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Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins Alexandra Gavryushkina University of Auckland
Ecology, Evolution and Organismal Biology Ecology, Evolution and Organismal Biology Publications 2017 Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins Alexandra Gavryushkina University of Auckland Tracy A. Heath Iowa State University, [email protected] Daniel T. Ksepka Bruce Museum David Welch University of Auckland Alexei J. Drummond University of Auckland Follow this and additional works at: http://lib.dr.iastate.edu/eeob_ag_pubs Part of the Ecology and Evolutionary Biology Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ eeob_ag_pubs/207. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Ecology, Evolution and Organismal Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Ecology, Evolution and Organismal Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Syst. Biol. 66(1):57–73, 2017 © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] DOI:10.1093/sysbio/syw060 Advance Access publication August 24, 2016 Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins , ,∗ , ALEXANDRA GAVRYUSHKINA1 2 ,TRACY A. -
A Rhinopristiform Sawfish (Genus Pristis) from the Middle Eocene (Lutetian) of Southern Peru and Its Regional Implications
Carnets Geol. 20 (5) E-ISSN 1634-0744 DOI 10.4267/2042/70759 A rhinopristiform sawfish (genus Pristis) from the middle Eocene (Lutetian) of southern Peru and its regional implications Alberto COLLARETA 1, 2 Luz TEJADA-MEDINA 3, 4 César CHACALTANA-BUDIEL 3, 5 Walter LANDINI 1, 6 Alí ALTAMIRANO-SIERRA 7, 8 Mario URBINA-SCHMITT 7, 9 Giovanni BIANUCCI 1, 10 Abstract: Modern sawfishes (Rhinopristiformes: Pristidae) are circumglobally distributed in warm wa- ters and are common in proximal marine and even freshwater habitats. The fossil record of modern pristid genera (i.e., Pristis and Anoxypristis) dates back to the early Eocene and is mostly represented by isolated rostral spines and oral teeth, with phosphatised rostra representing exceptional occurren- ces. Here, we report on a partial pristid rostrum, exhibiting several articulated rostral spines, from middle Eocene strata of the Paracas Formation (Yumaque Member) exposed in the southern Peruvian East Pisco Basin. This finely preserved specimen shows anatomical structures that are unlikely to leave a fossil record, e.g., the paracentral grooves that extend along the ventral surface of the rostrum. Ba- sed on the morphology of the rostral spines, this fossil sawfish is here identified as belonging to Pristis. To our knowledge, this discovery represents the geologically oldest known occurrence of Pristidae from the Pacific Coast of South America. Although the fossil record of pristids from the East Pisco Basin spans from the middle Eocene to the late Miocene, sawfishes are no longer present in the modern cool, upwelling-influenced coastal waters of southern Peru. Given the ecological preferences of the extant members of Pristis, the occurrence of this genus in the Paracas deposits suggests that middle Eocene nearshore waters in southern Peru were warmer than today. -
71St Annual Meeting Society of Vertebrate Paleontology Paris Las Vegas Las Vegas, Nevada, USA November 2 – 5, 2011 SESSION CONCURRENT SESSION CONCURRENT
ISSN 1937-2809 online Journal of Supplement to the November 2011 Vertebrate Paleontology Vertebrate Society of Vertebrate Paleontology Society of Vertebrate 71st Annual Meeting Paleontology Society of Vertebrate Las Vegas Paris Nevada, USA Las Vegas, November 2 – 5, 2011 Program and Abstracts Society of Vertebrate Paleontology 71st Annual Meeting Program and Abstracts COMMITTEE MEETING ROOM POSTER SESSION/ CONCURRENT CONCURRENT SESSION EXHIBITS SESSION COMMITTEE MEETING ROOMS AUCTION EVENT REGISTRATION, CONCURRENT MERCHANDISE SESSION LOUNGE, EDUCATION & OUTREACH SPEAKER READY COMMITTEE MEETING POSTER SESSION ROOM ROOM SOCIETY OF VERTEBRATE PALEONTOLOGY ABSTRACTS OF PAPERS SEVENTY-FIRST ANNUAL MEETING PARIS LAS VEGAS HOTEL LAS VEGAS, NV, USA NOVEMBER 2–5, 2011 HOST COMMITTEE Stephen Rowland, Co-Chair; Aubrey Bonde, Co-Chair; Joshua Bonde; David Elliott; Lee Hall; Jerry Harris; Andrew Milner; Eric Roberts EXECUTIVE COMMITTEE Philip