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      Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

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          Abstract

          With the recent revolution in sequencing, we revisit the unresolved question of what influences the range and values of genetic diversity across taxa.

          Abstract

          Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.

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          The genetics of inbreeding depression.

          Deborah Charlesworth, John Willis (2009)
          Inbreeding depression - the reduced survival and fertility of offspring of related individuals - occurs in wild animal and plant populations as well as in humans, indicating that genetic variation in fitness traits exists in natural populations. Inbreeding depression is important in the evolution of outcrossing mating systems and, because intercrossing inbred strains improves yield (heterosis), which is important in crop breeding, the genetic basis of these effects has been debated since the early twentieth century. Classical genetic studies and modern molecular evolutionary approaches now suggest that inbreeding depression and heterosis are predominantly caused by the presence of recessive deleterious mutations in populations.
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            The hitch-hiking effect of a favourable gene.

            J. M. Smith, J. Haigh (1974)
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              The effect of deleterious mutations on neutral molecular variation.

              B. Charlesworth, M. Morgan, D Charlesworth (1993)
              Selection against deleterious alleles maintained by mutation may cause a reduction in the amount of genetic variability at linked neutral sites. This is because a new neutral variant can only remain in a large population for a long period of time if it is maintained in gametes that are free of deleterious alleles, and hence are not destined for rapid elimination from the population by selection. Approximate formulas are derived for the reduction below classical neutral values resulting from such background selection against deleterious mutations, for the mean times to fixation and loss of new mutations, nucleotide site diversity, and number of segregating sites. These formulas apply to random-mating populations with no genetic recombination, and to populations reproducing exclusively asexually or by self-fertilization. For a given selection regime and mating system, the reduction is an exponential function of the total mutation rate to deleterious mutations for the section of the genome involved. Simulations show that the effect decreases rapidly with increasing recombination frequency or rate of outcrossing. The mean time to loss of new neutral mutations and the total number of segregating neutral sites are less sensitive to background selection than the other statistics, unless the population size is of the order of a hundred thousand or more. The stationary distribution of allele frequencies at the neutral sites is correspondingly skewed in favor of rare alleles, compared with the classical neutral result. Observed reductions in molecular variation in low recombination genomic regions of sufficiently large size, for instance in the centromere-proximal regions of Drosophila autosomes or in highly selfing plant populations, may be partly due to background selection against deleterious mutations.
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                Author and article information

                Journal
                Journal ID (nlm-ta): PLoS Biol
                Journal ID (iso-abbrev): PLoS Biol
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosbiol
                Title: PLoS Biology
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Print): 1544-9173
                ISSN (Electronic): 1545-7885
                Publication date Collection: September 2012
                Publication date (Print): September 2012
                Publication date (Electronic): 11 September 2012
                Volume: 10
                Issue: 9
                Electronic Location Identifier: e1001388
                Affiliations
                [1 ]Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
                [2 ]Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
                [3 ]Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
                [4 ]Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
                Author notes

                The authors have declared that no competing interests exist.

                Unsolved Mysteries discuss a topic of biological importance that is poorly understood and in need of research attention.

                Article
                Publisher ID: PBIOLOGY-D-12-00786
                DOI: 10.1371/journal.pbio.1001388
                PMC ID: 3439417
                PubMed ID: 22984349
                SO-VID: a9314cb0-5ed8-4c3a-a4a8-6c9a9320a742
                Copyright statement: Copyright @ 2012
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Page count
                Pages: 9
                Funding
                E.M.L. was partially supported by National Institutes of Health Grant T32 GM007197. M.P. is a Howard Hughes Early Career Scientist. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Unsolved Mystery
                Subject: Biology
                Subject: Ecology
                Subject: Biodiversity
                Subject: Conservation Science
                Subject: Evolutionary Biology
                Subject: Evolutionary Genetics
                Subject: Evolutionary Processes
                Subject: Evolutionary Theory
                Subject: Population Biology
                Subject: Population Genetics
                Subject: Effective Population Size
                Subject: Genetic Drift
                Subject: Genetic Polymorphism
                Subject: Natural Selection
                Subject: Neutral Theory

                ScienceOpen disciplines: Life sciences
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                ScienceOpen disciplines: Life sciences

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