1
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Hancock ZB, Cardinale DS. Back to the fundamentals: a reply to Basener and Sanford 2018. J Math Biol 2024; 88:54. [PMID: 38568223 DOI: 10.1007/s00285-024-02077-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
Fisher's fundamental theorem of natural selection has haunted theoretical population genetic literature since it was proposed in 1930, leading to numerous interpretations. Most of the confusion stemmed from Fisher's own obscure presentation. By the 1970s, a clearer view of Fisher's theorem had been achieved and it was found that, regardless of its utility or significance, it represents a general theorem of evolutionary biology. Basener and Sanford (J Math Biol 76:1589-1622, 2018) writing in JOMB, however, paint a different picture of the fundamental theorem as one hindered by its assumptions and incomplete due to its failure to explicitly incorporate mutational effects. They argue that Fisher saw his theorem as a "mathematical proof of Darwinian evolution". In this reply, we show that, contrary to Basener and Sanford, Fisher's theorem is a general theorem that applies to any evolving population, and that, far from their assertion that it needed to be expanded, the theorem already implicitly incorporates ancestor-descendant variation. We also show that their numerical simulations produce unrealistic results. Lastly, we argue that Basener and Sanford's motivations were in undermining not merely Fisher's theorem, but the concept of universal common descent itself.
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Affiliation(s)
- Zachary B Hancock
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48103, USA.
| | - Daniel Stern Cardinale
- Division of Life Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
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2
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Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang YE, Ge S, Guo YL. Forces driving transposable element load variation during Arabidopsis range expansion. THE PLANT CELL 2024; 36:840-862. [PMID: 38036296 PMCID: PMC10980350 DOI: 10.1093/plcell/koad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhi-Qin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Fu Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Min Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin-Tong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yong E Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Akalu YT, Bogunovic D. Inborn errors of immunity: an expanding universe of disease and genetic architecture. Nat Rev Genet 2024; 25:184-195. [PMID: 37863939 DOI: 10.1038/s41576-023-00656-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2023] [Indexed: 10/22/2023]
Abstract
Inborn errors of immunity (IEIs) are generally considered to be rare monogenic disorders of the immune system that cause immunodeficiency, autoinflammation, autoimmunity, allergy and/or cancer. Here, we discuss evidence that IEIs need not be rare disorders or exclusively affect the immune system. Namely, an increasing number of patients with IEIs present with severe dysregulations of the central nervous, digestive, renal or pulmonary systems. Current challenges in the diagnosis of IEIs that result from the segregated practice of specialized medicine could thus be mitigated, in part, by immunogenetic approaches. Starting with a brief historical overview of IEIs, we then discuss the technological advances that are facilitating the immunogenetic study of IEIs, progress in understanding disease penetrance in IEIs, the expanding universe of IEIs affecting distal organ systems and the future of genetic, biochemical and medical discoveries in this field.
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Affiliation(s)
- Yemsratch T Akalu
- Center for Inborn Errors of Immunity, Precision Immunology Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dusan Bogunovic
- Center for Inborn Errors of Immunity, Precision Immunology Institute, Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Singh RS. A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine. J Mol Evol 2023; 91:711-720. [PMID: 37665357 PMCID: PMC10597872 DOI: 10.1007/s00239-023-10131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Genetics and molecular biology research have progressed for over a century; however, no laws of biology resembling those of physics have been identified, despite the expectations of some physicists. It may be that it is not the properties of matter alone but evolved properties of matter in combination with atomic physics and chemistry that gave rise to the origin and complexity of life. It is proposed that any law of biology must also be a product of evolution that co-evolved with the origin and progression of life. It was suggested that molecular complexity and redundancy exponentially increase over time and have the following relationship: DNA sequence complexity (Cd) < molecular complexity (Cm) < phenotypic complexity (Cp). This study presents a law of redundancy, which together with the law of complexity, is proposed as an evolutionary law of biology. Molecular complexity and redundancy are inseparable aspects of biochemical pathways, and molecular redundancy provides the first line of defense against environmental challenges, including those of deleterious mutations. Redundancy can create problems for precision medicine because in addition to the issues arising from the involvement of multiple genes, redundancy arising from alternate pathways between genotypes and phenotypes can complicate gene detection for complex diseases and mental disorders. This study uses cancer as an example to show how cellular complexity, molecular redundancy, and hidden variation affect the ability of cancer cells to evolve and evade detection and elimination. Characterization of alternate biochemical pathways or "escape routes" can provide a step in the fight against cancer.
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Affiliation(s)
- Rama S Singh
- Professor Emeritus, Department of Biology and Origins Institute, McMaster University, 1280 Main Street W., Hamilton, ON, L8S 4K1, Canada.
