Michael Lynch (geneticist)

Last updated
Michael Lynch
Born (1951-12-06) December 6, 1951 (age 72)
Auburn, New York, U.S.
Alma mater University of Minnesota
Known forcontributions to Population Genetics, Quantitative Genetics,
Awards
Scientific career
Fields Genetics, Population genetics, Evolution
Institutions Indiana University, Arizona State University

Michael Lynch (born December 6, 1951) is an American geneticist who is the Director of the Biodesign Institute for Mechanisms of Evolution at Arizona State University, Tempe, Arizona.

Contents

Biography

Lynch held a Distinguished Professorship of Evolution, Population Genetics and Genomics at Indiana University, Bloomington, Indiana. Besides over 250 [1] [2] papers, especially in population genetics, he has written a two volume textbook with Bruce Walsh. Alongside this textbook he has also published two other books. He promotes neutral theories to explain genomic architecture based on the effects of population sizes in different lineages; [3] he presented this point of view in his 2007 book "The Origins of Genome Architecture". [4] In 2009, he was elected to the National Academy of Sciences (Evolutionary Biology). Lynch was a Biology undergraduate at St. Bonaventure University and received a B.S. in Biology in 1973. He obtained his PhD from the University of Minnesota (Ecology and Behavioral Biology) in 1977.

Research

Evolution of genome architecture

Population genetics principles, phylogenetic analyses, rate calculations, and allele frequency spectra of derived SNPs are employed to understand evolutionary mechanisms behind eukaryotic genome complexity. [5] Hypotheses around the ideas that eukaryotic genome complexity evolved as a result of a passive response to reduced population size, deleterious newly arisen introns in species of Daphnia, [6] genomic response to alterations in population size and mutation rates in E. coli [7] and the evolutionary fates of duplicate genes in of species of Paramecium using complete genomic sequencing are investigated. [8]

Role of mutation in evolution

Most mutations are mildly deleterious [9] and can eventually lead to decreased evolutionary fitness in a species. Using the Tree of Life, Lynch investigates the significant variation across diverse invertebrates and simple eukaryotic and prokaryotic organisms using a mutation-accumulation strategy. [10] To address this mutation diversity and the load of mutation on survival in some species, a novel method involving a mutation accumulation strategy that is followed by whole genome sequencing allows for estimation of error rates in transcription and variation among eukaryotic lineages. [11] The work done to estimate this variation translates to population genetic theories for mutation rates and how somatic mutations can eventually evolve to multicellularity. These approaches promote the evolutionary ideas of the drift-barrier hypothesis. [12]

Role of recombination in evolution

A major drawback of sexual recombination is the separation of complexes of alleles that have adapted together. Study of Daphnia pulex , a microcrustacean that has the ability to reproduce sexually and asexually based upon which is advantageous at particular evolutionary time points, allows for direct quantification and comparison of recombination rates in mobile genetic elements in sexual and asexual lineages. [13] This species of Daphnia's asexual lineage is rather young in an evolutionary time perspective and rapidly go extinct. [14] It is hypothesized that this rapid extinction is caused by a loss of heterozygosity caused by asexual reproduction as well as gene conversion exposing them to pre-existing deleterious mutations. [9] A new reference genome assembly of this species has recently been generated [15] and attention to the role of recombination in Daphnia has been of hallmark importance to Lynch's research in recent years.

Evolutionary cell biology

Currently, no formal field of evolutionary cell biology exists. The link between the evolution of phenotypes and molecular evolution is found at the level of cellular architecture. Recent work spearheaded by Michael Lynch and his lab seeks to link traditional evolutionary theory with molecular and cellular biology alongside comparative cellular biology observations. Using Paramecium as a model species, studies of the evolutionary basis of: evolution of cellular surveillance mechanisms, barriers as a result of random genetic drift on molecular perfection, multimeric proteins, vesicle transport and gene expression. [16] [17]

Honors and awards

See also

Related Research Articles

<span class="mw-page-title-main">Genetic recombination</span> Production of offspring with combinations of traits that differ from those found in either parent

Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes ; & (2) intrachromosomal recombination, occurring through crossing over.

Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.

Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

<span class="mw-page-title-main">Muller's ratchet</span> Accumulation of harmful mutations

In evolutionary genetics, Muller's ratchet is a process which, in the absence of recombination, results in an accumulation of irreversible deleterious mutations. This happens because in the absence of recombination, and assuming reverse mutations are rare, offspring bear at least as much mutational load as their parents. Muller proposed this mechanism as one reason why sexual reproduction may be favored over asexual reproduction, as sexual organisms benefit from recombination and consequent elimination of deleterious mutations. The negative effect of accumulating irreversible deleterious mutations may not be prevalent in organisms which, while they reproduce asexually, also undergo other forms of recombination. This effect has also been observed in those regions of the genomes of sexual organisms that do not undergo recombination.

<span class="mw-page-title-main">Genetic variation</span> Difference in DNA among individuals or populations

Genetic variation is the difference in DNA among individuals or the differences between populations among the same species. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources of genetic variation, but other mechanisms, such as genetic drift, contribute to it, as well.

In evolutionary genetics, mutational meltdown is a sub class of extinction vortex in which the environment and genetic predisposition mutually reinforce each other. Mutational meltdown is the accumulation of harmful mutations in a small population, which leads to loss of fitness and decline of the population size, which may lead to further accumulation of deleterious mutations due to fixation by genetic drift.

Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

<span class="mw-page-title-main">Evolution of sexual reproduction</span>

Evolution of sexual reproduction describes how sexually reproducing animals, plants, fungi and protists could have evolved from a common ancestor that was a single-celled eukaryotic species. Sexual reproduction is widespread in eukaryotes, though a few eukaryotic species have secondarily lost the ability to reproduce sexually, such as Bdelloidea, and some plants and animals routinely reproduce asexually without entirely having lost sex. The evolution of sexual reproduction contains two related yet distinct themes: its origin and its maintenance. Bacteria and Archaea (prokaryotes) have processes that can transfer DNA from one cell to another, but it is unclear if these processes are evolutionarily related to sexual reproduction in Eukaryotes. In eukaryotes, true sexual reproduction by meiosis and cell fusion is thought to have arisen in the last eukaryotic common ancestor, possibly via several processes of varying success, and then to have persisted.

Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.

<span class="mw-page-title-main">Mutation rate</span> Rate at which mutations occur during some unit of time

In genetics, the mutation rate is the frequency of new mutations in a single gene, nucleotide sequence, or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates are given for specific classes of mutations. Point mutations are a class of mutations which are changes to a single base. Missense, nonsense, and synonymous mutations are three subtypes of point mutations. The rate of these types of substitutions can be further subdivided into a mutation spectrum which describes the influence of the genetic context on the mutation rate.

Genetic load is the difference between the fitness of an average genotype in a population and the fitness of some reference genotype, which may be either the best present in a population, or may be the theoretically optimal genotype. The average individual taken from a population with a low genetic load will generally, when grown in the same conditions, have more surviving offspring than the average individual from a population with a high genetic load. Genetic load can also be seen as reduced fitness at the population level compared to what the population would have if all individuals had the reference high-fitness genotype. High genetic load may put a population in danger of extinction.

<span class="mw-page-title-main">Thelytoky</span> Type of parthenogenesis in which females are produced from unfertilized eggs

Thelytoky is a type of parthenogenesis and is the absence of mating and subsequent production of all female diploid offspring as for example in aphids. Thelytokous parthenogenesis is rare among animals and reported in about 1,500 species, about 1 in 1000 of described animal species, according to a 1984 study. It is more common in invertebrates, like arthropods, but it can occur in vertebrates, including salamanders, fish, and reptiles such as some whiptail lizards.

Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain. When one gene goes through a selective sweep, any other nearby polymorphisms that are in linkage disequilibrium will tend to change their allele frequencies too. Selective sweeps happen when newly appeared mutations are advantageous and increase in frequency. Neutral or even slightly deleterious alleles that happen to be close by on the chromosome 'hitchhike' along with the sweep. In contrast, effects on a neutral locus due to linkage disequilibrium with newly appeared deleterious mutations are called background selection. Both genetic hitchhiking and background selection are stochastic (random) evolutionary forces, like genetic drift.

The evolution of biological complexity is one important outcome of the process of evolution. Evolution has produced some remarkably complex organisms – although the actual level of complexity is very hard to define or measure accurately in biology, with properties such as gene content, the number of cell types or morphology all proposed as possible metrics.

