Selecting Among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients
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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. -
Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris Rarus) in a Successive Generation Closed Colony
diversity Article Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony Lei Cai 1,2,3, Miaomiao Hou 1,2, Chunsen Xu 1,2, Zhijun Xia 1,2 and Jianwei Wang 1,4,* 1 The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China; [email protected] (L.C.); [email protected] (M.H.); [email protected] (C.X.); [email protected] (Z.X.) 2 University of Chinese Academy of Sciences, Beijing 100049, China 3 Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China 4 National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China * Correspondence: [email protected] Received: 10 November 2020; Accepted: 11 December 2020; Published: 18 December 2020 Abstract: The complex genetic architecture of closed colonies during successive passages poses a significant challenge in the understanding of the genetic background. Research on the dynamic changes in genetic structure for the establishment of a new closed colony is limited. In this study, we developed 51 single nucleotide polymorphism (SNP) markers for the rare minnow (Gobiocypris rarus) and conducted genetic diversity and structure analyses in five successive generations of a closed colony using 20 SNPs. The range of mean Ho and He in five generations was 0.4547–0.4983 and 0.4445–0.4644, respectively. No significant differences were observed in the Ne, Ho, and He (p > 0.05) between the five closed colony generations, indicating well-maintained heterozygosity. -
Genetic Linkage Analysis
BASIC SCIENCE SEMINARS IN NEUROLOGY SECTION EDITOR: HASSAN M. FATHALLAH-SHAYKH, MD Genetic Linkage Analysis Stefan M. Pulst, MD enetic linkage analysis is a powerful tool to detect the chromosomal location of dis- ease genes. It is based on the observation that genes that reside physically close on a chromosome remain linked during meiosis. For most neurologic diseases for which the underlying biochemical defect was not known, the identification of the chromo- Gsomal location of the disease gene was the first step in its eventual isolation. By now, genes that have been isolated in this way include examples from all types of neurologic diseases, from neu- rodegenerative diseases such as Alzheimer, Parkinson, or ataxias, to diseases of ion channels lead- ing to periodic paralysis or hemiplegic migraine, to tumor syndromes such as neurofibromatosis types 1 and 2. Arch Neurol. 1999;56:667-672 With the advent of new genetic markers tin gene, diagnosis using flanking mark- and automated genotyping, genetic map- ers requires the analysis of several family ping can be conducted extremely rap- members. idly. Genetic linkage maps have been gen- erated for the human genome and for LINKAGE OF GENES model organisms and have provided the basis for the construction of physical maps When Mendel observed an “independent that permit the rapid mapping of disease assortment of traits” (Mendel’s second traits. law), he was fortunate to have chosen traits As soon as a chromosomal location that were not localized close to one an- for a disease phenotype has been estab- other on the same chromosome.1 Subse- lished, genetic linkage analysis helps quent studies revealed that many genes determine whether the disease pheno- were indeed linked, ie, that traits did not type is only caused by mutation in a assort or segregate independently, but that single gene or mutations in other genes traits encoded by these linked genes were can give rise to an identical or similar inherited together. -
Descriptors for Genetic Markers Technologies
• Descriptors for genetic markers technologies Version 1.0, February 2004 Carmen De Vicente, Thomas Metz and Adriana Alercia <www.futureharvest.org> IPGRI is a Future Harvest Centre supported by the Consultative Group on International Agricultural Research (CGIAR) ii DESCRIPTORS FOR GENETIC MARKERS TECHNOLOGIES The International Plant Genetic Resources Institute (IPGRI) is an independent international scientific organization that seeks to advance the conservation and use of plant genetic diversity for the well-being of present and future generations. It is one of 16 Future Harvest Centres supported by the Consultative Group on International Agricultural Research (CGIAR), an association of public and private