Currie, President; Blaire Van Valkenburgh, Past President; Catherine Forster, Vice President; Christopher Bell, Secretary; Ted Vlamis, Treasurer; Julia Clarke, Member at Large; Kristina Curry Rogers, Member at Large; Lars Werdelin, Member at Large SYMPOSIUM CONVENORS Roger B.J. Benson, Richard J. Butler, Nadia B. Fröbisch, Hans C.E. Larsson, Mark A. Loewen, Philip D. Mannion, Jim I. Mead, Eric M. Roberts, Scott D. Sampson, Eric D. Scott, Kathleen Springer PROGRAM COMMITTEE Jonathan Bloch, Co-Chair; Anjali Goswami, Co-Chair; Jason Anderson; Paul Barrett; Brian Beatty; Kerin Claeson; Kristina Curry Rogers; Ted Daeschler; David Evans; David Fox; Nadia B. Fröbisch; Christian Kammerer; Johannes Müller; Emily Rayfield; William Sanders; Bruce Shockey; Mary Silcox; Michelle Stocker; Rebecca Terry November 2011—PROGRAM AND ABSTRACTS 1 Members and Friends of the Society of Vertebrate Paleontology, The Host Committee cordially welcomes you to the 71st Annual Meeting of the Society of Vertebrate Paleontology in Las Vegas. -
2017 Chicxulub Revealed
THE UNIVERSITY TEXAS OF AUSTIN AT JACKSON• SCHOOL GEOSCIENCES OF 2017 NEWSLETTER• Newsletter2 017 Chicxulub Revealed A first look at rocks from the crater left by the asteroid that wiped out non-avian dinosaurs WELCOME Dear Alumni and Friends he devastation that Hurricane Harvey brought to Texas communities in August was a tragic reminder of how vital it is to understand our planet and T its processes. Shortly after the hurricane struck, our scientists, through our Rapid Response program, began to conduct research to understand how Harvey has impacted the coast and offshore Gulf of Mexico. This research will help determine the best ways to deal with many coastal issues in the aftermath of the storm, and how we might better prepare for such events in the future. You can read more about the mission on page 18. Rapid response efforts on the effects of abrupt, catastrophic geoscience events COVER: GRANITE FROM THE PEAK RING OF provide critical science that can benefit society. This is what we strive to do here at the THE CHICXULUB CRATER FORMED BY THE Jackson School of Geosciences. This year’s Newsletter holds some tremendous examples. ASTEROID STRIKE THAT WIPED OUT ALL NON- AVIAN DINOSAURS I’d like to draw your attention to the story on page 58 about the scientific coring mission led by Peter Flemings to bring back samples of methane hydrate from ABOVE: MEMBERS OF THE JACKSON beneath the Gulf of Mexico. This is a cutting-edge research project on a potential SCHOOL-LED TEAM CORING FOR SAMPLES OF METHANE HYDRATE IN THE GULF OF MEXICO future energy source that very few schools in the world would be able to mount. -
Bayesian Phylogenetic Estimation of Fossil Ages
Bayesian phylogenetic estimation of fossil ages Alexei J. Drummond1;2;3 and Tanja Stadler3;4 1Centre for Computational Evolution, University of Auckland, Auckland, New Zealand; 2Department of Computer Science, University of Auckland, Auckland, 1010, New Zealand; 3Department of Biosystems Science & Engineering, Eidgen¨ossischeTechnische Hochschule Z¨urich, 4058 Basel, Switzerland; 4Swiss Institute of Bioinformatics (SIB), Switzerland. Corresponding author: Alexei J. Drummond, Centre for Computational Evolution, University of Auckland, Auckland, New Zealand; E-mail: [email protected] Abstract Recent advances have allowed for both morphological fossil evi- dence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both di- vergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized data sets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two data sets of 5.7% and 13.2% respectively. The median relative standard error (RSD) was 9.2% and 7.2% respectively, suggesting good precision, although with some outliers. In fact in the two data sets we analyze the phylogenetic estimates of fossil age is on average < 2 My from the midpoint age of the geological strata from which it was ex- cavated. -
At the Root of the Early Penguin Neck: a Study of the Only Two Cervicodorsal Spines Recovered from the Eocene of Antarctica Piotr Jadwiszczak