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5
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Matheson J, Bertram J, Masel J. Human deleterious mutation rate implies high fitness variance, with declining mean fitness compensated by rarer beneficial mutations of larger effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555871. [PMID: 37732183 PMCID: PMC10508744 DOI: 10.1101/2023.09.01.555871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Each new human has an expected Ud = 2 - 10 new deleterious mutations. This deluge of deleterious mutations cannot all be purged, and therefore accumulate in a declining fitness ratchet. Using a novel simulation framework designed to efficiently handle genome-wide linkage disequilibria across many segregating sites, we find that rarer, beneficial mutations of larger effect are sufficient to compensate fitness declines due to the fixation of many slightly deleterious mutations. Drift barrier theory posits a similar asymmetric pattern of fixations to explain ratcheting genome size and complexity, but in our theory, the cause is Ud > 1 rather than small population size. In our simulations, Ud ~2 - 10 generates high within-population variance in relative fitness; two individuals will typically differ in fitness by 15-40%. Ud ~2 - 10 also slows net adaptation by ~13%-39%. Surprisingly, fixation rates are more sensitive to changes in the beneficial than the deleterious mutation rate, e.g. a 10% increase in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.
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Affiliation(s)
- Joseph Matheson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology, Behavior, and Evolution, University of California San Diego, San Diego, CA, 92093, USA
| | - Jason Bertram
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Mathematics, University of Western Ontario, London ON, Canada
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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6
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Hao S, Zhao X, Fan Y, Liu Z, Zhang X, Li W, Yuan H, Zhang J, Zhang Y, Ma T, Tao H. Prevalence and spectrum of cancer predisposition germline mutations in young patients with the common late-onset cancers. Cancer Med 2023; 12:18394-18404. [PMID: 37610374 PMCID: PMC10524041 DOI: 10.1002/cam4.6445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/30/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Pathogenic germline variants (PGVs) can play a vital role in the oncogenesis process in carriers. Previous studies have recognized that PGVs contribute to early onset of tumorigenesis in certain cancer types, for example, colorectal cancer and breast cancer. However, the reported prevalence data of cancer-associated PGVs were highly inconsistent due to nonuniform patient cohorts, sequencing methods, and prominent difficulties in pathogenicity interpretation of variants. In addition to the above difficulties, due to the rarity of cases, the prevalence of cancer PGV carriers in young cancer patients affected by late-onset cancer types has not been comprehensively evaluated to date. METHODS A total of 131 young cancer patients (1-29 years old at diagnosis) were enrolled in this study. The patients were affected by six common late-onset cancer types, namely, lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, and head-neck cancer. Cancer PGVs were identified and analyzed. based on NGS-based targeted sequencing followed by bioinformatic screening and strict further evaluations of variant pathogenicity. RESULTS Twenty-three cancer PGVs in 21 patients were identified, resulting in an overall PGV prevalence of 16.0% across the six included cancer types, which was approximately double the prevalence reported in a previous pancancer study. Nine of the 23 PGVs are novel, thus expanding the cancer PGV spectrum. Seven of the 23 (30.4%) PGVs are potential therapeutic targets of olaparib, with potential implications for clinical manipulation. Additionally, a small prevalence of somatic mutations of some classic cancer hallmark genes in young patients, in contrast to all-age patients, was revealed. CONCLUSION This study demonstrates the high prevalence of PGVs in young cancer patients with the common late-onset cancers and the potentially significant clinical implications of cancer PGVs, the findings highlight the value of PGV screening in young patients across lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, or head-neck cancer.
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Affiliation(s)
- Shaoyu Hao
- Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Ximeng Zhao
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Yue Fan
- Department of Integrated Traditional Chinese Medicine and Western MedicineZhong Shan Hospital, Fudan UniversityShanghaiChina
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Xiang Zhang
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Wei Li
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | | | - Jie Zhang
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | | | - Tonghui Ma
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
- Department of GastroenterologyZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
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7
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Wientjes YCJ, Bijma P, van den Heuvel J, Zwaan BJ, Vitezica ZG, Calus MPL. The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations. Genetics 2023; 225:iyad141. [PMID: 37506255 PMCID: PMC10471209 DOI: 10.1093/genetics/iyad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Genetic selection has been applied for many generations in animal, plant, and experimental populations. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allelic architecture are different for the recently introduced technique of genomic selection compared to traditional selection methods and whether they depend on the genetic architectures of traits. Here, we investigate the allele frequency changes of old and new causal loci under 50 generations of phenotypic, pedigree, and genomic selection, for a trait controlled by either additive, additive and dominance, or additive, dominance, and epistatic effects. Genomic selection resulted in slightly larger and faster changes in allele frequencies of causal loci than pedigree selection. For each locus, allele frequency change per generation was not only influenced by its statistical additive effect but also to a large extent by the linkage phase with other loci and its allele frequency. Selection fixed a large number of loci, and 5 times more unfavorable alleles became fixed with genomic and pedigree selection than with phenotypic selection. For pedigree selection, this was mainly a result of increased genetic drift, while genetic hitchhiking had a larger effect on genomic selection. When epistasis was present, the average allele frequency change was smaller (∼15% lower), and a lower number of loci became fixed for all selection methods. We conclude that for long-term genetic improvement using genomic selection, it is important to consider hitchhiking and to limit the loss of favorable alleles.
