its importance to the fossil hominin record, the geological age of Little Foot has been the subject of significant debate. Two main hypotheses have been proposed regarding the formation and age of Member 2 and by association StW 573. The first, proposes that Member 2 formed relatively rapidly, starting to accumulate at around 2.8 million years ago and that the unit is isolated to the Silberberg Grotto - the underlying chambers and passages forming later. The second proposes that Member 2 formed slowly, its accumulation starting before 3.67 million years ago and that the deposit extends into the Milner Hall and close to the base of the cave system. Both assume a primary association between StW 573 and Member 2, although which sediments in the Silberberg Grotto are associated with Member 2 has also been questioned. Recently a third alternative hypothesis questioning the association of StW 573 to Member 2 sediments proposed a two-stage burial scenario in which sediments associated with StW 573 represent a secondary and mixed-age deposit reworked from a higher cave. The stratigraphic and sedimentological implications of these hypotheses are tested here through the application of a multiscale investigation of Member 2, with reference to the taphonomy of the Little Foot skeleton. The complete infilling sequence of Member 2 is described and depositional units are tracked across all exposures of the deposit in the Silberberg Grotto and into the Milner Hall. Facies development follows patterns characteristic of colluvially accumulated taluses with 30-40 degrees angles of repose developing coarser distal facies. Sediments are generally stratified and conformably deposited in a sequence of silty sands eroded from well-developed lateritic soils on the landscape surface. Voids, clasts and bioclasts are organized consistently across and through Member 2 according to the underlying deposit geometry, indicating a gradual deposit accretion with no distinct collapse facies evident, no successive debris flow accumulation, and only localized intra-unit post-depositional modification. The stratigraphy and sedimentology of Member 2 supports a simple single-stage accumulation process through which Member 2 partially fills the Silberberg Grotto and extends into the deeper chambers and passages of the Sterkfontein Caves. Through this work we demonstrate at multiple scales the primary association between the sediments of Member 2 and the StW 573 Little Foot skeleton.

10: Nanjinganthus: An Unexpected Flower from the Jurassic of China
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Posted to bioRxiv 27 Dec 2017

Nanjinganthus: An Unexpected Flower from the Jurassic of China
1,187 downloads paleontology

Qiang FU, Jose Bienvenido DIEZ, Mike POLE, Manuel GARCIA-AVILA, Zhong-Jian LIU, Hang CHU, Yemao HOU, Pengfei YIN, Guo-Qiang ZHANG, Kaihe DU, Xin WANG

The origin of angiosperms has been the focus of intensive botanical debate for well over a century. The great diversity of angiosperms in the Early Cretaceous makes the Jurassic rather expected to elucidate the origin of angiosperm. Former reports of early angiosperms are frequently based on a single specimen, making many conclusions tentative. Here, based on observations of 284 individual flowers preserved on 28 slabs in various states and orientations, we describe a fossil flower, Nanjinganthus dendrostyla gen. et sp. nov., from the South Xiangshan Formation (Early Jurassic) of China. The large number of specimens and various preservations allows us to give an evidenced interpretation of the flower. The complete enclosure of ovules in Nanjinganthus is fulfilled by a combination of an invaginated and ovarian roof. Characterized by its actinomorphic flower with a dendroid style, cup-form receptacle, and angio-ovuly, Nanjinganthus is a bona fide angiosperm from the Jurassic. Nanjinganthus re-confirms the existence of Jurassic angiosperms and provides first-hand raw data for new analyses on the origin and history of angiosperms.

11: MUSCLES OF FACIAL EXPRESSION IN EXTINCT SPECIES OF THE GENUS HOMO
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Posted to bioRxiv 01 Sep 2016

MUSCLES OF FACIAL EXPRESSION IN EXTINCT SPECIES OF THE GENUS HOMO
1,043 downloads paleontology

Arturo Tozzi

We display a detailed description of mimetic muscles in extinct human species, framed in comparative and phylogenetic contexts. Using known facial landmarks, we assessed the arrangement of muscles of facial expression in Homo sapiens, neanderthalensis, erectus, heidelbergensis and ergaster. In modern humans, several perioral muscles are proportionally smaller in size (levator labii superioris, zygomaticus minor, zygomaticus major and triangularis) and/or located more medially (levator labii superioris, zygomaticus minor and quadratus labii inferioris) than in other human species. As mimetic musculature is examined in the most ancient specimens up to the most recent, there is a general trend towards an increase in size of corrugator supercillii and triangularis. Homo ergaster's mimetic musculature closely resembles modern Homo, both in size and in location; furthermore, Homo erectus and Homo neanderthalensis share many muscular features. The extinct human species had an elaborate and highly graded facial communication system, but it remained qualitatively different from that reported in modern Homo. Compared with other human species, Homo sapiens clearly exhibits a lower degree of facial expression, possibly correlated with more sophisticated social behaviours and with enhanced speech capabilities. The presence of anatomical variation among species of the genus Homo raises important questions about the possible taxonomic value of mimetic muscles.