RESEARCH/REVIEW ARTICLE At the root of the early penguin neck: a study of the only two cervicodorsal spines recovered from the Eocene of Antarctica Piotr Jadwiszczak Institute of Biology, University of Bialystok, Swierkowa 20B, PL-15-950, Bialystok, Poland Keywords Abstract Antarctic Peninsula; La Meseta Formation; Palaeogene; early Sphenisciformes; The spinal column of early Antarctic penguins is poorly known, mainly due to cervicodorsal vertebrae. the scarcity of articulated vertebrae in the fossil record. One of the most interesting segments of this part of the skeleton is the transitional series located Correspondence at the root of the neck. Here, two such cervicodorsal series, comprising rein- Piotr Jadwiszczak, Institute of Biology, terpreted known material and a new specimen from the Eocene of Seymour University of Bialystok, Swierkowa 20B, Island (Antarctic Peninsula), were investigated and contrasted with those PL-15-950 Bialystok, Poland. of modern penguins and some fossil bones. The new specimen is smaller E-mail: [email protected] than the counterpart elements in recent king penguins, whereas the second series belonged to a large-bodied penguin from the genus Palaeeudyptes. It had been assigned by earlier researchers to P. gunnari (a species of ‘‘giant’’ penguins) and a Bayesian analysis*a Bayes factor approach based on size of an associated tarsometatarsus*strongly supported such an assignment. Morphological and functional studies revealed that mobility within the aforementioned segment probably did not differ substantially between extant and studied fossil penguins. There were, however, intriguing morphological differences between the smaller fossil specimen and the comparative material related to the condition of the lateral excavation in the first cervicodorsal vertebra and the extremely small size of the intervertebral foramen located just prior to the first ‘‘true’’ thoracic vertebra. -
Supplementary Information
Supplementary Information Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits Andrea Estandía, R. Terry Chesser, Helen F. James, Max A. Levy, Joan Ferrer Obiol, Vincent Bretagnolle, Jacob González-Solís, Andreanna J. Welch This pdf file includes: Supplementary Information Text Figures S1-S7 SUPPLEMENTARY INFORMATION TEXT Fossil calibrations The fossil record of Procellariiformes is sparse when compared with other bird orders, especially its sister order Sphenisciformes (Ksepka & Clarke 2010, Olson 1985c). There are, however, some fossil Procellariiformes that are both robustly dated and identified and therefore suitable for fossil calibrations. Our justification of these fossils, below, follows best practices described by Parham et al. (2012) where possible. For all calibration points only a minimum age was set with no upper constraint specified, except for the root of the tree. 1. Node between Sphenisciformes/Procellariiformes Minimum age: 60.5 Ma Maximum age: 61.5 Ma Taxon and specimen: Waimanu manneringi (Slack et al. 2006); CM zfa35 (Canterbury Museum, Christchurch, New Zealand), holotype comprising thoracic vertebrae, caudal vertebrae, pelvis, femur, tibiotarsus, and tarsometatarsus. Locality: Basal Waipara Greensand, Waipara River, New Zealand. Phylogenetic justification: Waimanu has been resolved as the basal penguin taxon using morphological data (Slack et al. 2006), as well as combined morphological and molecular datasets (Ksepka et al. 2006, Clarke et al. 2007). Morphological and molecular phylogenies agree on the monophyly of Sphenisciformes and Procellariiformes (Livezey & Zusi 2007, Prum et al. 2015). Waimanu manneringi was previously used by Prum et al. (2015) to calibrate Sphenisiciformes, and see Ksepka & Clarke (2015) for a review of the utility of this fossil as a robust calibration point. -
Bird Fossils from the Takatika Grit, Chatham Island