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Affiliation(s)
- Yvonne C J Wientjes
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | | | - Mario P L Calus
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
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8
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Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions. Genes (Basel) 2023; 14:genes14030649. [PMID: 36980921 PMCID: PMC10048334 DOI: 10.3390/genes14030649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents–progeny sequencing to investigate the mutation rate and spectrum of the domestic silkworm (Bombyx mori) among normal and two temperature stress conditions (32 °C and 0 °C). The rate of single-nucleotide mutations in the normal temperature rearing condition was 0.41 × 10−8 (95% confidence interval, 0.33 × 10−8–0.49 × 10−8) per site per generation, which was up to 1.5-fold higher than in four previously studied insects. Moreover, the mutation rates of the silkworm under the stresses are significantly higher than in normal conditions. Furthermore, the mutation rate varies less in gene regions under normal and temperature stresses. Together, these findings expand the known diversity of the mutation rate among eukaryotes but also have implications for evolutionary analysis that assumes a constant mutation rate among species and environments.
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9
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Gill SE, Chain FJJ. Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum. J Mol Evol 2023; 91:24-32. [PMID: 36484794 PMCID: PMC9849192 DOI: 10.1007/s00239-022-10081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplication using mutation accumulation lines have estimated that genes are duplicated and deleted at orders of magnitude greater rates than the spontaneous point mutation rate. In our study, we tested whether spontaneous gene deletion and gene duplication rates are also high in Dictyostelium discoideum, a eukaryote with among the lowest point mutation rates (2.5 × 10-11 per site per generation) and an AT-rich genome (GC content of 22%). We calculated mutation rates of gene deletions and duplications using whole-genome sequencing data originating from a mutation accumulation experiment and determined the association between the copy number mutations and GC content. Overall, we estimated an average of 3.93 × 10-8 gene deletions and 1.18 × 10-8 gene duplications per gene per generation. While orders of magnitude greater than their point mutation rate, these rates are much lower compared to gene deletion and duplication rates estimated from mutation accumulation lines in other organisms (that are on the order of ~ 10-6 per gene/generation). The deletions and duplications were enriched in regions that were AT-rich even compared to the genomic background, in contrast to our expectations if low GC content was contributing to low mutation rates. The low deletion and duplication mutation rates in D. discoideum compared to other eukaryotes mirror their low point mutation rates, supporting previous work suggesting that this organism has high replication fidelity and effective molecular machinery to avoid the accumulation of mutations in their genome.
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Affiliation(s)
- Shelbi E Gill
- Department of Biology, University of Massachusetts Lowell, Lowell, MA, 01854-2874, USA.
| | - Frédéric J J Chain
- Department of Biology, University of Massachusetts Lowell, Lowell, MA, 01854-2874, USA.
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10
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Moral foundations tracked over 200 years of lexicographic data, and their predictors. ANTHROPOLOGICAL REVIEW 2022. [DOI: 10.18778/1898-6773.85.2.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prediction that reduction of negative selection decreases group-level competitiveness, as reflected in increased individual-focused and diminished group-focused moral foundations, is tested. To measure this hypothesized shift in moral foundations, we conduct a culturomic analysis of the utilization frequencies of items sourced from the moral foundations item pool, tracked among Britannic populations from 1800 to 1999 using Google Ngram Viewer. The resultant higher-order factor, which tracks increasing individualizing values and decreasing binding values, is termed Asabiyyah (capturing social cohesion and collective purpose). Two predictors of this factor are examined: change in the strength of intergroup competition and change in levels of indicators of developmental instability. Both the strength of intergroup competition and levels of developmental instability associate with Asabiyyah. Rising developmental instability mediates the impact of inter-group competition, indicating that reduced between-group competition might have relaxed negative selection against mutations, which might reduce Asabiyyah via their effects on inter-genomic transactions. These results must be interpreted carefully, given the clear real-world evidence that explicit commitment to group-oriented values often features in harmful and maladaptive social and political ideologies of an extreme character.
