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Genomics and Its Impact on Science and Society: the Human Genome Project and Beyond
DOE/SC-0083 Genomics and Its Impact on Science and Society The Human Genome Project and Beyond U.S. Department of Energy Genome Research Programs: genomics.energy.gov A Primer ells are the fundamental working units of every living system. All the instructions Cneeded to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instruc- tions required to create a particular organism with protein complex its own unique traits. The genome is an organism’s complete set of DNA. Genomes vary widely in size: The smallest known genome for a free-living organism (a bac- terium) contains about 600,000 DNA base pairs, while human and mouse genomes have some From Genes to Proteins 3 billion (see p. 3). Except for mature red blood cells, all human cells contain a complete genome. Although genes get a lot of attention, the proteins DNA in each human cell is packaged into 46 chro- perform most life functions and even comprise the mosomes arranged into 23 pairs. Each chromosome is majority of cellular structures. Proteins are large, complex a physically separate molecule of DNA that ranges in molecules made up of chains of small chemical com- length from about 50 million to 250 million base pairs. pounds called amino acids. Chemical properties that A few types of major chromosomal abnormalities, distinguish the 20 different amino acids cause the including missing or extra copies or gross breaks and protein chains to fold up into specific three-dimensional rejoinings (translocations), can be detected by micro- structures that define their particular functions in the cell. -
Hands-On Human Evolution: a Laboratory Based Approach
Hands-on Human Evolution: A Laboratory Based Approach Developed by Margarita Hernandez Center for Precollegiate Education and Training Author: Margarita Hernandez Curriculum Team: Julie Bokor, Sven Engling A huge thank you to….. Contents: 4. Author’s note 5. Introduction 6. Tips about the curriculum 8. Lesson Summaries 9. Lesson Sequencing Guide 10. Vocabulary 11. Next Generation Sunshine State Standards- Science 12. Background information 13. Lessons 122. Resources 123. Content Assessment 129. Content Area Expert Evaluation 131. Teacher Feedback Form 134. Student Feedback Form Lesson 1: Hominid Evolution Lab 19. Lesson 1 . Student Lab Pages . Student Lab Key . Human Evolution Phylogeny . Lab Station Numbers . Skeletal Pictures Lesson 2: Chromosomal Comparison Lab 48. Lesson 2 . Student Activity Pages . Student Lab Key Lesson 3: Naledi Jigsaw 77. Lesson 3 Author’s note Introduction Page The validity and importance of the theory of biological evolution runs strong throughout the topic of biology. Evolution serves as a foundation to many biological concepts by tying together the different tenants of biology, like ecology, anatomy, genetics, zoology, and taxonomy. It is for this reason that evolution plays a prominent role in the state and national standards and deserves thorough coverage in a classroom. A prime example of evolution can be seen in our own ancestral history, and this unit provides students with an excellent opportunity to consider the multiple lines of evidence that support hominid evolution. By allowing students the chance to uncover the supporting evidence for evolution themselves, they discover the ways the theory of evolution is supported by multiple sources. It is our hope that the opportunity to handle our ancestors’ bone casts and examine real molecular data, in an inquiry based environment, will pique the interest of students, ultimately leading them to conclude that the evidence they have gathered thoroughly supports the theory of evolution. -
Alan Robert Templeton
Alan Robert Templeton Charles Rebstock Professor of Biology Professor of Genetics & Biomedical Engineering Department of Biology, Campus Box 1137 Washington University St. Louis, Missouri 63130-4899, USA (phone 314-935-6868; fax 314-935-4432; e-mail [email protected]) EDUCATION A.B. (Zoology) Washington University 1969 M.A. (Statistics) University of Michigan 1972 Ph.D. (Human Genetics) University of Michigan 1972 PROFESSIONAL EXPERIENCE 1972-1974. Junior Fellow, Society of Fellows of the University of Michigan. 1974. Visiting Scholar, Department of Genetics, University of Hawaii. 1974-1977. Assistant Professor, Department of Zoology, University of Texas at Austin. 1976. Visiting Assistant Professor, Dept. de Biologia, Universidade de São Paulo, Brazil. 