New material of Erketu ellisoni.

27 p. : ill. ; 26 cm. "October 22, 2010."Phylogenetic relationships among the diverse Cretaceous sauropods of East Asia have long been controversial. Debate has centered on whether there is any evidence for an endemic clade of Asian species ("Euhelopodidae") and on the placement of these taxa within the context of higher sauropod phylogeny. While most Cretaceous sauropod taxa from Asia are recognized as part of Somphospondyli, recent discoveries have suggested Brachiosauridae may have dispersed into Asia as well. We present new fossils and analyses bearing on these issues. Additional material of the holotype individual of Erketu ellisoni recovered on a subsequent visit to the type locality expands the character data available for this unique sauropod. Associated sauropod dorsal and caudal vertebrae were collected from the same horizon, at a location approximately 2 km from the holotype excavation. The dorsal vertebra exhibits synapomorphies suggesting a representative of Titanosauria co-occurred with Erketu ellisoni. These new specimens, as well as recent discoveries of contemporary Asian sauropod taxa, allow a basis for phylogenetic reappraisal of Erketu and related taxa. Phylogenetic results support a sister group relationship between the Asian Cretaceous sauropods Erketu and Qiaowanlong. Although Qiaowanlong was described as a brachiosaurid, it joins Erketu on the somphospondylian side of the Brachiosauridae-Somphospondyli divergence, erasing the evidence for the dispersal of Brachiosauridae into Asia

Bayesian total evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilized birth-death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least 1.1.4) and morph-models (v. at least 1.0.4).Comment: 50 pages, 6 figure

Fossil record of penguins.

77 p. : ill., map ; 26 cm. "Issued June 3, 2010." Includes bibliographical references (p. 47-53).We present the first detailed description of Perudyptes devriesi, a basal penguin from the middle Eocene (~42 Ma) Paracas Formation of Peru, and a new analysis of all published extinct penguin species as well as controversial fragmentary specimens. The Perudyptes devriesi holotype includes key regions of the skull and significant postcranial material, thus helping to fill a major phylogenetic and stratigraphic (~20 million year) gap between the earliest fossil penguins (Waimanu manneringi and Waimanu tuatahi, ~58-61.6 Ma) and the next oldest partial skeletons. Perudyptes devriesi is diagnosable by five autapomorphies: (1) an anteroventrally directed postorbital process, (2) marked anterior expansion of the parasphenoid rostrum, (3) posterior trochlear ridge of the humerus projecting distal to the middle trochlear ridge and conformed as a large, broadly curved surface, (4) convex articular surface for the antitrochanter of the femur, and (5) extremely weak anterior projection of the lateral condyle of the tibiotarsus. The skull of Perudyptes is characterized by deep temporal fossae and an elongate, narrow beak that differs from other reported stem penguins in its short mandibular symphysis. The wing skeleton of Perudyptes preserves a combination of plesiomorphic features also observed in the basal penguin Waimanu and derived features shared with more crownward penguins. Features of the wing optimized as primitive for Sphenisciformes include retention of a discrete dorsal supracondylar tubercle on the humerus and presence of a modestly projected pisiform process on the carpometacarpus. Derived features present in Perudyptes and all more crownward penguins, but absent in Waimanu, include a more flattened humerus, development of a trochlea for the tendon of m. scapulotriceps at the distal end of the humerus, and bowing of the anterior face of the carpometacarpus. A combined molecular and morphological dataset for Spheniciformes was expanded by adding 25 osteological and soft tissue characters as well as 11 taxa. In agreement with previous results, Perudyptes devriesi is identified as one of the most basal members of Sphenisciformes. This analysis also confirms the placement of the middle/late Miocene (~11-13 Ma) fossil Spheniscus muizoni as a member of the Spheniscus clade and places the late Miocene (~10 Ma) Madrynornis mirandus as sister taxon to extant Eudyptes. These two species, known from relatively complete partial skeletons, are the oldest crown clade penguin fossils and represent well-corroborated temporal calibration points for the Spheniscus-Eudyptula divergence and Megadyptes-Eudyptes divergence, respectively. Our results reaffirm that the Miocene penguin taxon Palaeospheniscus, recently proposed to represent a member of the crown radiation, belongs outside of the crown clade Spheniscidae. The phylogenetic positions of small Eocene Antarctic penguin taxa (Delphinornis, Marambiornis, and Mesetaornis) recently proposed as possible direct ancestors to crown Spheniscidae were further evaluated using alternate coding strategies for incorporating scorings from isolated elements that preserve critical morphologies and are thought to represent these taxa, although they cannot yet be reliably assigned to individual species. Under all scoring regimes, Delphinornis, Marambiornis, and Mesetaornis were recovered as distantly related to Spheniscidae. Using synapomorphies identified in the primary analysis, we evaluated the phylogenetic position of fragmentary specimens, including the holotypes of valid but poorly known species, specimens currently unassignable to the species level, and morphologically distinct specimens that have not yet been named. All pre-Miocene specimens can be excluded from Spheniscidae based on presence of plesiomorphies lost in all crown penguins, consistent with a recent radiation for the penguin crown clade. This study provides additional support for a scenario of penguin evolution characterized by an origin of flightlessness near the K-T boundary, dispersal throughout the Southern Hemisphere during the early Paleogene, and a late Cenozoic origin for the crown clade Spheniscidae. Stratigraphic distribution and phylogenetic relationships of fossil penguins are consistent with distinct radiations during the Eocene, Oligocene, and Miocene. While the Eocene and Oligocene penguin faunas are similar in many respects, the Miocene fauna is characterized by smaller average size and novel cranial morphologies, suggesting that an ecological shift in diet occurred close to the origin of crown Spheniscidae