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11
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OUP accepted manuscript. Hum Reprod Update 2022; 28:457-479. [DOI: 10.1093/humupd/dmac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/17/2022] [Indexed: 11/12/2022] Open
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12
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Catania F, Baedke J, Fábregas-Tejeda A, Nieves Delgado A, Vitali V, Long LAN. Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture. Bioessays 2021; 43:e2100049. [PMID: 33829521 DOI: 10.1002/bies.202100049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet-driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet-driven microbiome changes lead to dysbiosis, they can also shape life-history traits and fuel human evolution. We posit that dietary shifts prompt mismatched microbiome-host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra-holobiont stress response, which encourages the holobiont to re-establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change-related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life-history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate-related dietary challenges for policy and health interventions.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jan Baedke
- Department of Philosophy I, Ruhr University Bochum, Bochum, Germany
| | | | - Abigail Nieves Delgado
- Knowledge, Technology & Innovation, Wageningen University, Wageningen, The Netherlands.,Freudenthal Institute, Utrecht University, Utrecht, The Netherlands
| | - Valerio Vitali
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Le Anh Nguyen Long
- Department of Public Administration, University of Twente, Enschede, The Netherlands
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13
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Singh RS, Singh KK, Singh SM. Origin of Sex-Biased Mental Disorders: An Evolutionary Perspective. J Mol Evol 2021; 89:195-213. [PMID: 33630117 PMCID: PMC8116267 DOI: 10.1007/s00239-021-09999-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/06/2021] [Indexed: 12/12/2022]
Abstract
Sexual dimorphism or sex bias in diseases and mental disorders have two biological causes: sexual selection and sex hormones. We review the role of sexual selection theory and bring together decades of molecular studies on the variation and evolution of sex-biased genes and provide a theoretical basis for the causes of sex bias in disease and health. We present a Sexual Selection-Sex Hormone theory and show that male-driven evolution, including sexual selection, leads to: (1) increased male vulnerability due to negative pleiotropic effects associated with male-driven sexual selection and evolution; (2) increased rates of male-driven mutations and epimutations in response to early fitness gains and at the cost of late fitness; and (3) enhanced female immunity due to antagonistic responses to mutations that are beneficial to males but harmful to females, reducing female vulnerability to diseases and increasing the thresholds for disorders such as autism. Female-driven evolution, such as reproduction-related fluctuation in female sex hormones in association with stress and social condition, has been shown to be associated with increased risk of certain mental disorders such as major depression disorder in women. Bodies have history, cells have memories. An evolutionary framework, such as the Sexual Selection–Sex Hormone theory, provides a historical perspective for understanding how the differences in the sex-biased diseases and mental disorders have evolved over time. It has the potential to direct the development of novel preventive and treatment strategies.
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Affiliation(s)
- Rama S Singh
- Department of Biology, McMaster University, Hamilton, Canada.
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Canada.,Krembil Research Institute, University Health Network, Toronto, Canada
| | - Shiva M Singh
- Department of Biology, University of Western Ontario, London, Canada
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14
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Innan H, Vaiman D, Veitia RA. Predictable increase in female reproductive window: A simple model connecting age of reproduction, menopause, and longevity. Bioessays 2021; 43:e2000233. [PMID: 33569823 DOI: 10.1002/bies.202000233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 01/08/2023]
Abstract
With the ever-increasing lifespan along with societal changes, women can marry and procreate later than in previous centuries. However, pathogenic genetic variants segregating in the population can lead to female subfertility or infertility well before the average age of normal menopause, leading to counter-selection of such deleterious alleles. In reviewing this field, we speculate that a logical consequence would be the later occurrence of menopause and the extension of women's reproductive lifespan. We illustrate this point with a simple model that applies to other variants that contribute to female infertility, including epigenetic variation. We also consider the effect of medical interventions and lifestyle.
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Affiliation(s)
- Hideki Innan
- Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Daniel Vaiman
- Université de Paris, Paris, France.,Institut Cochin, Paris, France
| | - Reiner A Veitia
- Université de Paris, Paris, France.,CNRS, Institut Jacques Monod, Paris, France.,Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Paris-Saclay, Paris, France
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15
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Smirnov E, Chmúrčiaková N, Liška F, Bažantová P, Cmarko D. Variability of Human rDNA. Cells 2021; 10:cells10020196. [PMID: 33498263 PMCID: PMC7909238 DOI: 10.3390/cells10020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
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16
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Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nat Rev Genet 2021; 22:269-283. [PMID: 33408383 PMCID: PMC7787134 DOI: 10.1038/s41576-020-00305-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Nearly all genetic variants that influence disease risk have human-specific origins; however, the systems they influence have ancient roots that often trace back to evolutionary events long before the origin of humans. Here, we review how advances in our understanding of the genetic architectures of diseases, recent human evolution and deep evolutionary history can help explain how and why humans in modern environments become ill. Human populations exhibit differences in the prevalence of many common and rare genetic diseases. These differences are largely the result of the diverse environmental, cultural, demographic and genetic histories of modern human populations. Synthesizing our growing knowledge of evolutionary history with genetic medicine, while accounting for environmental and social factors, will help to achieve the promise of personalized genomics and realize the potential hidden in an individual's DNA sequence to guide clinical decisions. In short, precision medicine is fundamentally evolutionary medicine, and integration of evolutionary perspectives into the clinic will support the realization of its full potential.