1977-1981. Associate Professor, Departments of Biology and Genetics, Washington University. 1981-present. Professor, Departments of Biology and Genetics, Washington University. 1983-1987. Genetics Study Section, NIH (also served as an ad hoc reviewer several times). 1984-1992: 1996-1997. Head, Evolutionary and Population Biology Program, Washington University. 1985. Visiting Professor, Department of Human Genetics, University of Michigan. 1986. Distinguished Visiting Scientist, Museum of Zoology, University of Michigan. 1986-present. Research Associate of the Missouri Botanical Garden. 1992. Elected Visiting Fellow, Merton College, University of Oxford, Oxford, United Kingdom. 2000. Visiting Professor, Technion Institute of Technology, Haifa, Israel 2001-present. Charles Rebstock Professor of Biology 2001-present. Professor of Biomedical Engineering, School of Engineering, Washington University 2002-present. Visiting Professor, Rappaport Institute, Medical School of the Technion, Israel. 2007-2010. Senior Research Associate, The Institute of Evolution, University of Haifa, Israel. 2009-present. Professor, Division of Statistical Genomics, Washington University 2010-present. -
Changes in Life History and Population Size Can Explain the Relative Neutral Diversity Levels on X and Autosomes in Extant Human Populations
Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations Guy Amstera,1, David A. Murphya, William R. Milligana, and Guy Sellaa,b,c,1 aDepartment of Biological Sciences, Columbia University, New York, NY 10027; bDepartment of Systems Biology, Columbia University, New York, NY 10032; and cProgram for Mathematical Genomics, Columbia University, New York, NY 10032 Edited by Brian Charlesworth, University of Edinburgh, Edinburgh, United Kingdom, and approved July 7, 2020 (received for review October 22, 2019) In human populations, the relative levels of neutral diversity on generally—the effects of selection at linked sites should be stronger the X and autosomes differ markedly from each other and from on the X (ref. 18, but see ref. 3). To evaluate these effects empiri- the naïve theoretical expectation of 3/4. Here we propose an ex- cally, several studies have examined how diversity levels on the X and planation for these differences based on new theory about the autosomes vary with genetic distance from putatively selected re- effects of sex-specific life history and given pedigree-based esti- gions, for example from coding and conserved noncoding regions mates of the dependence of human mutation rates on sex and (11, 13–15, 19, 20). In most hominids, including humans, such age. We demonstrate that life history effects, particularly longer comparisons confirm the theoretical expectation that selection at generation times in males than in females, are expected to have linked loci reduces X:A diversity ratios (11, 15, 20). They further had multiple effects on human X-to-autosome (X:A) diversity ra- suggest that the effects are minimal sufficiently far from genes (11, tios, as a result of male-biased mutation rates, the equilibrium X:A 19), thereby providing an opportunity to examine the effects of ratio of effective population sizes, and the differential responses other factors shaping X:A diversity ratios in isolation by considering to changes in population size. -
Genetics and Genomics of Human Population Structure 20
Genetics and Genomics of Human Population Structure 20 Sohini Ramachandran , Hua Tang , Ryan N. Gutenkunst , and Carlos D. Bustamante Abstract Recent developments in sequencing technology have created a fl ood of new data on human genetic variation, and this data has yielded new insights into human popu- lation structure. Here we review what both early and more recent studies have taught us about human population structure and history. Early studies showed that most human genetic variation occurs within populations rather than between them, and that genetically related populations often cluster geographically. Recent studies based on much larger data sets have recapitulated these observations, but have also demonstrated that high-density genotyping allows individuals to be reliably assigned to their population of origin. In fact, for admixed individuals, even the ancestry of particular genomic regions can often be reli- ably inferred. Recent studies have also offered detailed information about the composition of specifi c populations from around the world, revealing how history has shaped their genetic makeup. We also briefl y review quantitative models of human genetic history, including the role natural selection has played in shaping human genetic variation. Contents 20.2.3 Characterizing Locus-Specifi c Ancestry ...................................................... 