BIRD FOSSILS FROM THE TAKATIKA GRIT, CHATHAM ISLAND, NEW ZEALAND A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geology At the University of Canterbury By Jacob Christopher Blokland University of Canterbury 2017 Figure I: An interpretation of Archaeodyptes stilwelli. Original artwork by Jacob Blokland. i ACKNOWLEDGEMENTS The last couple years have been exciting and challenging. It has been a pleasure to work with great people, and be involved with new research that will hopefully be of contribution to science. First of all, I would like to thank my two supervisors, Dr Catherine Reid and Dr Paul Scofield, for tirelessly reviewing my work and providing feedback. I literally could not have done it without you, and your time, patience and efforts are very much appreciated. Thank you for providing me with the opportunity to do a vertebrate palaeontology based thesis. I would like to extend my deepest gratitude to Catherine for encouragement regarding my interest in palaeontology since before I was an undergraduate, and providing great information regarding thesis and scientific format. I am also extremely grateful to Paul for welcoming me to use specimens from Canterbury Museum, and providing useful information and recommendations for this project through your expertise in this particular discipline. I would also like to thank Associate Professor Jeffrey Stilwell for collecting the fossil specimens used in this thesis, and for the information you passed on regarding the details of the fossils. Thank you to Geoffrey Guinard for allowing me to use your data from your published research in this study. -
Antarctic Peninsula Paleontology Project Matt Lamanna
Philadelphia College of Osteopathic Medicine DigitalCommons@PCOM PCOM Scholarly Papers 2-11-2016 Science AMA Series: Antarctic Peninsula Paleontology Project Matt Lamanna Julia Clarke Pat O'Connor Ross MacPhee Erik Gorscak See next page for additional authors Follow this and additional works at: http://digitalcommons.pcom.edu/scholarly_papers Part of the Paleontology Commons Recommended Citation Lamanna, Matt; Clarke, Julia; O'Connor, Pat; MacPhee, Ross; Gorscak, Erik; West, Abby; Torres, Chris; Claeson, Kerin M.; Jin, Meng; Salisbury, Steve; Roberts, Eric; and Jinnah, Zubair, "Science AMA Series: Antarctic Peninsula Paleontology Project" (2016). PCOM Scholarly Papers. Paper 1677. http://digitalcommons.pcom.edu/scholarly_papers/1677 This Article is brought to you for free and open access by DigitalCommons@PCOM. It has been accepted for inclusion in PCOM Scholarly Papers by an authorized administrator of DigitalCommons@PCOM. For more information, please contact [email protected]. Authors Matt Lamanna, Julia Clarke, Pat O'Connor, Ross MacPhee, Erik Gorscak, Abby West, Chris Torres, Kerin M. Claeson, Meng Jin, Steve Salisbury, Eric Roberts, and Zubair Jinnah This article is available at DigitalCommons@PCOM: http://digitalcommons.pcom.edu/scholarly_papers/1677 REDDIT Science AMA Series: We’re a group of paleontologists and geologists on our way to Antarctica to look for fossils of non-avian dinosaurs, ancient birds, and more. AUA! ANTARCTICPALEO R/SCIENCE Hi Reddit! Our research team—collectively working as part of the Antarctic Peninsula Paleontology Project, or AP3—is on a National Science Foundation-supported research vessel on its way to Antarctica. This will be our third expedition to explore the Antarctic Peninsula for fossils spanning the end of the Age of Dinosaurs (the Late Cretaceous) to the dawn of the Age of Mammals (the early Paleogene). -
Phylogenetically Vetted and Stratigraphically Constrained Fossil Calibrations Within Aves
Palaeontologia Electronica palaeo-electronica.org Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves Daniel Ksepka and Julia Clarke ABSTRACT Understanding the timing of the crown radiation of birds is a major goal of avian molecular systematists and paleontologists. Despite the availability of ever-larger molecular datasets and increasingly sophisticated methods for phylogeny reconstruc- tion and divergence time estimation, relatively little attention has been paid to outlining and applying fossil calibrations. As the avian fossil record has become better sampled, and more extinct taxa have been incorporated into a phylogenetic framework, the potential for this record to serve as a powerful source of temporal data for divergence dating analyses has increased. Nonetheless, the desire for abundant calibrations must be balanced by careful vetting of candidate fossils, especially given the prevalence of inaccurate fossil calibrations in the recent past. In this contribution, we provide seven phylogenetically vetted fossil calibrations for major divergences within crown Aves rep- resenting the splits between (1) Anatoidea, (2) Sphenisciformes, (3) Coracioidea, (4) Apodidae, (5) Coliiformes, (6) Psittaciformes, and (7) Upupiformes, and the respective extant sister taxon for each of these clades. Each calibration is based an individual specimen, which maintains the clearest possible chain of inference for converting the relevant stratigraphic horizon to a numerical date. Minimum ages for each fossil are tightly constrained and incorporate associated dating errors, and the distributions of younger fossils from the clades of interest are summarized to provide a starting point for workers interested in estimating confidence intervals or outlining prior age distribu- tion curves. Daniel Ksepka. National Evolutionary Synthesis Center, Durham, North Carolina, 27706, USA. -
Phylogenetic Characters in the Humerus and Tarsometatarsus of Penguins
vol. 35, no. 3, pp. 469–496, 2014 doi: 10.2478/popore−2014−0025 Phylogenetic characters in the humerus and tarsometatarsus of penguins Martín CHÁVEZ HOFFMEISTER School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, BS8 1RJ, Bristol, United Kingdom and Laboratorio de Paleoecología, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile <[email protected]> Abstract: The present review aims to improve the scope and coverage of the phylogenetic matrices currently in use, as well as explore some aspects of the relationships among Paleogene penguins, using two key skeletal elements, the humerus and tarsometatarsus. These bones are extremely important for phylogenetic analyses based on fossils because they are commonly found solid specimens, often selected as holo− and paratypes of fossil taxa. The resulting dataset includes 25 new characters, making a total of 75 characters, along with eight previously uncoded taxa for a total of 48. The incorporation and analysis of this corrected subset of morphological characters raise some interesting questions consider− ing the relationships among Paleogene penguins, particularly regarding the possible exis− tence of two separate clades including Palaeeudyptes and Paraptenodytes, the monophyly of Platydyptes and Paraptenodytes, and the position of Anthropornis. Additionally, Noto− dyptes wimani is here recovered in the same collapsed node as Archaeospheniscus and not within Delphinornis, as in former analyses. Key words: Sphenisciformes, limb bones, phylogenetic analysis, parsimony method, revised dataset. Introduction Since the work of O’Hara (1986), the phylogeny of penguins has been a sub− ject of great interest. During the last decade, several authors have explored the use of molecular (e.g., Subramanian et al. -
Paleogene Equatorial Penguins Challenge the Proposed Relationship Between Biogeography, Diversity, and Cenozoic Climate Change
Paleogene equatorial penguins challenge the proposed relationship between biogeography, diversity, and Cenozoic climate change Julia A. Clarkea,b,c,d, Daniel T. Ksepkac, Marcelo Stucchie, Mario Urbinaf, Norberto Gianninig,h, Sara Bertellii,g, Yanina Narva´ ezj, and Clint A. Boyda aDepartment of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Campus Box 8208, Raleigh, NC 27695; bDepartment of Paleontology, North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601-1029; Divisions of cPaleontology and gVertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024; eAsociacio´n para la Investigacio´n y Conservacio´n de la Biodiversidad, Los Agro´logos 220, Lima 12, Peru´; fDepartment of Vertebrate Paleontology, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Avenida Arenales 1256, Lima 14, Peru´; hProgram de Investigaciones de Biodiversidad Argentina (Consejo Nacional de Investigaciones Cientı´ficas y Te´cnicas), Facultad de Ciencias Naturales, Instituto Miguel Lillo de la Universidad Nacional de Tucuma´n, Miguel Lillo 205, CP 4000, Tucuma´n, Argentina; iThe Dinosaur Institute, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007; and jDepartment of Geology, Centro de Investigacio´n Cientı´ficay de Educacio´n Superior de Ensenada, Kilometer 107 Carretera Tijuana–Ensenada, 22860 Ensenada, Baja California, Me´xico Edited by R. Ewan Fordyce, University of Otago, Dunedin, New Zealand, and accepted by the Editorial Board May 21, 2007 (received for review December 14, 2006) New penguin fossils from the Eocene of Peru force a reevaluation of presence of at least five penguin taxa (ref.