Defining Genetic Diversity (Within a Population)
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Effective Population Size and Genetic Conservation Criteria for Bull Trout
North American Journal of Fisheries Management 21:756±764, 2001 q Copyright by the American Fisheries Society 2001 Effective Population Size and Genetic Conservation Criteria for Bull Trout B. E. RIEMAN* U.S. Department of Agriculture Forest Service, Rocky Mountain Research Station, 316 East Myrtle, Boise, Idaho 83702, USA F. W. A LLENDORF Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA Abstract.ÐEffective population size (Ne) is an important concept in the management of threatened species like bull trout Salvelinus con¯uentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively. Although Ne strongly depends on census population size, it also depends on demographic and life history characteristics that complicate any estimates. This is an especially dif®cult problem for species like bull trout, which have overlapping generations; biologists may monitor annual population number but lack more detailed information on demographic population structure or life history. We used a generalized, age-structured simulation model to relate Ne to adult numbers under a range of life histories and other conditions characteristic of bull trout populations. Effective population size varied strongly with the effects of the demographic and environmental variation included in our simulations. Our most realistic estimates of Ne were between about 0.5 and 1.0 times the mean number of adults spawning annually. We conclude that cautious long-term management goals for bull trout populations should include an average of at least 1,000 adults spawning each year. Where local populations are too small, managers should seek to conserve a collection of interconnected populations that is at least large enough in total to meet this minimum. -
Patterns of Genetic Diversity Are the Result Of
Perceiving patterns in nature is a beginning to and seed dispersal, its mating system, and its natural understanding the basis of biological diversity, sensing range) can be used to establish a reasonable idea of its some order in what may otherwise seem chaotic or random spatial genetic pattern. Sometimes environmental spatial arrays. Spatial patterns in genetic diversity, also features are indicators of the spatial genetic patterns if a called ‘genetic structure’ or ‘spatial genetic structure,’ species is adapted to changes in these features. For often reflect biologically meaningful processes. example, a species that occurs at a range of elevations Recognizing these patterns, giving genes a ‘physical may show a gradient in genetic diversity that address,’ and understanding their basis can provide a corresponds with adaptations to various elevations. stronger scientific basis for conservation and restoration However, these natural processes may not all be consistent decisions by making use of biologically meaningful or pushing in the same direction. For example, a units. These patterns are the result of natural processes, population may be locally adapted to microclimate and the characteristics of the species, and historical events. moisture availability (which would suggest local genetic structure) but also have long-distance seed and pollen [ patterns of genetic dispersal (that would tend to mix up the genes with diversity are the result of other populations and undermine local adaptations). So natural processes, the direct genetic studies are needed for confirmation of the genetic structure. characteristics of the species, A traditional approach to describing spatial patterns in and historical events ] genetic diversity of plants is to sample individuals widely Spatial patterns reflect the natural genetic processes across the species’ range and present a picture of the (described in Volume 3) — migration, natural selection, overall genetic structure based on various kinds of data. -
Microevolution and the Genetics of Populations Microevolution Refers to Varieties Within a Given Type
Chapter 8: Evolution Lesson 8.3: Microevolution and the Genetics of Populations Microevolution refers to varieties within a given type. Change happens within a group, but the descendant is clearly of the same type as the ancestor. This might better be called variation, or adaptation, but the changes are "horizontal" in effect, not "vertical." Such changes might be accomplished by "natural selection," in which a trait within the present variety is selected as the best for a given set of conditions, or accomplished by "artificial selection," such as when dog breeders produce a new breed of dog. Lesson Objectives ● Distinguish what is microevolution and how it affects changes in populations. ● Define gene pool, and explain how to calculate allele frequencies. ● State the Hardy-Weinberg theorem ● Identify the five forces of evolution. Vocabulary ● adaptive radiation ● gene pool ● migration ● allele frequency ● genetic drift ● mutation ● artificial selection ● Hardy-Weinberg theorem ● natural selection ● directional selection ● macroevolution ● population genetics ● disruptive selection ● microevolution ● stabilizing selection ● gene flow Introduction Darwin knew that heritable variations are needed for evolution to occur. However, he knew nothing about Mendel’s laws of genetics. Mendel’s laws were rediscovered in the early 1900s. Only then could scientists fully understand the process of evolution. Microevolution is how individual traits within a population change over time. In order for a population to change, some things must be assumed to be true. In other words, there must be some sort of process happening that causes microevolution. The five ways alleles within a population change over time are natural selection, migration (gene flow), mating, mutations, or genetic drift. -
Gene Flow by Pollen Into Small Populations
