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Molecular Clock: Insights and Pitfalls
Molecular clock: insights and pitfalls • An historical presentation of the molecular clock. • Birth of the molecular clock • Neutral Theory of evolution • The Nearly Neutral Theory of Evolution • The molecular clock is a « sloppy » clock. • A variable « tick rate » • Different rates for different groups • Calibrating a molecular phylogenetic tree • Dating Methods --- Introductory seminar on the use of molecular tools in natural history collections - 6-7 November 2007, RMCA --- A historical presentation of the molecular clock -1951-1955: Sanger sequenced the first protein, the insulin. Give the potential for using molecular sequences to construct phylogeny -1962: Zuckerkandl and Pauling: AA differences between the hemoglobin of different species is correlated with the time passed since they diverged. Divergence time (T) dAB / 2 A B Rate = (dAB / 2) / T C D --- Introductory seminar on the use of molecular tools in natural history collections - 6-7 November 2007, RMCA --- A historical presentation of the molecular clock Fixed or lost by chance Kimura, 1968 Eliminated by selection Fixed by selection Selection theory more in agreement with the rate of morphological evolution (Modified from Bromham and Penny, 2003) --- Introductory seminar on the use of molecular tools in natural history collections - 6-7 November 2007, RMCA --- The Neutral Theory of molecular evolution Eliminated by selection Fixed by selection Kimura, 1968 Fixed or lost by chance GENETIC DRIFT ν ν Molecular rate of evolution = Mutation rate 2N e * 1/2N e = (Modified from -
Washington University Record, April 1, 1993
Washington University School of Medicine Digital Commons@Becker Washington University Record Washington University Publications 4-1-1993 Washington University Record, April 1, 1993 Follow this and additional works at: http://digitalcommons.wustl.edu/record Recommended Citation "Washington University Record, April 1, 1993" (1993). Washington University Record. Book 615. http://digitalcommons.wustl.edu/record/615 This Article is brought to you for free and open access by the Washington University Publications at Digital Commons@Becker. It has been accepted for inclusion in Washington University Record by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS iecord Vol. 17 No. 25 April 1,1993 Architecture class teaches universal design, sensitivity Architecture students recently tried experiencing the world from the perspective of people with disabilities. For a few hours, students maneuvered in wheelchairs, wore blindfolds over their eyes or plugs in their ears to try to get a sense of the needs of people with physi- cal impairments. Some students also spent an entire day in wheelchairs. One took the bus to the St. Louis Galleria, another tried to go out to dinner. For Michele Lewis, a graduate stu- dent in the course, just being at home was difficult. "I even had trouble getting into my building, and there are people living there who are in wheelchairs," she said. "The hallways are too skinny, I couldn't reach my toothbrush and the stove is too high. How are you supposed to know when your water is boiling when you can't see it?" This empathic experience is part of a course taught by Mary Ann Lazarus, vice president at Hellmuth, Obata, and Kassabaum (HOK), an international Sophomore Becky Sladky signs up to be a host for April Welcome, an expanded student recruitment program. -
U-Pb Geochronology and the Calibration of Metazoan Evolution: Progress and Promise
Eleventh Annual V. M. Goldschmidt Conference (2001) 3867.pdf U-PB GEOCHRONOLOGY AND THE CALIBRATION OF METAZOAN EVOLUTION: PROGRESS AND PROMISE. S. A. Bowring, M. W. Martin, and J. P. Grotzinger. Intensive efforts by paleontologists, evolutionary and developmental biologists, and geologists are leading to a much better understanding of the first appearance and subsequent explosive diversification of animals. The recognition of thin zircon-bearing air-fall ash beds interlayered with fossil-bearing rocks has allowed the establishment of a high-precision temporal framework for animal evolution. Refined laboratory techniques permit analytical uncertainties that translate to age uncertainties of less than 1 Ma and the potential for global correlations at even higher resolution (100-300 ka) when combined with integrated paleontological, chemostratigraphic, and geological data. This framework, will allow evaluation of models that invoke both intrinsic and extrinsic triggers for Metazoan evolution and the Cambrian radiation. In particular, many have pointed out that the first appearance of metazoan fossils follows a period characterized by dramatic climate fluctuations and large fluctuations in the sequestration of carbon. The oldest dated Metazoan fossils (Ediacarans) are younger than ca. 575 Ma and appear to just post-date the youngest Neoproterozoic glacial deposits ca. 580 Ma. The Doushantuo phosphatic rocks of south China preserve spectacular animal fossils but have not been precisely dated. Geochronological data from Neoproterozoic to Cambrian rocks in North America, Namibia, Great Britain, Siberia, and Oman indicate that Ediacaran fossils range from at least 575 Ma (Newfoundland) to <543 Ma (Namibia). Shelly fossils (Cloudina and Namacalathus) are > 548 to ca. 542 Ma. Complex trace-fossils occur at least as far back as 555 Ma (White Sea, Russia). -
