Neanderthals and Denisovans As Biological Invaders
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Ecological Correlates of Ghost Lineages in Ruminants
Paleobiology, 38(1), 2012, pp. 101–111 Ecological correlates of ghost lineages in ruminants Juan L. Cantalapiedra, Manuel Herna´ndez Ferna´ndez, Gema M. Alcalde, Beatriz Azanza, Daniel DeMiguel, and Jorge Morales Abstract.—Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation. Juan L. Cantalapiedra, Gema Alcalde, and Jorge Morales. Departamento de Paleobiologı´a, Museo Nacional de Ciencias Naturales, UCM-CSIC, Pinar 25, 28006 Madrid, Spain. E-mail: [email protected] Manuel Herna´ndez Ferna´ndez. Departamento de Paleontologı´a, Facultad de Ciencias Geolo´gicas, Universidad Complutense de Madrid y Departamento de Cambio Medioambiental, Instituto de Geociencias, Consejo Superior de Investigaciones Cientı´ficas, Jose´ Antonio Novais 2, 28040 Madrid, Spain Daniel DeMiguel. -
Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
The Middle Stone Age of East Africa and the Beginnings of Regional Identity
Journal of Worm Prehistory, Vol. 2, No. 3. 1988 The Middle Stone Age of East Africa and the Beginnings of Regional Identity J. Desmond Clark ~ The history of research into the Middle Stone Age of East Africa and the present state of knowledge of this time period is examined for the region as a whole, with special reference to paleoenvironments. The known MSA sites and occurrences are discussed region by region and attempts are made to fit them into a more precise chronological framework and to assess their cultural affinities. The conclusion is reached that the Middle Stone Age lasted for some 150,000 years but considerably more systematic and in-depth research is needed into this time period, which is now perceived as of great significance since it appears to span the time of the evolution of anatomically Modern humans in the continent, perhaps in Last Africa. KEY WORDS: Middle Stone Age; Sangoan/Lupemban; long chronology; Archaic Homo sapiens; Modern H. sapiens. • . when we eventually find the skulls of the makers of the African Mousterian they will prove to be of non-Homo sapiens type, although probably not of Neanderthal type, but merely an allied race of Homo rhodesiensis. The partial exception.., of the Stillbay culture group is therefore explicable on the grounds that Homo sapiens influence was already at work. (Leakey, 1931, p. 326) The other view is that the cradle of the Aurignacian races lies hidden somewhere in the Sahara area, probably in the south-east, and that an early wave of movement carried one branch of the stock via Somaliland and the Straits of Bab el-Mandeb into Arabia, and thence to some unknown secondary centre of distribution in Asia. -
Phylogeny of a Rapidly Evolving Clade: the Cichlid Fishes of Lake Malawi
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 5107–5110, April 1999 Evolution Phylogeny of a rapidly evolving clade: The cichlid fishes of Lake Malawi, East Africa (adaptive radiationysexual selectionyspeciationyamplified fragment length polymorphismylineage sorting) R. C. ALBERTSON,J.A.MARKERT,P.D.DANLEY, AND T. D. KOCHER† Department of Zoology and Program in Genetics, University of New Hampshire, Durham, NH 03824 Communicated by John C. Avise, University of Georgia, Athens, GA, March 12, 1999 (received for review December 17, 1998) ABSTRACT Lake Malawi contains a flock of >500 spe- sponsible for speciation, then we expect that sister taxa will cies of cichlid fish that have evolved from a common ancestor frequently differ in color pattern but not morphology. within the last million years. The rapid diversification of this Most attempts to determine the relationships among cichlid group has been attributed to morphological adaptation and to species have used morphological characters, which may be sexual selection, but the relative timing and importance of prone to