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Affiliation(s)
- Mary Lauren Benton
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.252890.40000 0001 2111 2894Department of Computer Science, Baylor University, Waco, TX USA
| | - Abin Abraham
- grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN USA
| | - Abigail L. LaBella
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Patrick Abbot
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Antonis Rokas
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - John A. Capra
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
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17
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Woodley Of Menie MA, Kanazawa S, Pallesen J, Sarraf MA. Paternal Age is Negatively Associated with Religious Behavior in a Post-60s But Not a Pre-60s US Birth Cohort: Testing a Prediction from the Social Epistasis Amplification Model. JOURNAL OF RELIGION AND HEALTH 2020; 59:2733-2752. [PMID: 32006140 DOI: 10.1007/s10943-020-00987-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Participation in social behaviors that enhance group-level fitness may be influenced by mutations that affect patterns of social epistasis in human populations. Mutations that cause individuals to not participate in these behaviors may weaken the ability of members of a group to coordinate and regulate behavior, which may in turn negatively affect fitness. To investigate the possibility that de novo mutations degrade these adaptive social behaviors, we examine the effect of paternal age (as a well-established proxy for de novo mutation load) on one such social behavior, namely religious observance, since religiosity may be a group-level cultural adaptation facilitating enhanced social coordination. Using two large samples (Wisconsin Longitudinal Study and AddHealth), each of a different US birth cohort, paternal age was used to hierarchically predict respondent's level of church attendance after controlling for multiple covariates. The effect is absent in WLS (β = .007, ns, N = 4560); however, it is present in AddHealth (β = - .046, p < .05, N = 4873) increasing the adjusted model R2 by .005. The WLS respondents were (mostly) born in the 1930s, whereas the AddHealth respondents were (mostly) born in the 1970s. This may indicate that social-epistatic regulation of behavior has weakened historically in the USA, which might stem from and enhance the ability for de novo mutations to influence behavior among more recently born cohorts-paralleling the secular rise in the heritability of age at sexual debut after the sexual revolution.
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Affiliation(s)
- Michael A Woodley Of Menie
- Center Leo Apostel for Interdisciplinary Studies, Vrije Universiteit Brussel, Brussels, Belgium.
- Unz Foundation, Palo Alto, CA, USA.
| | - Satoshi Kanazawa
- School of Management, London School of Economics and Political Science, London, UK
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18
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Affiliation(s)
- Russell T. Warne
- Utah Valley University, 800 West University Parkway MC 115, Orem, UT 84604, E-mail:
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19
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Makarieva AM, Nefiodov AV, Li BL. Life's Energy and Information: Contrasting Evolution of Volume- versus Surface-Specific Rates of Energy Consumption. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E1025. [PMID: 33286794 PMCID: PMC7597118 DOI: 10.3390/e22091025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/02/2022]
Abstract
As humanity struggles to find a path to resilience amidst global change vagaries, understanding organizing principles of living systems as the pillar for human existence is rapidly growing in importance. However, finding quantitative definitions for order, complexity, information and functionality of living systems remains a challenge. Here, we review and develop insights into this problem from the concept of the biotic regulation of the environment developed by Victor Gorshkov (1935-2019). Life's extraordinary persistence-despite being a strongly non-equilibrium process-requires a quantum-classical duality: the program of life is written in molecules and thus can be copied without information loss, while life's interaction with its non-equilibrium environment is performed by macroscopic classical objects (living individuals) that age. Life's key energetic parameter, the volume-specific rate of energy consumption, is maintained within universal limits by most life forms. Contrary to previous suggestions, it cannot serve as a proxy for "evolutionary progress". In contrast, ecosystem-level surface-specific energy consumption declines with growing animal body size in stable ecosystems. High consumption by big animals is associated with instability. We suggest that the evolutionary increase in body size may represent a spontaneous loss of information about environmental regulation, a manifestation of life's algorithm ageing as a whole.
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Affiliation(s)
- Anastassia M. Makarieva
- Theoretical Physics Division, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia
- USDA-China MOST Joint Research Center for AgroEcology and Sustainability, University of California, Riverside, CA 92521-0124, USA
| | - Andrei V. Nefiodov
- Theoretical Physics Division, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia
| | - Bai-Lian Li
- USDA-China MOST Joint Research Center for AgroEcology and Sustainability, University of California, Riverside, CA 92521-0124, USA
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20
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Abstract
Extant humans are currently increasing their genetic load, which is informing present and future human microevolution. This has been a gradual process that has been rising over the last centuries as a consequence of improved sanitation, nutritional improvements, advancements in microbiology and medical interventions, which have relaxed natural selection. Moreover, a reduction in infant and child mortality and changing societal attitudes towards fertility have led to a decrease in total fertility rates (TFRs) since the 19th century. Generally speaking, decreases in differential fertility and mortality have meant that there is less opportunity for natural selection to eliminate deleterious mutations from the human gene pool. It has been argued that the average human may carry ~250-300 mutations that are mostly deleterious, as well as several hundred less-deleterious variants. These deleterious alleles in extant humans mean that our fitness is being constrained. While such alleles are viewed as reducing human fitness, they may also have had an adaptive function in the past, such as assisting in genetic complexity, sexual recombination and diploidy. Saying this, our current knowledge on these fitness compromising alleles is still lacking.