594 20.1 Introduction ............................................................... 590 20.3 Global Patterns of Human Population Structure ....... 595 20.1.1 Evolutionary Forces Shaping 20.3.1 The Apportionment of Human Human Genetic Variation ........................... 590 Diversity ..................................................... 595 20.2 Quantifying Population Structure ............................. 592 20.3.2 The History and Geography of Human Genes ......................................... 596 20.2.1 FST and Genetic Distance ............................ 592 20.2.2 Model-Based Clustering 20.3.3 Genetic Structure of Human Populations .. -
A Brief History of Human Disease Genetics
Review A brief history of human disease genetics https://doi.org/10.1038/s41586-019-1879-7 Melina Claussnitzer1,2,3, Judy H. Cho4,5,6, Rory Collins7,8, Nancy J. Cox9, Emmanouil T. Dermitzakis10,11, Matthew E. Hurles12, Sekar Kathiresan2,13,14, Eimear E. Kenny4,6,15, Received: 16 July 2019 Cecilia M. Lindgren2,16,17, Daniel G. MacArthur2,13,18, Kathryn N. North19,20, Sharon E. Plon21,22, Accepted: 13 November 2019 Heidi L. Rehm2,13,18,23, Neil Risch24, Charles N. Rotimi25, Jay Shendure26,27,28, Nicole Soranzo12,29 & Mark I. McCarthy17,30,31,32* Published online: 8 January 2020 A primary goal of human genetics is to identify DNA sequence variants that infuence biomedical traits, particularly those related to the onset and progression of human disease. Over the past 25 years, progress in realizing this objective has been transformed by advances in technology, foundational genomic resources and analytical tools, and by access to vast amounts of genotype and phenotype data. Genetic discoveries have substantially improved our understanding of the mechanisms responsible for many rare and common diseases and driven development of novel preventative and therapeutic strategies. Medical innovation will increasingly focus on delivering care tailored to individual patterns of genetic predisposition. medicine, which was previously restricted to a few specific clinical Anniversary indications, is poised to go mainstream. collection: This Review charts recent milestones in the history of human disease go.nature.com/ genetics and provides an opportunity to reflect on lessons learned by nature150 the human genetics community. We focus first on the long-standing division between genetic discovery efforts targeting rare variants with large effects and those seeking alleles that influence predispo- sition to common diseases. -
What Is the Human Genome Project?
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Supervised Undergraduate Student Research Chancellor’s Honors Program Projects and Creative Work Spring 4-2000 What is the Human Genome Project? Lauren Leigh Taylor University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_chanhonoproj Recommended Citation Taylor, Lauren Leigh, "What is the Human Genome Project?" (2000). Chancellor’s Honors Program Projects. https://trace.tennessee.edu/utk_chanhonoproj/434 This is brought to you for free and open access by the Supervised Undergraduate Student Research and Creative Work at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Chancellor’s Honors Program Projects by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Lauren Taylor Senior Project- (very partial) Dr.Koontz, mentor Dr. Broadhead- I should have this ready to tum in by next Tuesday or Wednesday. Thanks for your grace-- Intro As part of the University of Tennessee Honors Program, I am required to submit a senior project, consisting of research and creative analysis supervised by a faculty mentor. Although these project topics may cover any subject, most students choose a topic that falls within their undergraduate course of study. I have chosen to do this as well. As a Biology major, I have undergone ample preparation to enter a highly advanced field of modern science and medicine. One of the "hot topics" of science today is the international collaboration of scientists working to map the human genome, known as the Human Genome Project. -
Human Evolution