Ornithomimosaur remains

4 p. : 1 ill. ; 26 cm.Includes bibliographical references (p. 4).The 1998 American Museum of Natural History-Mongolian Academy of Sciences expedition uncovered partial ornithomimosaur remains from the Xanadu sublocality at Uhkaa Tolgod. The specimen includes the rostral portion of the snout, the anterior portion of the mandible, and vertebral fragments. These remains cannot be assigned with certainty to any known ornithomimosaur genus. Examination of these materials allows new comments on ornithomimosaur palatal anatomy

A Phylogenomic Supertree of Birds

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well

The Fossil Calibration Database—A New Resource for Divergence Dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important—often least appreciated—step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the databas

High-coverage genomes to elucidate the evolution of penguins

Background: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results: Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. Conclusions: We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.Fil: Pan, Hailin. Bgi-shenzhen; ChinaFil: Cole, Theresa L. University Of Otago; CanadáFil: Bi, Xupeng. Bgi-shenzhen; ChinaFil: Fang, Miaoquan. Bgi-shenzhen; ChinaFil: Zhou, Chengran. Bgi-shenzhen; ChinaFil: Yang, Zhengtao. Bgi-shenzhen; ChinaFil: Ksepka, Daniel T. Bruce Museum; Estados UnidosFil: Hart, Tom. University of Oxford; Reino UnidoFil: Bouzat, Juan L.. Bowling Green State University; Estados UnidosFil: Boersma, P. Dee. University of Washington; Estados UnidosFil: Bost, Charles-André. Centre Detudes Biologiques de Chizé; FranciaFil: Cherel, Yves. Centre Detudes Biologiques de Chizé; FranciaFil: Dann, Peter. Phillip Island Nature Parks; AustraliaFil: Mattern, Thomas. University of Otago; Nueva ZelandaFil: Ellenberg, Ursula. Global Penguin Society; Estados Unidos. La Trobe University; AustraliaFil: Garcia Borboroglu, Jorge Pablo. University of Washington; Estados Unidos. Global Penguin Society; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Argilla, Lisa S.. Otago Polytechnic; Nueva ZelandaFil: Bertelsen, Mads F.. Copenhagen Zoo; Dinamarca. University of Copenhagen; DinamarcaFil: Fiddaman, Steven R.. University of Oxford; Reino UnidoFil: Howard, Pauline. Hornby Veterinary Centre; Nueva Zelanda. South Island Wildlife Hospital; Nueva ZelandaFil: Labuschagne, Kim. National Zoological Garden; SudáfricaFil: Miller, Gary. University of Western Australia; Australia. University of Tasmania; AustraliaFil: Parker, Patricia. University of Missouri St. Louis; Estados UnidosFil: Phillips, Richard A.. Natural Environment Research Council; Reino UnidoFil: Quillfeldt, Petra. Justus-Liebig-Universit ̈ at Giessen; AlemaniaFil: Ryan, Peter G.. University of Cape Town; SudáfricaFil: Taylor, Helen. Vet Services Hawkes Bay Ltd; Nueva Zelanda. Wairoa Farm Vets; Nueva ZelandaFil: Zhang, De-Xing. Chinese Academy of Sciences; República de ChinaFil: Zhang, Guojie. BGI-Shenzhen; China. Chinese Academy of Sciences; República de China. University of Copenhagen; DinamarcaFil: McKinlay, Bruce. Department of Conservation; Nueva Zeland

The Fossil Calibration Database, A New Resource for Divergence Dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important, and often least appreciated, step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for non- specialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open- access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as one key pipeline for peer-reviewed calibrations to enter the database

Earth history and the passerine superradiation.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation

The evolution of mammalian brain size

Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relationship across species and that any deviation from this slope is due to selection on brain size. Using the largest fossil and extant dataset yet assembled, we find that shifts in allometric slope underpin major transitions in mammalian evolution and are often primarily characterized by marked changes in body size. Our results reveal that the largest-brained mammals achieved large relative brain sizes by highly divergent paths. These findings prompt a reevaluation of the traditional paradigm of relative brain size and open new opportunities to improve our understanding of the genetic and developmental mechanisms that influence brain size