An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. -
Molecular Clocks Fossil Evidence Is Sparse and Imprecise Rose Hoberman (Or Nonexistent)
The Holy Grail Molecular Clocks Fossil evidence is sparse and imprecise Rose Hoberman (or nonexistent) Predict divergence times by comparing molecular data Rate Constancy? •Given 110 MYA – a phylogenetic tree – branch lengths (rt) – a time estimate for one (or more) node C D R M H • Can we date other nodes in the tree? • Yes... if the rate of molecular change is constant across all branches Page & Holmes p240 Protein Variability Evidence for Rate Constancy in Hemoglobin • Protein structures & functions differ – Proportion of neutral sites differ • Rate constancy does not hold across different protein types Large carniverous marsupial • However... – Each protein does appear to have a characteristic rate of evolution Page and Holmes p229 1 The Outline Molecular Clock • Methods for estimating time under a molecular Hypothesis clock – Estimating genetic distance • Amount of genetic difference between – Determining and using calibration points sequences is a function of time since – Sources of error separation. • Rate heterogeneity – reasons for variation • Rate of molecular change is constant – how its taken into account when estimating times (enough) to predict times of divergence • Reliability of time estimates • Estimating gene duplication times Measuring Evolutionary time with a Estimating Genetic Differences molecular clock 1. Estimate genetic distance If all nt equally likely, observed difference d = number amino acid replacements would plateau at 0.75 2. Use paleontological data to determine date of common ancestor Simply counting -
Aspen Ecology in Rocky Mountain National Park: Age Distribution, Genetics, and the Effects of Elk Herbivory
Aspen Ecology in Rocky Mountain National Park: Age Distribution, Genetics, and the Effects of Elk Herbivory By Linda C. Zeigenfuss, Dan Binkley, Gerald A. Tuskan, William H. Romme, Tongming Yin, Stephen DiFazio, and Francis J. Singer Open-File Report 2008–1337 U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior DIRK KEMPTHORNE, Secretary U.S. Geological Survey Mark D. Myers, Director U.S. Geological Survey, Reston, Virginia 2008 For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod Telephone: 1-888-ASK-USGS For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment: World Wide Web: http://www.usgs.gov Telephone: 1-888-ASK-USGS Suggested citation: Zeigenfuss, L.C., Binkley, D., Tuskan, G.A., Romme, W.H., Yin, T., DiFazio, S., and Singer, F.J. 2008, Aspen Ecology in Rocky Mountain National Park: Age distribution, genetics, and the effects of elk herbivory: U.S. Geological Survey Open-File Report 2008–1337, 52 p. Available online only Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted material contained within this report. Cover photo courtesy of Carolyn Widman ii Contents Executive Summary............................................................................................................................................................1 -
AMPK Against NASH Non-Alcoholic Steatohepatitis (NASH) Is Activation Were Elevated in LAKO Mice the Most Severe Form of Non-Alcoholic on NASH-Inducing Diets
RESEARCH HIGHLIGHTS collected from people representing published the first report of Journal Club all major global populations. mtDNA mutations causing a The most important discovery of disease — Leber’s hereditary optic mtDNA IN THE CROSSROADS OF their work was that the highest neuropathy. As disease- causing EVOLUTION AND DISEASE degree of mtDNA variation was mutations are amenable to natural found among Africans, attesting to selection, how could one consider Mitochondrial DNA (mtDNA) their anti quity. The other finding the mtDNA to be merely a neutral sequences are currently studied was that although mtDNA from marker? It was this contradiction mainly by three disciplines: across the globe contained African that drew me into studying molecular evolution (including types, Africans had many unique mitochondrial biology and to anthropology), functional mtDNA types. discovering that even common genomics and