convergence (8). Molecular sequences normally these mechanisms is not known. A phylogeny of the group provide the independent estimate of phylogeny needed to infer would help identify the role each mechanism has played in the evolutionary mechanisms. The Lake Malawi cichlids, however, evolution of the flock. Previous attempts to reconstruct the are speciating faster than alleles can become fixed within a relationships among these taxa using molecular methods have species (9, 10). The coalescence of mtDNA haplotypes found been frustrated by the persistence of ancestral polymorphisms within populations predates the origin of many species (11). In within species. -
Major Clades of Agaricales: a Multilocus Phylogenetic Overview
Mycologia, 98(6), 2006, pp. 982–995. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Major clades of Agaricales: a multilocus phylogenetic overview P. Brandon Matheny1 Duur K. Aanen Judd M. Curtis Laboratory of Genetics, Arboretumlaan 4, 6703 BD, Biology Department, Clark University, 950 Main Street, Wageningen, The Netherlands Worcester, Massachusetts, 01610 Matthew DeNitis Vale´rie Hofstetter 127 Harrington Way, Worcester, Massachusetts 01604 Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708 Graciela M. Daniele Instituto Multidisciplinario de Biologı´a Vegetal, M. Catherine Aime CONICET-Universidad Nacional de Co´rdoba, Casilla USDA-ARS, Systematic Botany and Mycology de Correo 495, 5000 Co´rdoba, Argentina Laboratory, Room 304, Building 011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350 Dennis E. Desjardin Department of Biology, San Francisco State University, Jean-Marc Moncalvo San Francisco, California 94132 Centre for Biodiversity and Conservation Biology, Royal Ontario Museum and Department of Botany, University Bradley R. Kropp of Toronto, Toronto, Ontario, M5S 2C6 Canada Department of Biology, Utah State University, Logan, Utah 84322 Zai-Wei Ge Zhu-Liang Yang Lorelei L. Norvell Kunming Institute of Botany, Chinese Academy of Pacific Northwest Mycology Service, 6720 NW Skyline Sciences, Kunming 650204, P.R. China Boulevard, Portland, Oregon 97229-1309 Jason C. Slot Andrew Parker Biology Department, Clark University, 950 Main Street, 127 Raven Way, Metaline Falls, Washington 99153- Worcester, Massachusetts, 01609 9720 Joseph F. Ammirati Else C. Vellinga University of Washington, Biology Department, Box Department of Plant and Microbial Biology, 111 355325, Seattle, Washington 98195 Koshland Hall, University of California, Berkeley, California 94720-3102 Timothy J. -
Persistence of Middle Stone Age Technology to the Pleistocene/Holocene Transition Supports a Complex Hominin Evolutionary Scenario in West Africa
This is a repository copy of Persistence of Middle Stone Age technology to the Pleistocene/Holocene transition supports a complex hominin evolutionary scenario in West Africa. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/129212/ Version: Accepted Version Article: Scerri, E.M.L., Blinkhorn, J., Niang, K. et al. (2 more authors) (2017) Persistence of Middle Stone Age technology to the Pleistocene/Holocene transition supports a complex hominin evolutionary scenario in West Africa. Journal of Archaeological Science: Reports, 11. pp. 639-646. ISSN 2352-409X https://doi.org/10.1016/j.jasrep.2017.01.003 Reuse This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) licence. This licence only allows you to download this work and share it with others as long as you credit the authors, but you can’t change the article in any way or use it commercially. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Persistence of Middle Stone Age technology to the Pleistocene/Holocene transition supports a complex hominin evolutionary scenario in West Africa Eleanor M.L. Scerria*, James Blinkhornb, Khady Niangc, Mark D. Batemand, Huw S. Groucutta a Research -
Krapina and Other Neanderthal Clavicles: a Peculiar Morphology?