Note added by authors December 4, 2018: This study is grounded in and strongly supports Darwinian evolution, including the understanding that all life has evolved from a common biological origin over several billion years. This work follows mainstream views of human evolution. We do not propose there was a single "Adam" or "Eve". We do not propose any catastrophic events. HUMAN EVOLUTION Vol. 33 - n. 1-2 (1-30) - 2018 Stoeckle M.Y. Why should mitochondria define species? Program for the Human Environment The Rockefeller University 1230 York AVE More than a decade of DNA barcoding encompassing New York, NY 10065 about five million specimens covering 100,000 animal USA species supports the generalization that mitochondrial Email: [email protected] DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synony- Thaler D.S. mous substitutions. What evolutionary mechanisms ac- Biozentrum, University of Basel count for synonymous clusters being largely coincident Klingelbergstrasse 50/70 with species? The answer depends on whether variants CH - 4056 Basel Switzerland are phenotypically neutral. To the degree that variants are Email: [email protected] selectable, purifying selection limits variation within spe- [email protected] cies and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic DOI: 10.14673/HE2018121037 hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial bar- codes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. -
The Economic Impact and Functional Applications of Human Genetics and Genomics
The Economic Impact and Functional Applications of Human Genetics and Genomics Commissioned by the American Society of Human Genetics Produced by TEConomy Partners, LLC. Report Authors: Simon Tripp and Martin Grueber May 2021 TEConomy Partners, LLC (TEConomy) endeavors at all times to produce work of the highest quality, consistent with our contract commitments. However, because of the research and/or experimental nature of this work, the client undertakes the sole responsibility for the consequence of any use or misuse of, or inability to use, any information or result obtained from TEConomy, and TEConomy, its partners, or employees have no legal liability for the accuracy, adequacy, or efficacy thereof. Acknowledgements ASHG and the project authors wish to thank the following organizations for their generous support of this study. Invitae Corporation, San Francisco, CA Regeneron Pharmaceuticals, Inc., Tarrytown, NY The project authors express their sincere appreciation to the following indi- viduals who provided their advice and input to this project. ASHG Government and Public Advocacy Committee Lynn B. Jorde, PhD ASHG Government and Public Advocacy Committee (GPAC) Chair, President (2011) Professor and Chair of Human Genetics George and Dolores Eccles Institute of Human Genetics University of Utah School of Medicine Katrina Goddard, PhD ASHG GPAC Incoming Chair, Board of Directors (2018-2020) Distinguished Investigator, Associate Director, Science Programs Kaiser Permanente Northwest Melinda Aldrich, PhD, MPH Associate Professor, Department of Medicine, Division of Genetic Medicine Vanderbilt University Medical Center Wendy Chung, MD, PhD Professor of Pediatrics in Medicine and Director, Clinical Cancer Genetics Columbia University Mira Irons, MD Chief Health and Science Officer American Medical Association Peng Jin, PhD Professor and Chair, Department of Human Genetics Emory University Allison McCague, PhD Science Policy Analyst, Policy and Program Analysis Branch National Human Genome Research Institute Rebecca Meyer-Schuman, MS Human Genetics Ph.D. -
Determining De Novo Mutation Rates Knowing the Human De Novo Mutation Rate Is Important for Understanding Our Evolution and the Origins of Genetic Diseases
RESEARCH HIGHLIGHTS IN BRIEF GENE THERAPY Single-stranded RNAs for potent RNAi In the development of gene-based therapies, delivery of ssRNAs is simpler than it is for dsRNAs (as this requires lipid formulation, for example). However, ssRNAs have previously been found to be far less potent for gene silencing. Lima et al. have now overcome this limitation by chemical modifications of ssRNAs that increase their stability. They show that these modified ssRNAs act through the RNAi pathway as guide strands for Argonaute 2 to induce specific gene silencing. Yu et al. demonstrate the therapeutic potential of these RNAs in a mouse model of Huntington’s disease using ssRNAs that target the mutant HTT allele. The gene-silencing efficiency for the ssRNAs seems to be similar to equivalent dsRNAs. ORIGINAL RESEARCH PAPERS Lima, W. F. et al. Single-stranded siRNAs activate RNAi in animals. Cell 150, 883–894 (2012) | Yu, D. et al. Single-stranded RNAs use RNAi to potently and allele-selectively inhibit mutant