Proc. Natl. Acad. Sci. USA Vol. 86, pp. 9044-9047, November 1989 Population Biology Gene flow by pollen into small populations: Data from experimental and natural stands of wild radish (Raphanus sativus/spatial isolation/interpopulation mating) NORMAN C. ELLSTRANDt, B. DEVLINt, AND DIANE L. MARSHALL§ Department of Botany and Plant Sciences and Program in Genetics, University of California, Riverside, CA 92521-0124 Communicated by R. W. Allard, August 14, 1989 (received for review August 18, 1988) ABSTRACT Gene flow can have an especially strong im- much from population to population, whether it varies within pact on the evolution of small populations. However, empirical a population over a season, and whether it varies with spatial studies on the actual rates and patterns of gene flow into small isolation from the nearest conspecific. More data are needed populations are few. Thus, we sought to measure gene flow into that focus more closely on a number ofpopulations ofa single small populations of wild radish, Raphanus sativus. We found species. significant differences in gene flow receipt among experimental Therefore, we selected wild radish, Raphanus sativus L. populations and within those populations over a season. A (Brassicaceae), to measure patterns of gene flow by pollen maximum-likelihood estimate revealed that almost all of the into small populations. This species is especially suitable for gene flow into these synthetic populations had its origin in both experimental and descriptive gene flow studies because relatively distant (>650 m), large natural populations rather it is a common outcrossing weed in southern California (8), than the proximal (255400 m), small synthetic populations. -
Lecture 9: Population Genetics
Lecture 9: Population Genetics Plan of the lecture I. Population Genetics: definitions II. Hardy-Weinberg Law. III. Factors affecting gene frequency in a population. Small populations and founder effect. IV. Rare Alleles and Eugenics The goal of this lecture is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. It will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision). I. Population genetics: definitions Population – group of interbreeding individuals of the same species that are occupying a given area at a given time. Population genetics is the study of the allele frequency distribution and change under the influence of the 4 evolutionary forces: natural selection, mutation, migration (gene flow), and genetic drift. Population genetics is concerned with gene and genotype frequencies, the factors that tend to keep them constant, and the factors that tend to change them in populations. All the genes at all loci in every member of an interbreeding population form gene pool. Each gene in the genetic pool is present in two (or more) forms – alleles. Individuals of a population have same number and kinds of genes (except sex genes) and they have different combinations of alleles (phenotypic variation). The applications of Mendelian genetics, chromosomal abnormalities, and multifactorial inheritance to medical practice are quite evident. Physicians work mostly with patients and families. However, as important as they may be, genes affect populations, and in the long run their effects in populations have a far more important impact on medicine than the relatively few families each physician may serve. -
Working at the Interface of Phylogenetics and Population
Molecular Ecology (2007) 16, 839–851 doi: 10.1111/j.1365-294X.2007.03192.x WorkingBlackwell Publishing Ltd at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae) A. L. RUSSELL,* J. RANIVO,†‡ E. P. PALKOVACS,* S. M. GOODMAN‡§ and A. D. YODER¶ *Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, †Département de Biologie Animale, Université d’Antananarivo, Antananarivo, BP 106, Madagascar, ‡Ecology Training Program, World Wildlife Fund, Antananarivo, BP 906 Madagascar, §The Field Museum of Natural History, Division of Mammals, 1400 South Lake Shore Drive, Chicago, IL 60605, USA, ¶Department of Ecology and Evolutionary Biology, PO Box 90338, Duke University, Durham, NC 27708, USA Abstract New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeo- graphical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylo- genetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar’s Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. -
Hemizygous Or Haploid Sex Diploid Sex
9781405132770_4_002.qxd 1/19/09 2:22 PM Page 16 Table 2.1 Punnett square to predict genotype frequencies for loci on sex chromosomes and for all loci in males and females of haplo-diploid species. Notation in this table is based on birds where the sex chromosomes are Z and W (ZZ males and ZW females) with a diallelic locus on the Z chromosome possessing alleles A and a at frequencies p and q, respectively. In general, genotype frequencies in the homogametic or diploid sex are identical to Hardy–Weinberg expectations for autosomes, whereas genotype frequencies are equal to allele frequencies in the heterogametic or haploid sex. Hemizygous or haploid sex Diploid sex Genotype Gamete Frequency Genotype Gamete Frequency ZW Z-A p ZZ Z-A p Z-a q Z-a q W Expected genotype frequencies under random mating Homogametic sex Z-A Z-A p2 Z-A Z-a 2pq Z-a Z-a q2 Heterogametic sex Z-A W p Z-a W q ·· 9781405132770_4_002.qxd 1/19/09 2:22 PM Page 19 Table 2.2 Example DNA profile for three simple tandem repeat (STR) loci commonly used in human forensic cases. Locus names refer to the human chromosome (e.g. D3 means third chromosome) and chromosome region where the SRT locus is found. Locus D3S1358 D21S11 D18S51 Genotype 17, 18 29, 30 18, 18 ·· 9781405132770_4_002.qxd 1/19/092:22PMPage20 Table 2.3 Allele frequencies for nine STR loci commonly used in forensic cases estimated from 196 US Caucasians sampled randomly with respect to geographic location. -
Saving Our Tree HUMAN GENETICS