Krapina and Other Neanderthal Clavicles : A Peculiar Morphology? Jean-Luc Voisin To cite this version: Jean-Luc Voisin. Krapina and Other Neanderthal Clavicles : A Peculiar Morphology?. Periodicum Biologorum, 2006, 108 (3), pp.331-339. halshs-00352689 HAL Id: halshs-00352689 https://halshs.archives-ouvertes.fr/halshs-00352689 Submitted on 13 Jan 2009 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. PERIODICUM BIOLOGORUM UDC 57:61 VOL. 108, No 3, 331–339, 2006 CODEN PDBIAD ISSN 0031-5362 Original scientific paper Krapina and Other Neanderthal Clavicles: A Peculiar Morphology? Abstract JEAN-LUC VOISIN The clavicle is the less studied element of the shoulder girdle, even if it is USM 103 a very important bone for human evolution because it permits all move- Institut de Paléontologie Humaine ments outside the parasagittal plan. In this work, clavicle curvatures are 1 rue René Panhard 75013 Paris studied by projecting them on a cranial and a dorsal plan, which are perpen- E-mail: [email protected] dicular. In cranial view, there is no difference within the genus Homo, and [email protected] Neanderthal clavicles are not more S-shaped than modern human ones. -
Timeline from Ice Ages to European Arrival in New England
TIMELINE FROM ICE AGES TO EUROPEAN ARRIVAL IN NEW ENGLAND Mitchell T. Mulholland & Kit Curran Department of Anthropology, University of Massachusetts Amherst 500 Years Before Present CONTACT Europeans Arrive PERIOD 3,000 YBP WOODLAND Semi-permanent villages in which cultivated food crops are stored. Mixed-oak forest, chestnut. Slash and burn agriculture changes appearance of landscape. Cultivated plants: corn, beans, and squash. Bows and arrows, spears used along with more wood, bone tools. 6,000 YBP LATE Larger base camps; small groups move seasonally ARCHAIC through mixed-oak forest, including some tropical plants. Abundant fish and game; seeds and nuts. 9,000 YBP EARLY & Hunter/gatherers using seasonal camping sites for MIDDLE several months duration to hunt deer, turkey, ARCHAIC and fish with spears as well as gathering plants. 12,000 YBP PALEOINDIAN Small nomadic hunting groups using spears to hunt caribou and mammoth in the tundra Traditional discussions of the occupation of New England by prehistoric peoples divide prehistory into three major periods: Paleoindian, Archaic and Woodland. Paleoindian Period (12,000-9,000 BP) The Paleoindian Period extended from approximately 12,000 years before present (BP) until 9,000 BP. During this era, people manufactured fluted projectile points. They hunted caribou as well as smaller animals found in the sparse, tundra-like environment. In other parts of the country, Paleoindian groups hunted larger Pleistocene mammals such as mastodon or mammoth. In New England there is no evidence that these mammals were utilized by humans as a food source. People moved into New England after deglaciation of the region concluded around 14,000 BP. -
K = Kenyanthropus Platyops “Kenya Man” Discovered by Meave Leaky
K = Kenyanthropus platyops “Kenya Man” Discovered by Meave Leaky and her team in 1998 west of Lake Turkana, Kenya, and described as a new genus dating back to the middle Pliocene, 3.5 MYA. A = Australopithecus africanus STS-5 “Mrs. Ples” The discovery of this skull in 1947 in South Africa of this virtually complete skull gave additional credence to the establishment of early Hominids. Dated at 2.5 MYA. H = Homo habilis KNM-ER 1813 Discovered in 1973 by Kamoya Kimeu in Koobi Fora, Kenya. Even though it is very small, it is considered to be an adult and is dated at 1.9 MYA. E = Homo erectus “Peking Man” Discovered in China in the 1920’s, this is based on the reconstruction by Sawyer and Tattersall of the American Museum of Natural History. Dated at 400-500,000 YA. (2 parts) L = Australopithecus afarensis “Lucy” Discovered by Donald Johanson in 1974 in Ethiopia. Lucy, at 3.2 million years old has been considered the first human. This is now being challenged by the discovery of Kenyanthropus described by Leaky. (2 parts) TC = Australopithecus africanus “Taung child” Discovered in 1924 in Taung, South Africa by M. de Bruyn. Raymond Dart established it as a new genus and species. Dated at 2.3 MYA. (3 parts) G = Homo ergaster “Nariokotome or Turkana boy” KNM-WT 15000 Discovered in 1984 in Nariokotome, Kenya by Richard Leaky this is the first skull dated before 100,000 years that is complete enough to get accurate measurements to determine brain size. Dated at 1.6 MYA. -
Denisovan Portrait Drawn From