<span class="mw-page-title-main">Clonal interference</span> Phenomenon in evolutionary biology

Clonal interference is a phenomenon in evolutionary biology, related to the population genetics of organisms with significant linkage disequilibrium, especially asexually reproducing organisms. The idea of clonal interference was introduced by American geneticist Hermann Joseph Muller in 1932. It explains why beneficial mutations can take a long time to get fixated or even disappear in asexually reproducing populations. As the name suggests, clonal interference occurs in an asexual lineage ("clone") with a beneficial mutation. This mutation would be likely to get fixed if it occurred alone, but it may fail to be fixed, or even be lost, if another beneficial-mutation lineage arises in the same population; the multiple clones interfere with each other.

A genetic lineage includes all descendants of a given genetic sequence, typically following a new mutation. It is not the same as an allele because it excludes cases where different mutations give rise to the same allele, and includes descendants that differ from the ancestor by one or more mutations. The genetic sequence can be of different sizes, e.g. a single gene or a haplotype containing multiple adjacent genes along a chromosome. Given recombination, each gene can have a separate genetic lineages, even as the population shares a single organismal lineage. In asexual microbes or somatic cells, cell lineages exactly match genetic lineages, and can be traced.

<i>Paramecium aurelia</i> Species of single-celled organism

Paramecium aurelia are unicellular organisms belonging to the genus Paramecium of the phylum Ciliophora. They are covered in cilia which help in movement and feeding.Paramecium can reproduce sexually, asexually, or by the process of endomixis. Paramecium aurelia demonstrate a strong "sex reaction" whereby groups of individuals will cluster together, and emerge in conjugant pairs. This pairing can last up to 12 hours, during which the micronucleus of each organism will be exchanged. In Paramecium aurelia, a cryptic species complex was discovered by observation. Since then, some have tried to decode this complex using genetic data.

<i>Daphnia pulex</i> Species of small freshwater animal

Daphnia pulex is the most common species of water flea. It has a cosmopolitan distribution: the species is found throughout the Americas, Europe, and Australia. It is a model species, and was the first crustacean to have its genome sequenced.

<i>Daphnia pulicaria</i> Species of small freshwater animal

Daphnia pulicaria is a species of freshwater crustaceans found within the genus of Daphnia, which are often called "water fleas," and they are commonly used as model organisms for scientific research. Like other species of Daphnia, they reproduce via cyclic parthenogenesis. D. pulicaria are filter-feeders with a diet primarily consisting of algae, including Ankistrodesmus falcatus, and they can be found in deep lakes located in temperate climates. Furthermore, D. pulicaria are ecologically important herbivorous zooplankton, which help control algal populations and are a source of food for some fish. D. pulicaria are closely related to Daphnia pulex, and numerous studies have investigated the nature and strength of this relationship because these species can produce Daphnia pulex-pulicaria hybrids. In recent years, D. pulicaria along with other Daphnia species have been negatively affected by invasive predators, such as Bythotrephes longimanus.

Eukaryote hybrid genomes result from interspecific hybridization, where closely related species mate and produce offspring with admixed genomes. The advent of large-scale genomic sequencing has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number.