12: History is written by the victors: the effect of the push of the past on the fossil record
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Posted to bioRxiv 27 Sep 2017

History is written by the victors: the effect of the push of the past on the fossil record
1,003 downloads paleontology

Graham E. Budd, Richard P Mann

Phylogenies may be modelled using 'birth-death' models for speciation and extinction, but even when a homogeneous rate of diversification is used, survivorship biases can generate remarkable rate heterogeneities through time. One such bias has been termed the 'push of the past', by which the length of time a clade has survived is conditioned on the rate of diversification that happened to pertain at its origin. This creates the illusion of a secular rate slow-down through time that is, rather, a reversion to the mean. Here we model the controls on the push of the past, and the effect it has on clade origination times, and show that it largely depends on underlying extinction rates. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilisation, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalised to the diversification process as a whole without additional study of small and extinct clades.

13: The multi-peak adaptive landscape of crocodylomorph body size evolution
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Posted to bioRxiv 31 Aug 2018

The multi-peak adaptive landscape of crocodylomorph body size evolution
948 downloads paleontology

Pedro L Godoy, Roger B J Benson, Mario Bronzati, Richard J Butler

Background: Little is known about the long-term patterns of body size evolution in Crocodylomorpha, the > 200-million-year-old group that includes living crocodylians and their extinct relatives. Extant crocodylians are mostly large-bodied (3-7 m) predators. However, extinct crocodylomorphs exhibit a wider range of phenotypes, and many of the earliest taxa were much smaller (< 1.2 m). This suggests a pattern of size increase through time that could be caused by multi-lineage evolutionary trends of size increase or by selective extinction of small-bodied species. In this study, we characterise patterns of crocodylomorph body size evolution using a model fitting-approach (with cranial measurements serving as proxies). We also estimate body size disparity through time and quantitatively test hypotheses of biotic and abiotic factors as potential drivers of crocodylomorph body size evolution. Results: Crocodylomorphs reached an early peak in body size disparity during the Late Jurassic, and underwent essentially continually decreases in disparity since then. A multi-peak Ornstein-Uhlenbeck model outperforms all other evolutionary models fitted to our data (including both uniform and non-uniform), indicating that the macroevolutionary dynamics of crocodylomorph body size are better described within the concept of an adaptive landscape, with most body size variation emerging after shifts to new macroevolutionary regimes (analogous to adaptive zones). We did not find support for a consistent evolutionary trend towards larger sizes among lineages (i.e., Cope's rule), or strong correlations of body size with climate. Instead, the intermediate to large body sizes of some crocodylomorphs are better explained by group-specific adaptations. In particular, the evolution of a more aquatic lifestyle (especially marine) correlates with increases in average body size, though not without exceptions. Conclusions: Shifts between macroevolutionary regimes provide a better explanation of crocodylomorph body size evolution than do climatic factors, suggesting a central role for lineage-specific adaptations rather than climatic forcing. Shifts leading to larger body sizes occurred in most aquatic and semi-aquatic groups. This, combined with extinctions of groups occupying smaller body size regimes (particularly during the Late Cretaceous and Cenozoic), gave rise to the upward-shifted body size distribution of extant crocodylomorphs compared to their smaller-bodied terrestrial ancestors.

14: A new genus of horse from Pleistocene North America
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Posted to bioRxiv 24 Jun 2017

A new genus of horse from Pleistocene North America
938 downloads paleontology

Peter D. Heintzman, Grant D Zazula, Ross DE MacPhee, Eric Scott, James A. Cahill, Brianna K McHorse, Joshua D. Kapp, Mathias Stiller, Matthew J Wooller, Ludovic Orlando, John R Southon, Duane G Froese, Beth Shapiro

The extinct New World stilt-legged, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event.