analyses of genetic These two findings, in addition population variants of mtDNA are disorders. Strangely, these discip- to other data, prompted Cann et al. both subjected to natural selection lines can use the relatively short mtDNA (1987) to propose that the origin and alter the tendency to develop sequence of mtDNA in opposing has been of all current human populations genetic disorders. manners, by attributing to it either considered (at least the maternal lineage) is Dan Mishmar Department of Life Sciences, lack of function, as is the case an excellent likely African. Many criticized in (some) molecular evolution this study, especially because Ben- Gurion University of the Negev, marker for Be’er- Sheva, Israel. studies, or conversely, functional their African samples originated e- mail: [email protected] mainly from Afro-Americans relevance in the aetiology of tracing ancient The author declares no competing interests genetic disorders. -
MOLECULAR CLOCKS Definition Introduction
MOLECULAR CLOCKS 583 Kishino, H., Thorne, J. L., and Bruno, W. J., 2001. Performance of Thorne, J. L., Kishino, H., and Painter, I. S., 1998. Estimating the a divergence time estimation method under a probabilistic model rate of evolution of the rate of molecular evolution. Molecular of rate evolution. Molecular Biology and Evolution, 18,352–361. Biology and Evolution, 15, 1647–1657. Kodandaramaiah, U., 2011. Tectonic calibrations in molecular dat- Warnock, R. C. M., Yang, Z., Donoghue, P. C. J., 2012. Exploring ing. Current Zoology, 57,116–124. uncertainty in the calibration of the molecular clock. Biology Marshall, C. R., 1997. Confidence intervals on stratigraphic ranges Letters, 8, 156–159. with nonrandom distributions of fossil horizons. Paleobiology, Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., 23, 165–173. and Tavaré, S., 2011. Dating primate divergences through an Müller, J., and Reisz, R. R., 2005. Four well-constrained calibration integrated analysis of palaeontological and molecular data. Sys- points from the vertebrate fossil record for molecular clock esti- tematic Biology, 60,16–31. mates. Bioessays, 27, 1069–1075. Yang, Z., and Rannala, B., 2006. Bayesian estimation of species Parham, J. F., Donoghue, P. C. J., Bell, C. J., et al., 2012. Best practices divergence times under a molecular clock using multiple fossil for justifying fossil calibrations. Systematic Biology, 61,346–359. calibrations with soft bounds. Molecular Biology and Evolution, Peters, S. E., 2005. Geologic constraints on the macroevolutionary 23, 212–226. history of marine animals. Proceedings of the National Academy Zuckerkandl, E., and Pauling, L., 1962. Molecular disease, evolution of Sciences, 102, 12326–12331. -
Pseudotsuga Menziesii)
120 - PART 1. CONSENSUS DOCUMENTS ON BIOLOGY OF TREES Section 4. Douglas-Fir (Pseudotsuga menziesii) 1. Taxonomy Pseudotsuga menziesii (Mirbel) Franco is generally called Douglas-fir (so spelled to maintain its distinction from true firs, the genus Abies). Pseudotsuga Carrière is in the kingdom Plantae, division Pinophyta (traditionally Coniferophyta), class Pinopsida, order Pinales (conifers), and family Pinaceae. The genus Pseudotsuga is most closely related to Larix (larches), as indicated in particular by cone morphology and nuclear, mitochondrial and chloroplast DNA phylogenies (Silen 1978; Wang et al. 2000); both genera also have non-saccate pollen (Owens et al. 1981, 1994). Based on a molecular clock analysis, Larix and Pseudotsuga are estimated to have diverged more than 65 million years ago in the Late Cretaceous to Paleocene (Wang et al. 2000). The earliest known fossil of Pseudotsuga dates from 32 Mya in the Early Oligocene (Schorn and Thompson 1998). Pseudostuga is generally considered to comprise two species native to North America, the widespread Pseudostuga menziesii and the southwestern California endemic P. macrocarpa (Vasey) Mayr (bigcone Douglas-fir), and in eastern Asia comprises three or fewer endemic species in China (Fu et al. 1999) and another in Japan. The taxonomy within the genus is not yet settled, and more species have been described (Farjon 1990). All reported taxa except P. menziesii have a karyotype of 2n = 24, the usual diploid number of chromosomes in Pinaceae, whereas the P. menziesii karyotype is unique with 2n = 26. The two North American species are vegetatively rather similar, but differ markedly in the size of their seeds and seed cones, the latter 4-10 cm long for P. -
Evidence for a Convergent Slowdown in Primate Molecular Rates and Its Implications for the Timing of Early Primate Evolution
Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution Michael E. Steipera,b,c,d,1 and Erik R. Seifferte aDepartment of Anthropology, Hunter College of the City University of New York (CUNY), New York, NY 10065; Programs in bAnthropology and cBiology, The Graduate Center, CUNY, New York, NY 10016; dNew York Consortium in Evolutionary Primatology, New York, NY; and eDepartment of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794-8081 Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved February 28, 2012 (received for review November 29, 2011) A long-standing problem in primate evolution is the discord divergences—that molecular rates were exceptionally rapid in between paleontological and molecular clock estimates for the the earliest primates, and that these rates have convergently time of crown primate origins: the earliest crown primate fossils slowed over the course of primate evolution. Indeed, a conver- are ∼56 million y (Ma) old, whereas molecular estimates for the gent rate slowdown has been suggested as an explanation for the haplorhine-strepsirrhine split are often deep in the Late Creta- large differences between the molecular and fossil evidence for ceous. One explanation for this phenomenon is that crown pri- the timing of placental mammalian evolution generally (18, 19). mates existed in the Cretaceous but that their fossil remains However, this hypothesis has not been directly tested within have not yet been found. Here we provide strong evidence that a particular mammalian group. this discordance is better-explained by a convergent molecular Here we test this “convergent rate slowdown” hypothesis in rate slowdown in early primate evolution. -
Recent Human Evolution
A common ancestor at 500 ka? H. heid. in Europe and Africa LCA of Nea. and sapiens? The origin of our species (H. sapiens) TWO origins to explain: 1.The shared (species) features 2. Non-shared (regional/racial) features Origins of modern human behaviour? Complex technology “Houses Networking” Symbolic burials Art Models of modern human origins 1984 1970 1987: Mitochondrial Eve hits the headlines! Mitochondrial DNA and human evolution Nature 325, 31-36 Rebecca L. Cann, Mark Stoneking & Allan C. Wilson (1987) African female ancestor ~200ka The pendulum starts swinging! 2000 1995 1995 1984 1970 The African record H. sapiens: fossils suggest an African origin for the modern pattern ~ 150-200ka? Age ka ~260 ~150? ~160? ~195? >130 Tim White Lieberman Pinnacle Point Howiesonspoort Microliths Klasies Twin Rivers Enakpune Mumba ya Muto Shellfishing Grotta Moscerini Ochre Kapthurin Twin Rivers Klasies Qafzeh Blombos 300 ka 200 150 100 50 0 Taforalt Shell beads Skhul Enakpune Blombos ya Muto Early H. sapiens fossils Omo Kibish Herto “Modern” anatomy and behaviour have deep roots in Africa… ~60 ka: Modern Humans start to leave Africa… ? Out of Africa Mitochondrial DNA Out of Africa Y-chromosome DNA The evolution of regionality (“race”) DNA benetton Natural selection Bottlenecks + Founder Effects Sexual/cultural selection We are all the same (species), but we all look different (individuals, ♀/♂, regions, “races”). Species Individuals (Homo sapiens) large brain Natural Selection body shape high round skull Sexual Selection skin colour small face hair -
Unique Features of Human Skin
Center for Academic Research & Training in Anthropogeny (CARTA) Unique Features of Human Skin Public Symposium ! Friday, October 16, 2015 Chairs: Nina Jablonski, Pennsylvania State University Pascal Gagneux, UC San Diego This CARTA symposium is sponsored by: The G. Harold and Leila Y. Mathers Charitable Foundation ABSTRACTS Skin: A Window into the Evolution of the Human Super-Organism Richard Gallo, UC San Diego All life must establish an external barrier that simultaneously interacts with and defends itself from the outside world. Skin is our most important barrier, and human skin has many functions that are in common with other animals but also unique to our species. General skin functions include sensing danger, regulation of internal temperature, maintaining fluid balance and mounting visual sexual displays. Human life also depends on the capacity of our skin to protect us from specific environmental dangers and pathogens unique to us. The central teachings of the medical specialty of Dermatology have been that health is defined by the capacity of skin to perform all these functions while constantly resisting entry of microbial pathogens. However, a recent revolution in understanding skin biology has revealed that normal skin functions are performed not only by cells of human origin, but also by specialized microbes that have co-evolved with us to live in a mutually beneficial relationship. This presentation will provide an overview of the multiple cell types, both human and microbial, that comprise the human skin super-organism. Understanding this relationship changes how we should think about evolution, gene transfer and the impact of current hygiene and antibiotic therapies.