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21
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Carlaw TM, Zhang LH, Ross CJD. CRISPR/Cas9 Editing: Sparking Discussion on Safety in Light of the Need for New Therapeutics. Hum Gene Ther 2020; 31:794-807. [PMID: 32586150 DOI: 10.1089/hum.2020.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent advances in genome sequencing have greatly improved our ability to understand and identify the causes of genetic diseases. However, there remains an urgent need for innovative, safe, and effective treatments for these diseases. CRISPR-based genome editing systems have become important and powerful tools in the laboratory, and efforts are underway to translate these into patient therapies. Therapeutic base editing is one form of genome engineering that has gained much interest because of its simplicity, specificity, and effectiveness. Base editors are a fusion of a partially deactivated Cas9 enzyme with nickase function, together with a base-modifying enzyme. They are capable of precisely targeting and repairing a pathogenic mutation to restore the normal function of a gene, ideally without disturbing the rest of the genome. In the past year, research has identified new safety concerns of base editors and sparked new innovations to improve their safety. In this review, we provide an overview of the recent advances in the safety and effectiveness of therapeutic base editors and prime editing.
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Affiliation(s)
| | - Lin-Hua Zhang
- Faculty of Pharmaceutical Sciences; University of British Columbia, Vancouver, Canada
| | - Colin J D Ross
- Faculty of Pharmaceutical Sciences; University of British Columbia, Vancouver, Canada
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22
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Mathieson I. Human adaptation over the past 40,000 years. Curr Opin Genet Dev 2020; 62:97-104. [PMID: 32745952 PMCID: PMC7484260 DOI: 10.1016/j.gde.2020.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/10/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States.
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23
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The Muller’s Ratchet and Aging. Trends Genet 2020; 36:395-402. [DOI: 10.1016/j.tig.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/02/2020] [Accepted: 02/25/2020] [Indexed: 11/21/2022]
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24
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25
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Experimental evidence for effects of sexual selection on condition-dependent mutation rates. Nat Ecol Evol 2020; 4:737-744. [DOI: 10.1038/s41559-020-1140-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/10/2020] [Indexed: 01/13/2023]
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26
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Aris-Brosou S. Direct Evidence of an Increasing Mutational Load in Humans. Mol Biol Evol 2020; 36:2823-2829. [PMID: 31424543 DOI: 10.1093/molbev/msz192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.
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Affiliation(s)
- Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
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27
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Oliynyk RT. Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective. Int J Mol Sci 2019; 20:E5013. [PMID: 31658652 PMCID: PMC6834143 DOI: 10.3390/ijms20205013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
With the accumulation of scientific knowledge of the genetic causes of common diseases and continuous advancement of gene-editing technologies, gene therapies to prevent polygenic diseases may soon become possible. This study endeavored to assess population genetics consequences of such therapies. Computer simulations were used to evaluate the heterogeneity in causal alleles for polygenic diseases that could exist among geographically distinct populations. The results show that although heterogeneity would not be easily detectable by epidemiological studies following population admixture, even significant heterogeneity would not impede the outcomes of preventive gene therapies. Preventive gene therapies designed to correct causal alleles to a naturally-occurring neutral state of nucleotides would lower the prevalence of polygenic early- to middle-age-onset diseases in proportion to the decreased population relative risk attributable to the edited alleles. The outcome would manifest differently for late-onset diseases, for which the therapies would result in a delayed disease onset and decreased lifetime risk; however, the lifetime risk would increase again with prolonging population life expectancy, which is a likely consequence of such therapies. If the preventive heritable gene therapies were to be applied on a large scale, the decreasing frequency of risk alleles in populations would reduce the disease risk or delay the age of onset, even with a fraction of the population receiving such therapies. With ongoing population admixture, all groups would benefit over generations.
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Affiliation(s)
- Roman Teo Oliynyk
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand.
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand.
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28
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FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue. G3-GENES GENOMES GENETICS 2019; 9:2977-2987. [PMID: 31352405 PMCID: PMC6723130 DOI: 10.1534/g3.119.400438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With growing interest in monitoring mutational processes in normal tissues, tumor heterogeneity, and cancer evolution under therapy, the ability to accurately and economically detect ultra-rare mutations is becoming increasingly important. However, this capability has often been compromised by significant sequencing, PCR and DNA preparation error rates. Here, we describe FERMI (Fast Extremely Rare Mutation Identification) - a novel method designed to eliminate the majority of these sequencing and library-preparation errors in order to significantly improve rare somatic mutation detection. This method leverages barcoded targeting probes to capture and sequence DNA of interest with single copy resolution. The variant calls from the barcoded sequencing data are then further filtered in a position-dependent fashion against an adaptive, context-aware null model in order to distinguish true variants. As a proof of principle, we employ FERMI to probe bone marrow biopsies from leukemia patients, and show that rare mutations and clonal evolution can be tracked throughout cancer treatment, including during historically intractable periods like minimum residual disease. Importantly, FERMI is able to accurately detect nascent clonal expansions within leukemias in a manner that may facilitate the early detection and characterization of cancer relapse.