IN FOCUS NEWS trees across 13 provinces in the country’s north since the programme began in 1978. Around 2000, deserts across the country MAAYAN HAREL MAAYAN were expanding by 10,400 square kilometres a year, says the government. But in 2017, it reported that China’s deserts were shrinking by more than 2,400 square kilometres a year. A 2018 study1 of satellite data from the US National Oceanic and Atmospheric Administration found that forest cover has increased in line with government statistics, but suggested that changes in logging policy were more important than afforestation — planting forests where none were before. In 1999, the Chinese government began planting millions of trees in its Grain for Green Program, intended to repair dam- aged farmland in the northern Loess Plateau, which is roughly the size of France. And the afforestation drive is continuing apace: in 2018, the government announced a target of 30% forest coverage by 2050. At the moment, the coverage is around 22%. It’s still too early to determine whether it has solved the problem, says Congbin Fu, director of the Institute for Climate and Global Change Research at Nanjing University. Land restoration can take An artist’s impression of a young female Denisovan, based on skeletal traits derived from ancient DNA. several decades or even 100 years, he says. There are pitfalls to mass tree-planting. ANCIENT HUMANS Large parts of China — including some areas where trees are being planted — are getting drier. A paper2 co-authored by Sternberg found that arid areas in China had increased Denisovan portrait by roughly 1.6 million square kilometres, about the size of Iran, since 1980 — probably due largely to anthropogenic climate change. -
Periodontal Disease and Dental Caries from Krapina Neanderthal to Contemporary Man – Skeletal Studies
Clinical science Acta Medica Academica 2012;41(2):119-130 DOI: 10.5644/ama2006-124.45 Periodontal disease and dental caries from Krapina Neanderthal to contemporary man – skeletal studies Berislav Topić1, Hajrija Raščić-Konjhodžić2, Mojca Čižek Sajko3 1 Academy of Sciences and Arts Objective. The aim of this study was the quantification of alveolar of Bosnia and Herzegovina, Sarajevo bone resorption as well as the number and percentage of teeth with Bosnia and Herzegovina dental caries. Materials and Methods. Four samples of jaws and sin- 2 Faculty of Stomatology, University gle teeth were studied from four time periods, i.e. from the Krapina of Sarajevo, Sarajevo, Bosnia and Neanderthals (KN) who reportedly lived over 130,000 years ago, and Herzegovina groups of humans from the 1st, 10th and 20th centuries. Resorption of 3 Institute for Biostatistics and Medical the alveolar bone of the jaws was quantified by the tooth-cervical- Informatics, Faculty of Medicine height (TCH) index. Diagnosis of dental caries was made by inspec- Ljubljana, Slovenia tion and with a dental probe. TCH-index was calculated for a total of 1097 teeth from 135 jaws. Decay was calculated for a total of 3579 Corresponding author: teeth. Results. Resorptive changes of the alveolar bone in KN and 1st Berislav Topić century man were more pronounced on the vestibular surface than Academy of Sciences and Arts interdentally (p<0.05), while no significant difference could be con- of Bosnia and Herzegovina firmed for 10th and 20th century man (p=0.1). The number (percent- 71000 Sarajevo age) of decayed teeth was 0 (0%, n=281 teeth) in KN, 15 (1.7%; n=860 Bosnia and Herzegovina teeth) in 1st century, 24 (3.4%; n=697 teeth) in 10th century, and 207 [email protected] (11.9%, n=1741 teeth) in 20th century. -
No Evidence for Recent Selection at FOXP2 Among Diverse Human Populations
Article No Evidence for Recent Selection at FOXP2 among Diverse Human Populations Graphical Abstract Authors Elizabeth Grace Atkinson, Amanda Jane Audesse, Julia Adela Palacios, Dean Michael Bobo, Ashley Elizabeth Webb, Sohini Ramachandran, Brenna Mariah Henn Correspondence [email protected] (E.G.A.), [email protected] (B.M.H.) In Brief An in-depth examination of diverse sets of human genomes argues against a recent selective evolutionary sweep of FOXP2, a gene that was believed to be critical for speech evolution in early hominins. Highlights d No support for positive selection at FOXP2 in large genomic datasets d Sample composition and genomic scale significantly affect selection scans d An intronic ROI within FOXP2 is expressed in human brain cells and cortical tissue d This ROI contains a large amount of constrained, human- specific polymorphisms Atkinson et al., 2018, Cell 174, 1424–1435 September 6, 2018 ª 2018 Elsevier Inc. https://doi.org/10.1016/j.cell.2018.06.048 Article No Evidence for Recent Selection at FOXP2 among Diverse Human Populations Elizabeth Grace Atkinson,1,8,9,10,* Amanda Jane Audesse,2,3 Julia Adela Palacios,4,5 Dean Michael Bobo,1 Ashley Elizabeth Webb,2,6 Sohini Ramachandran,4 and Brenna Mariah Henn1,7,* 1Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA 2Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA 3Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA 4Department of Ecology and Evolutionary