huntingtin expression. Cell 150, 895–908 (2012) CLINICAL GENOMICS Sequencing to track bacterial infection outbreaks The use of genome sequencing to research disease outbreaks retrospectively has been demonstrated by high-profile cases, such as the recent cholera outbreak in Haiti. But can whole-genome sequencing be used to provide information that can be used in clinical decision making during an outbreak? Two recent studies suggest that it can. Köser et al. investigated a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in a neonatal unit and identified transmission events, using data from the Illumina MiSeq platform. The authors note that the timescale (1.5 days from DNA extraction to sequence) and cost of their study demonstrates that such information can be obtained on a clinically relevant time frame. -
Sociobiology and Law
Sociobiology and Law Allan Ardill LLB. (Hons), B.Bus. (Accounting), B.Bus. (HRM), A.Dip. Bus. (IR) A dissertation in fulfilment of the requirements for the degree of Doctor of Philosophy Griffith Law School Griffith University Gold Coast, Queensland, Australia. February 2008 2 Abstract The place of humans in nature and the nature of humans eludes us and yet there are those certain these issues can be reduced to biological explanations. Similarly, there are those rejecting the biological determinist hypothesis in favour of the equally unsubstantiated cultural construction hypothesis. This thesis draws on neo-Marxism and feminist intersectional post-positivist standpoint theory to posit biological and cultural determinism as privileged and flawed knowledge produced within relations of asymmetrical power. Instead “social construction” is preferred viewing knowledge of both nature and culture as partial and constructed within an historical, socioeconomic and political context according to asymmetrical power. Social constructionists prefer to question the role of power in the production of knowledge rather than asking questions about the place of humans in nature and the nature of humans; and trying to answer those questions through methods imbued with western, colonial, patriarchal, homophobic, and positivist ideals. As a starting point the postmodern view that knowledge is incomplete and has no ultimate authority is accepted. However, this thesis departs from postmodernism on the premise that knowledge is not all relative and can be critiqued by drawing on neo- Marxist and feminist intersectional post-positivist standpoint theory. Standpoint theory presumes a knowledge power nexus and contends accountable, ethical and responsible knowledge can be produced provided an “upwards perspective” is applied commencing with the standpoint of the most marginalised group within a given context. -
Genetic Variation and Human Evolution
| NSW Department of Education Genetic Variation and Human Evolution. This article is referenced in the Module 5 and 6 guide, IQ6-1: Can population genetic patterns be predicted with any accuracy? The article is no longer available online. It is archived at the American Society of Human Genetics www.ashg.org. The article provides background information about the use of mitochondrial DNA and Y- chromosome DNA studies to determine a possible path for human evolution. Students could carry out their own research after reading this article. Genetic Variation and Human Evolution Lynn B. Jorde, Ph.D. Department of Human Genetics University of Utah School of Medicine. The past two decades have witnessed an explosion of human genetic data. Innumerable DNA sequences and genotypes have been generated, and they have led to significant biomedical advances. In addition, these data have greatly increased our understanding of patterns of genetic diversity among individuals and populations. The purpose of this brief review is to show how our knowledge of genetic variation can contribute to an understanding of our similarities and differences, our origins, and our evolutionary history. Patterns of genetic diversity inform us about population history because each major demographic event leaves an imprint on a population's collective genomic diversity. A reduction in population size reduces genetic diversity, and an increase in population size eventually increases diversity. The exchange of migrants between populations inevitably results in greater genetic similarity, while isolation preserves genetic uniqueness. These demographic signatures are passed from generation to generation, such that the genomes of modern individuals reflect their demographic history.