15: Community stability and selective extinction during Earth's greatest mass extinction
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Posted to bioRxiv 01 Feb 2015

Community stability and selective extinction during Earth's greatest mass extinction
899 downloads paleontology

Peter D Roopnarine, Kenneth D Angielczyk

We modelled the resilience and transient dynamics of terrestrial paleocommunities from the Karoo Basin, South Africa, around the Permian-Triassic mass extinction. Using recently refined biostratigraphic data that suggest two pulses of extinction leading up to the Permian-Triassic boundary, we show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became stable during the mass extinction. Modelled food webs before and after the mass extinction have lower resilience and less stable transient dynamics compared to random food webs lacking in functional structure but of equal species richness. They are, however, more stable than random food webs of equal richness but with randomized functional structure. In contrast, models become increasingly more resilient and have more stable transient dynamics, relative to the random models, as the mass extinction progressed. The increased stability of the community that resulted from the first pulse of extinction was driven by significant selective extinction against small-bodied amniotes, and significantly greater probabilities of survival of large-bodied amniotes. These results point to a positive relationship between evolved patterns of functional diversity and emergent community dynamics, with observed patterns being more stable than alternative possibilities.

16: The case for species selection
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Posted to bioRxiv 28 Oct 2016

The case for species selection
896 downloads paleontology

Carl Simpson

The mere existence of speciation and extinction make macroevolutionary processes possible. Speciation and extinction introduce discontinuities in the microevolutionary change within lineages by initiating, disrupting, and terminating the continuity of species lineages. Within a clade, speciation and extinction become potent means of macroevolution in and of themselves. This process, termed species selection, is a macroevolutionary analogue of natural selection, with species playing an analogous part akin to that played by organisms in microevolution. That said, it has proven difficult to think about levels of selection. The concept of species sorting was introduced to help our thinking on this issue by identifying two aspects inherent in hierarchical systems can confuse our attempts to understand them: uncertainty in the level that selection acts and uncertainty about if the pattern of selection is in fact caused at all. Thanks to insights from evolutionary transitions in individuality, we now know more about how to identify the level of selection and how to parse the causal structure in hierarchical evolutionary circumstances. We know that if the fitness of organisms causes the fitness of more inclusive species then they must covary. However, there is no evidence of such a covariance between fitnesses at these two levels. This covariance is just not observed; neither between cells and organisms nor between organisms and species. Rather, speciation and extinction rates appear to be completely divorced from organismal fitness. With this insight, the concept of species sorting shrinks so that it only covers the two processes of species selection and drift. I argue that we are better off focusing on understanding the processes of species selection and drift and that there is therefore no further need for the concept of species sorting.

17: The Biogeography of coelurosaurian theropods and its impact on their evolutionary history
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Posted to bioRxiv 10 May 2019

The Biogeography of coelurosaurian theropods and its impact on their evolutionary history
874 downloads paleontology

Anyang Ding, Michael Pittman, Paul Upchurch, Jingmai O'Connor, Daniel Field, Xing Xu

The Coelurosauria are a group of mostly feathered theropods that gave rise to birds, the only dinosaurs that survived the Cretaceous-Paleogene extinction event and are still found today. Between their first appearance in the Middle Jurassic up to the end Cretaceous, coelurosaurs were party to dramatic geographic changes on the Earth's surface, including the breakup of the supercontinent Pangaea, and the formation of the Atlantic Ocean. These plate tectonic events are thought to have caused vicariance or dispersal of coelurosaurian faunas, influencing their evolution. Unfortunately, few coelurosaurian biogeographic hypotheses are supported by quantitative evidence. Here, we report the first, broadly-sampled quantitative analysis of coelurosaurian biogeography using the likelihood-based package BioGeoBEARS. Mesozoic geographic configurations and changes are reconstructed and employed as constraints in this analysis, including their associated uncertainties. We use a comprehensive time-calibrated coelurosaurian evolutionary tree produced from the Theropod Working Group phylogenetic data matrix. Six biogeographic models in the BioGeoBEARS package with different assumptions about the evolution of spatial distribution are tested against the geographic constraints. Our results statistically favour the DIVALIKE+J and DEC+J models, which allow vicariance and founder events, supporting continental vicariance as an important factor in coelurosaurian evolution. Ancestral range estimation indicates frequent dispersal events via the Apulian Route (connecting Europe and Africa during the Early Cretaceous) and the Bering Land Bridge (connecting North America and Asia during the Late Cretaceous). These quantitative results are consistent with commonly inferred Mesozoic dinosaurian dispersals and continental-fragmentation-induced vicariance events. In addition, we recognise the importance of Europe as a dispersal centre and gateway in the Early Cretaceous, as well as other vicariance events like those triggered by the disappearance of land-bridges.