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29
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Gyngell C, Bowman-Smart H, Savulescu J. Moral reasons to edit the human genome: picking up from the Nuffield report. JOURNAL OF MEDICAL ETHICS 2019; 45:514-523. [PMID: 30679191 PMCID: PMC6820147 DOI: 10.1136/medethics-2018-105084] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/02/2018] [Accepted: 12/11/2018] [Indexed: 05/12/2023]
Abstract
In July 2018, the Nuffield Council of Bioethics released its long-awaited report on heritable genome editing (HGE). The Nuffield report was notable for finding that HGE could be morally permissible, even in cases of human enhancement. In this paper, we summarise the findings of the Nuffield Council report, critically examine the guiding principles they endorse and suggest ways in which the guiding principles could be strengthened. While we support the approach taken by the Nuffield Council, we argue that detailed consideration of the moral implications of genome editing yields much stronger conclusions than they draw. Rather than being merely 'morally permissible', many instances of genome editing will be moral imperatives.
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Affiliation(s)
- Christopher Gyngell
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | | | - Julian Savulescu
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Faculty of Philosophy, Oxford Uehiro Centre for Practical Ethics, Oxford, UK
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30
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Zhang Y, Li Y, Li T, Shen X, Zhu T, Tao Y, Li X, Wang D, Ma Q, Hu Z, Liu J, Ruan J, Cai J, Wang HY, Lu X. Genetic Load and Potential Mutational Meltdown in Cancer Cell Populations. Mol Biol Evol 2019; 36:541-552. [PMID: 30649444 DOI: 10.1093/molbev/msy231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Large genomes with elevated mutation rates are prone to accumulating deleterious mutations more rapidly than natural selection can purge (Muller's ratchet). As a consequence, it may lead to the extinction of small populations. Relative to most unicellular organisms, cancer cells, with large and nonrecombining genome and high mutation rate, could be particularly susceptible to such "mutational meltdown." However, the most common type of mutation in organismal evolution, namely, deleterious mutation, has received relatively little attention in the cancer biology literature. Here, by monitoring single-cell clones from HeLa cell lines, we characterize deleterious mutations that retard the rate of cell proliferation. The main mutation events are copy number variations (CNVs), which, estimated from fitness data, happen at a rate of 0.29 event per cell division on average. The mean fitness reduction, estimated reaching 18% per mutation, is very high. HeLa cell populations therefore have very substantial genetic load and, at this level, natural population would likely face mutational meltdown. We suspect that HeLa cell populations may avoid extinction only after the population size becomes large enough. Because CNVs are common in most cell lines and tumor tissues, the observations hint at cancer cells' vulnerability, which could be exploited by therapeutic strategies.
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Affiliation(s)
- Yuezheng Zhang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Yawei Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xu Shen
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Tianqi Zhu
- National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Yong Tao
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Xueying Li
- School of Life Sciences, Peking University, Beijing, China
| | - Di Wang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Qin Ma
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Hu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Jialin Liu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Jue Ruan
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Jun Cai
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Xuemei Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
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31
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Abstract
Mutation provides the ultimate source of all new alleles in populations, including variants that cause disease and fuel adaptation. Recent whole genome sequencing studies have uncovered variation in the mutation rate among individuals and differences in the relative frequency of specific nucleotide changes (the mutation spectrum) between populations. Although parental age is a major driver of differences in overall mutation rate among individuals, the causes of variation in the mutation spectrum remain less well understood. Here, I use high-quality whole genome sequences from 29 inbred laboratory mouse strains to explore the root causes of strain variation in the mutation spectrum. My analysis leverages the unique, mosaic patterns of genetic relatedness among inbred mouse strains to identify strain private variants residing on haplotypes shared between multiple strains due to their recent descent from a common ancestor. I show that these strain-private alleles are strongly enriched for recent de novo mutations and lack signals of widespread purifying selection, suggesting their faithful recapitulation of the spontaneous mutation landscape in single strains. The spectrum of strain-private variants varies significantly among inbred mouse strains reared under standardized laboratory conditions. This variation is not solely explained by strain differences in age at reproduction, raising the possibility that segregating genetic differences affect the constellation of new mutations that arise in a given strain. Collectively, these findings imply the action of remarkably precise nucleotide-specific genetic mechanisms for tuning the de novo mutation landscape in mammals and underscore the genetic complexity of mutation rate control.
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32
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Ohno M. Spontaneous de novo germline mutations in humans and mice: rates, spectra, causes and consequences. Genes Genet Syst 2019; 94:13-22. [DOI: 10.1266/ggs.18-00015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Mizuki Ohno
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Science, Kyushu University
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33
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Chain FJJ, Flynn JM, Bull JK, Cristescu ME. Accelerated rates of large-scale mutations in the presence of copper and nickel. Genome Res 2019; 29:64-73. [PMID: 30487211 PMCID: PMC6314161 DOI: 10.1101/gr.234724.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
Mutation rate variation has been under intense investigation for decades. Despite these efforts, little is known about the extent to which environmental stressors accelerate mutation rates and influence the genetic load of populations. Moreover, most studies on stressors have focused on unicellular organisms and point mutations rather than large-scale deletions and duplications (copy number variations [CNVs]). We estimated mutation rates in Daphnia pulex exposed to low levels of environmental stressors as well as the effect of selection on de novo mutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103 generations of MA propagation, we sequenced 60 genomes and found significantly accelerated rates of deletions and duplications in MA lines exposed to ecologically relevant concentrations of metals. Whereas control lines had gene deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10-6 per gene per generation), the presence of nickel and copper increased these rates fourfold. The realized mutation rate under selection was reduced to 0.4× that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous recombination associated with regions of DNA fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand breaks with higher CNV rates. Our findings suggest that environmental stress, in particular multiple stressors, can have profound effects on large-scale mutation rates and mutational load of multicellular organisms.