HIGHLIGHTS EVOLUTION IN BRIEF Saving our tree HUMAN GENETICS Identification of a gene responsible for familial For several years, evolutionary biolo- Wolff–Parkinson–White syndrome. gists interested in gene flow between species have been investigating and Gollob, M. H. et al. N. Engl. J. Med. 344, 1823–1831 (2001) debating a controversial issue: the hor- Wolff–Parkinson–White (WPW) syndrome is an inherited heart izontal exchange of genes between dis- defect associated with arrhythmia, cardiac arrest and sudden death. tantly related species, its extent and Gollob et al. studied two large families with autosomal-dominant possible adaptive significance. WPW syndrome, and used a positional candidate-gene approach to Horizontal gene transfer (HGT) is an identify the causative gene, which encodes a regulatory subunit of important evolutionary force in appears in a cluster of bacterial AMP-activated protein kinase. This finding should shed light on prokaryotes, as their life cycles facilitate sequences, then the vertebrate gene the mechanisms that lead to heart arrhythmias. the exchange of genes between even was probably horizontally transferred distantly related species. However, this from bacteria. Conversely, if all GENETIC NETWORKS is trickier in multicellular organisms, eukaryotic sequences cluster together, in which the fixation of horizontally then HGT has probably not occurred Ordering genes in a flagella pathway by analysis of transferred genes can only occur if as this grouping is most parsimo- expression kinetics from living bacteria. they are transmitted through the germ niously explained by vertebrates hav- Kalir, S. et al. Science 292, 2080–2083 (2001) line. It was therefore surprising when ing acquired the sequence by descent the International Human Genome through other eukaryotes. -
Muller's Ratchet As a Mechanism of Frailty and Multimorbidity
bioRxivMuller’s preprint ratchetdoi: https://doi.org/10.1101/439877 and frailty ; this version posted[Type Octoberhere] 10, 2018. The copyright holder Govindarajufor this preprint and (which Innan was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Muller’s ratchet as a mechanism of frailty and multimorbidity 2 3 Diddahally R. Govindarajua,b,1, 2, and Hideki Innanc,1,2 4 5 aDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138; 6 and bThe Institute of Aging Research, Albert Einstein College of Medicine, Bronx, 7 NY 1046, and cGraduate University for Advanced Studies, Hayama, Kanagawa, 8 240-0193, Japan 9 10 11 12 Authors contributions: D.R.G., H.I designed study, performed research, contributed new 13 analytical tools, analyzed data and wrote the paper 14 15 The authors declare no conflict of interest 16 1D.R.G., and H.I. contributed equally to this work and listed alphabetically 17 2 Correspondence: Email: [email protected]; [email protected] 18 19 Senescence | mutation accumulation | asexual reproduction | somatic cell-lineages| 20 organs and organ systems |Muller’s ratchet | fitness decay| frailty and multimorbidity 21 22 23 24 25 26 27 28 29 30 31 32 1 bioRxivMuller’s preprint ratchetdoi: https://doi.org/10.1101/439877 and frailty ; this version posted[Type Octoberhere] 10, 2018. The copyright holder Govindarajufor this preprint and (which Innan was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 33 Mutation accumulation has been proposed as a cause of senescence. -
Genetic Structure and Eco-Geographical Differentiation of Lancea Tibetica in the Qinghai-Tibetan Plateau
G C A T T A C G G C A T genes Article Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau Xiaofeng Chi 1,2 , Faqi Zhang 1,2,* , Qingbo Gao 1,2, Rui Xing 1,2 and Shilong Chen 1,2,* 1 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China; [email protected] (X.C.); [email protected] (Q.G.); [email protected] (R.X.) 2 Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810001, China * Correspondence: [email protected] (F.Z.); [email protected] (S.C.) Received: 14 December 2018; Accepted: 24 January 2019; Published: 29 January 2019 Abstract: The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. -
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. -
Genetic Drift Lab
Genetic Drift Lab Small population sizes are more strongly influenced by random events than large populations. This means that the genetic frequencies of alleles in small populations are more likely to vary from one generation to the next from the original population. Often, genetic variation is rapidly lost in small populations and random events can create rapid genetic changes or microevolution in such cases. Populations may be subject to this random genetic drift (rapid movement of allele frequencies) by one of two events that reduce population size. 1. Bottlenecks - an incident reduces the overall number of individuals in a population and only a few survive to produce the next generation. Evidence of bottlenecks have been discovered in many species, such as cheetahs and the northern elephant seal. 2. Founder effect - a small number of individuals disperse and colonize new habitat, founding a new population. Organisms colonizing new habitats, such as islands, or migrating to new areas are also common. In both cases the surviving or founding individuals will often vary in genetic frequency from the parental populations (original sources). Also, small subsequent population size plays a big role in additional changes to the gene frequencies. I. Simulation of random events (coin tosses): Each student flips a coin 10 times. What are the expected number of heads for 10 flips? How many heads did you obtain for your 10 flips? _______ # students in your class ___________ # times heads appeared out of 10 trials for all students: 0 _____ 1 ______ 2 _______ 3 ______ 4 ______ 5 ______ 6 _____ 7 _______ 8 ______ 9 ______ 10 ______ How many total times did the replications meet the expected number of heads _______ How many times did the replications not meet this? __________ II.