18: Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals
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Posted to bioRxiv 29 Jan 2019

Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals
806 downloads paleontology

Benedict King, Robin M. D. Beck

The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for palaeontologists. Bayesian tip-dating (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip-dating affects the recovery of evolutionary relationships has yet to be fully explored. Here we show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip-dating are outliers when compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip-dating have better fit to stratigraphy than trees recovered by other methods, due to trees with better stratigraphic fit being assigned a higher prior probability. Differences in stratigraphic fit and tree topology between tip-dating and other methods appear to be concentrated in parts of the tree with weaker character signal and a stronger influence of the prior, as shown by successive deletion of the most incomplete taxa from a sauropod dataset. Tip-dating applied to Mesozoic mammals firmly rejects a monophyletic Allotheria, and strongly supports diphyly of haramiyidans, with the late Triassic Haramiyavia and Thomasia forming a clade with tritylodontids, which is distant from the middle Jurassic euharamiyidans. This result is not sensitive to the controversial age of the eutherian Juramaia. A Test of the age of Juramaia using a less restrictive prior reveals strong support from the data for an Early Cretaceous age. Our results suggest that tip-dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit a prior expectation that can be overturned by strong evidence from character data.

19: The locomotor and predatory habits of unenlagiines (Theropoda, Paraves): inferences based on morphometric studies and comparisons with Laurasian dromaeosaurids
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Posted to bioRxiv 18 Feb 2019

The locomotor and predatory habits of unenlagiines (Theropoda, Paraves): inferences based on morphometric studies and comparisons with Laurasian dromaeosaurids
796 downloads paleontology

Federico A. Gianechini, Marcos D. Ercoli, Ignacio Díaz-Martínez

Unenlagiinae is mostly recognized as a subclade of dromaeosaurids. They have the modified pedal digit II that characterize all dromeosaurids, which is typically related to predation. However, derived Laurasian dromaeosaurids (eudromaeosaurs) differ from unenlagiines in having a shorter metatarsus and pedal phalanx II-1, and more ginglymoid articular surfaces in metatarsals and pedal phalanges. Further, unenlagiines have a subarctometatarsal condition, which could have increased the mechanical efficiency during locomotion. All these discrepancies possibly reflect different locomotor and predatory habits. To evaluate this we conducted morphometric analyses and comparisons of qualitative morphological aspects. The former consisted in two phylogenetic principal component analyses, one of them based on lengths of femur, tibia and metatarsus, and width of metatarsus, and the other based on lengths of pedal phalanges. The data sampling covered several coelurosaurian and non-coelurosaurian taxa. The first analysis showed the unenlagiines close to taxa with long tibiae and long and slender metatarsi, which are features considered to provide high cursorial capacities. Instead, eudromaeosaurs are close to taxa with shorter tibiae and shorter and wider metatarsi, which can be considered with low cursorial capacities. The second analysis showed that eudromaeosaurs and unenlagiines have similar phalangeal proportions. Moreover, they share the elongation of distal phalanges, which is a feature related to the capacity of grasping. The shorter and wider metatarsus, more ginglymoid articular surfaces and a shorter pedal phalanx II-2 of eudromaeosaurs possibly allowed them to exert a greater gripping strength. Thus, they had the potential of hunting large prey. Instead, the longer and slender subarctometatarsus, lesser ginglymoid articular surfaces and a longer pedal phalanx II-2 of unenlagiines possibly gave to them greater cursorial capacities and the ability to hunt smaller and elusive prey on the ground. Thus, the different morphological evolutionary paths of dromaeosaurids lineages seem to indicate different locomotor and predatory specializations.

20: Earliest-known intentionally deformed human cranial fossil from Asia and the initiation of hereditary hierarchy in the early Holocene
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Posted to bioRxiv 26 Jan 2019

Earliest-known intentionally deformed human cranial fossil from Asia and the initiation of hereditary hierarchy in the early Holocene
785 downloads paleontology

Xijun Ni, Qiang Li, Thomas A. Stidham, Yangheshan Yang, Qiang Ji, Changzhu Jin, Khizar Samiullah

Hereditary hierarchy is one of the major features of complex societies. Without a written record, prehistoric evidence for hereditary hierarchy is rare. Intentional cranial deformation (ICD) is a cross-generational cultural practice that embodies social identity and culture beliefs in adults through the behavior of altering infant head shape. Therefore, ICD is usually regarded as an archeological clue for the occurrence of hereditary hierarchy. With a calibrated radiocarbon age of 11245-11200 years BP, a fossil skull of an adult male displaying ICD discovered in Northeastern China is among the oldest-known ICD practices in the world. Along with the other earliest global occurrences of ICD, this discovery points to the early initiation of complex societies among the non-agricultural local societies in Northeastern Asia in the early Holocene. A population increase among previously more isolated terminal Pleistocene/early Holocene hunter-gatherer groups likely increased their interactions, possibly fueling the formation of the first complex societies.

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