members who support efforts to mobilize cutting-edge science to reduce hunger and poverty, improve human nutrition and health, and protect the environment. IPGRI has its headquarters in Maccarese, near Rome, Italy, with offices in more than 20 other countries worldwide. The Institute operates through three programmes: (1) the Plant Genetic Resources Programme, (2) the CGIAR Genetic Resources Support Programme and (3) the International Network for the Improvement of Banana and Plantain (INIBAP). The international status of IPGRI is conferred under an Establishment Agreement which, by January 2003, had been signed by the Governments of Algeria, Australia, Belgium, Benin, Bolivia, Brazil, Burkina Faso, Cameroon, Chile, China, Congo, Costa Rica, Côte d’Ivoire, Cyprus, Czech Republic, Denmark, Ecuador, Egypt, Greece, Guinea, Hungary, India, Indonesia, Iran, Israel, Italy, Jordan, Kenya, Malaysia, Mauritania, Morocco, Norway, Pakistan, Panama, Peru, Poland, Portugal, Romania, Russia, Senegal, Slovakia, Sudan, Switzerland, Syria, Tunisia, Turkey, Uganda and Ukraine. Financial support for IPGRI’s research is provided by more than 150 donors, including governments, private foundations and international organizations. -
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. -
Single Nucleotide Polymorphism (SNP) Discovery in Mammals
Molecular Ecology (2004) 13, 1423–1431 doi: 10.1111/j.1365-294X.2004.02159.x SingleBlackwell Publishing, Ltd. nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach NICOLA AITKEN,* STEVEN SMITH,† CARSTEN SCHWARZ‡ and PHILLIP A. MORIN§ Laboratory for Conservation Genetics, Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103, Leipzig, Germany Abstract Single nucleotide polymorphisms (SNPs) have rarely been exploited in nonhuman and nonmodel organism genetic studies. This is due partly to difficulties in finding SNPs in species where little DNA sequence data exist, as well as to a lack of robust and inexpensive genotyping methods. We have explored one SNP discovery method for molecular ecology, evolution, and conservation studies to evaluate the method and its limitations for population genetics in mammals. We made use of ‘CATS’ (or ‘EPIC’) primers to screen for novel SNPs in mammals. Most of these primer sets were designed from primates and/or rodents, for amplifying intron regions from conserved genes. We have screened 202 loci in 16 repres- entatives of the major mammalian clades. Polymerase chain reaction (PCR) success correlated with phylogenetic distance from the human and mouse sequences used to design most primers; for example, specific PCR products from primates and the mouse amplified the most con- sistently and the marsupial and armadillo amplifications were least successful. Approxi- mately 24% (opossum) to 65% (chimpanzee) of primers produced usable PCR product(s) in the mammals tested. Products produced generally high but variable levels of readable sequence and similarity to the expected genes. In a preliminary screen of chimpanzee DNA, 12 SNPs were identified from six (of 11) sequenced regions, yielding a SNP on average every 400 base pairs (bp). -
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. -
Genome-Wide Mapping and Characterization of Microsatellites In
www.nature.com/scientificreports OPEN Genome-wide mapping and characterization of microsatellites in the swamp eel genome Received: 14 February 2017 Zhigang Li, Feng Chen, Chunhua Huang, Weixin Zheng, Chunlai Yu, Hanhua Cheng & Accepted: 26 April 2017 Rongjia Zhou Published: xx xx xxxx We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics. Swamp eel (Monopterus albus) taxonomically belongs to teleosts, the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, and Vertebrata). -
Genetic Markers and Plant Genetic Resource Management P
NCRPIS Publications and Papers North Central Regional Plant Introduction Station 1995 Genetic Markers and Plant Genetic Resource Management P. K. Bretting United States Department of Agriculture Mark P. Widrlechner Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/ncrpis_pubs Part of the Agricultural Science Commons, Agriculture Commons, and the Plant Breeding and Genetics Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ ncrpis_pubs/75. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Book Chapter is brought to you for free and open access by the North Central Regional Plant Introduction Station at Iowa State University Digital Repository. It has been accepted for inclusion in NCRPIS Publications and Papers by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Plant Breeding Reviews, Volume 13 Edited by Jules Janick © 1995 John Wiley & Sons, Inc. ISBN: 978-0-471-57343-2 12 P. K. BRETTING AND M. P. WIDRLECHNER C. Maintenance 1. Maintaining Trueness-to-Type a. Morphological Traits b. Secondary Metabolites c. Isozymes, Seed Proteins, and DNA Markers d. Comparative Studies e. Pollination Control Methods 2. Monitoring Shifts in Population Genetic Structure in Heterogeneous Germplasm a. Deviations from Random Mating b. Regeneration of Autogamous Species 3. Monitoring Genetic Shifts Caused by Differential Viability in Storage 4. Monitoring Genetic Shifts Caused by In Vitro Culture 5. Monitoring Germplasm Viability and Health D. Utilization 1. Developing Optimal Utilization Strategies from Genetic Marker Data 2. -
Mitochondrial DNA in Anthropological Research
AIMS Genetics, 3(2): 146-156. DOI: 10.3934/genet.2016.2.146 Received: 25 April 2016 Accepted: 11 July 2016 Published: 13 July 2016 http://www.aimspress.com/journal/Genetics Review A history of you, me, and humanity: mitochondrial DNA in anthropological research Jada Benn Torres* Laboratory of Genetic Anthropology, Department of Anthropology, Vanderbilt University, Nashville, TN 37325, USA * Correspondence: Email: [email protected]; Tel: +615-343-6120. Abstract: Within genetic anthropology, mitochondrial DNA (mtDNA) has garnered a prominent if not enduring place within the anthropological toolkit. MtDNA has provided new and innovative perspectives on the emergence and dispersal of our species, interactions with extinct human species, and illuminated relationships between human groups. In this paper, I provide a brief overview of the major findings ascertained from mtDNA about human origins, human dispersal across the globe, interactions with other hominin species, and the more recent uses of mtDNA in direct to consumer ancestry tests. Relative to nuclear DNA, mtDNA is a small section of the genome and due to its inheritance pattern provides a limited resolution of population history and an individual‘s genetic ancestry. Consequently, some scholars dismiss mtDNA as insignificant due to the limited inferences that may be made using the locus. Regardless, mtDNA provides some useful insights to understanding how social, cultural, and environmental factors have shaped patterns of genetic variability. Furthermore, with regard to the experiences of historically marginalized groups, in particular those of African descent throughout the Americas, mtDNA has the potential to fill gaps in knowledge that would otherwise remain unknown. Within anthropological sciences, the value of this locus for understanding human experience is maximized when contextualized with complementary lines of evidence. -
Glossary/Index
Glossary 03/08/2004 9:58 AM Page 119 GLOSSARY/INDEX The numbers after each term represent the chapter in which it first appears. additive 2 allele 2 When an allele’s contribution to the variation in a One of two or more alternative forms of a gene; a single phenotype is separately measurable; the independent allele for each gene is inherited separately from each effects of alleles “add up.” Antonym of nonadditive. parent. ADHD/ADD 6 Alzheimer’s disease 5 Attention Deficit Hyperactivity Disorder/Attention A medical disorder causing the loss of memory, rea- Deficit Disorder. Neurobehavioral disorders character- soning, and language abilities. Protein residues called ized by an attention span or ability to concentrate that is plaques and tangles build up and interfere with brain less than expected for a person's age. With ADHD, there function. This disorder usually first appears in persons also is age-inappropriate hyperactivity, impulsive over age sixty-five. Compare to early-onset Alzheimer’s. behavior or lack of inhibition. There are several types of ADHD: a predominantly inattentive subtype, a predomi- amino acids 2 nantly hyperactive-impulsive subtype, and a combined Molecules that are combined to form proteins. subtype. The condition can be cognitive alone or both The sequence of amino acids in a protein, and hence pro- cognitive and behavioral. tein function, is determined by the genetic code. adoption study 4 amnesia 5 A type of research focused on families that include one Loss of memory, temporary or permanent, that can result or more children raised by persons other than their from brain injury, illness, or trauma.