References

  1. ↑ "Publications | The Biodesign Institute | ASU". biodesign.asu.edu. Retrieved 2017-11-08.
  2. ↑ "Michael Lynch". scholar.google.com. Retrieved 2023-09-28.
  3. ↑ Lynch, Michael (2007-05-15). "The frailty of adaptive hypotheses for the origins of organismal complexity". Proceedings of the National Academy of Sciences. 104 (suppl_1): 8597–8604. doi: 10.1073/pnas.0702207104 . ISSN   0027-8424. PMC   1876435 . PMID   17494740.
  4. ↑ "The origins of genome architecture". Choice Reviews Online. 45 (2): 45–0862-45-0862. 2007-10-01. doi:10.5860/choice.45-0862. ISSN   0009-4978.
  5. ↑ Li, Wenli; Tucker, Abraham E.; Sung, Way; Thomas, W. Kelley; Lynch, Michael (2009-11-27). "Extensive, Recent Intron Gains in Daphnia Populations". Science. 326 (5957): 1260–1262. Bibcode:2009Sci...326.1260L. doi:10.1126/science.1179302. ISSN   0036-8075. PMC   3878872 . PMID   19965475.
  6. ↑ Li, Wenli; Kuzoff, Robert; Wong, Chen Khuan; Tucker, Abraham; Lynch, Michael (2014-09-01). "Characterization of Newly Gained Introns in Daphnia Populations". Genome Biology and Evolution. 6 (9): 2218–2234. doi:10.1093/gbe/evu174. PMC   4202315 . PMID   25123113.
  7. ↑ Lynch, Michael (2010). "Evolution of the mutation rate". Trends in Genetics. 26 (8): 345–352. doi:10.1016/j.tig.2010.05.003. PMC   2910838 . PMID   20594608.
  8. ↑ Lynch, Michael (2006-09-11). "Streamlining and Simplification of Microbial Genome Architecture". Annual Review of Microbiology. 60 (1): 327–349. doi:10.1146/annurev.micro.60.080805.142300. ISSN   0066-4227. PMID   16824010.
  9. 1 2 Loewe, Laurence; Hill, William G. (2010-04-27). "The population genetics of mutations: good, bad and indifferent". Philosophical Transactions of the Royal Society of London B: Biological Sciences. 365 (1544): 1153–1167. doi:10.1098/rstb.2009.0317. ISSN   0962-8436. PMC   2871823 . PMID   20308090.
  10. ↑ Lynch, Michael; Conery, John; Burger, Reinhard (1995-10-01). "Mutation Accumulation and the Extinction of Small Populations". The American Naturalist. 146 (4): 489–518. doi:10.1086/285812. ISSN   0003-0147.
  11. ↑ Lynch, Michael; Gabriel, Wilfried (1990-11-01). "Mutation Load and the Survival of Small Populations". Evolution. 44 (7): 1725–1737. doi: 10.1111/j.1558-5646.1990.tb05244.x . ISSN   1558-5646. PMID   28567811.
  12. ↑ Lynch, Michael; Ackerman, Matthew S.; Gout, Jean-Francois; Long, Hongan; Sung, Way; Thomas, W. Kelley; Foster, Patricia L. (2016-10-14). "Genetic drift, selection and the evolution of the mutation rate". Nature Reviews Genetics. 17 (11): 704–714. doi:10.1038/nrg.2016.104. ISSN   1471-0064. PMID   27739533.
  13. ↑ Jiang, Xiaoqian; Tang, Haixu; Ye, Zhiqiang; Lynch, Michael (2017-02-01). "Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex". Genome Biology and Evolution. 9 (2): 362–374. doi:10.1093/gbe/evw302. PMC   5381639 . PMID   28057730.
  14. ↑ Omilian, Angela R.; Cristescu, Melania E. A.; Dudycha, Jeffry L.; Lynch, Michael (2006-12-05). "Ameiotic recombination in asexual lineages of Daphnia". Proceedings of the National Academy of Sciences. 103 (49): 18638–18643. Bibcode:2006PNAS..10318638O. doi:10.1073/pnas.0606435103. ISSN   0027-8424. PMC   1693715 . PMID   17121990.
  15. ↑ Ye, Zhiqiang; Xu, Sen; Spitze, Ken; Asselman, Jana; Jiang, Xiaoqian; Ackerman, Matthew S.; Lopez, Jacqueline; Harker, Brent; Raborn, R. Taylor (2017-05-01). "A New Reference Genome Assembly for the Microcrustacean Daphnia pulex". G3: Genes, Genomes, Genetics. 7 (5): 1405–1416. doi:10.1534/g3.116.038638. ISSN   2160-1836. PMC   5427498 . PMID   28235826.
  16. ↑ McGrath, Casey L.; Gout, Jean-Francois; Doak, Thomas G.; Yanagi, Akira; Lynch, Michael (2014-08-01). "Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence". Genetics. 197 (4): 1417–1428. doi:10.1534/genetics.114.163287. ISSN   0016-6731. PMC   4125410 . PMID   24840360.
  17. ↑ Catania, Francesco; Wurmser, François; Potekhin, Alexey A.; Przyboś, Ewa; Lynch, Michael (2009-02-01). "Genetic Diversity in the Paramecium aurelia Species Complex". Molecular Biology and Evolution. 26 (2): 421–431. doi:10.1093/molbev/msn266. ISSN   0737-4038. PMC   3888249 . PMID   19023087.
  18. ↑ "Past and Present GSA Officers". GSA. Archived from the original on 4 December 2018. Retrieved 27 November 2018.
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