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Affiliation(s)
- Frédéric J J Chain
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Jullien M Flynn
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - James K Bull
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
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34
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Katju V, Bergthorsson U. Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches. Genome Biol Evol 2019; 11:136-165. [PMID: 30476040 PMCID: PMC6330053 DOI: 10.1093/gbe/evy252] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels-the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
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35
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Caution, Overload: The Troubled Past of Genetic Load. Genetics 2018; 210:747-755. [PMID: 30401761 DOI: 10.1534/genetics.118.301093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/22/2018] [Indexed: 11/18/2022] Open
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36
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You W, Henneberg M. Relaxed natural selection contributes to global obesity increase more in males than in females due to more environmental modifications in female body mass. PLoS One 2018; 13:e0199594. [PMID: 30021019 PMCID: PMC6051589 DOI: 10.1371/journal.pone.0199594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/11/2018] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE Relaxed natural selection, measured by Biological State Index (Ibs), results in unfavourable genes/mutations accumulation in population. Obesity is partly heritable. We aim to examine and compare the effects of relaxed natural selection on male and female obesity prevalence. METHODS Data for 191 countries of the world were captured for this ecological study. Curvilinear regressions, bivariate and partial correlations, linear mixed models and multivariate linear regression analyses were used to examine the relationship between Ibs and sex-specific obesity prevalence. Per capita GDP, urbanization and caloric intake were controlled for as the confounding factors. Fisher r-to-z transformation, R2 increment in multivariate regression and F-test were used to compare the correlations. RESULTS Curvilinear regressions, bivariate and partial correlations (controlled for GDP, urbanization and calories) revealed that Ibs was significantly correlated to obesity prevalence of both sexes, but significantly stronger to male than to female obesity prevalence. Curvilinear regression models also showed strong correlations. Mixed linear models, with effects of GDP, urbanisation and caloric intake controlled for, showed that male and female average obesity prevalence rates were significantly higher in countries with greater Ibs value than their equivalents in countries with lower Ibs. Between higher and lower Ibs countries, the gap of male obesity prevalence is 60% greater than the gap of female obesity prevalence. Stepwise multiple regression identified that Ibs was a significant predictor of obesity prevalence of both sexes. Multivariate regression showed that, adding Ibs as an obesity predictor, R2 increment in male model was significantly greater than in female model. CONCLUSIONS Relaxed natural selection may drive males and females to accumulate metabolic faulty genes equally. Probably due to greater environmental, personal intervention in regulating female body mass, relaxed natural selection shows less contributing effects to female obesity prevalence than to male obesity prevalence. Gene therapy to prevent obesity may need to be also taken into account.
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Affiliation(s)
- Wenpeng You
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Maciej Henneberg
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
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37
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Basener WF, Sanford JC. The fundamental theorem of natural selection with mutations. J Math Biol 2018; 76:1589-1622. [PMID: 29116373 PMCID: PMC5906570 DOI: 10.1007/s00285-017-1190-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/10/2017] [Indexed: 02/01/2023]
Abstract
The mutation-selection process is the most fundamental mechanism of evolution. In 1935, R. A. Fisher proved his fundamental theorem of natural selection, providing a model in which the rate of change of mean fitness is equal to the genetic variance of a species. Fisher did not include mutations in his model, but believed that mutations would provide a continual supply of variance resulting in perpetual increase in mean fitness, thus providing a foundation for neo-Darwinian theory. In this paper we re-examine Fisher's Theorem, showing that because it disregards mutations, and because it is invalid beyond one instant in time, it has limited biological relevance. We build a differential equations model from Fisher's first principles with mutations added, and prove a revised theorem showing the rate of change in mean fitness is equal to genetic variance plus a mutational effects term. We refer to our revised theorem as the fundamental theorem of natural selection with mutations. Our expanded theorem, and our associated analyses (analytic computation, numerical simulation, and visualization), provide a clearer understanding of the mutation-selection process, and allow application of biologically realistic parameters such as mutational effects. The expanded theorem has biological implications significantly different from what Fisher had envisioned.
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Affiliation(s)
- William F Basener
- Rochester Institute of Technology, 1 Lomb Memorial Drive, Rochester, NY, 14623, USA.
| | - John C Sanford
- Horticulture Section, NYSAES, 630 West North Street, Geneva, New York, 14456, USA
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38
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Woodley of Menie MA, Fernandes HB, Kanazawa S, Dutton E. Sinistrality is associated with (slightly) lower general intelligence: A data synthesis and consideration of the secular trend in handedness. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2018; 69:118-126. [DOI: 10.1016/j.jchb.2018.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/14/2018] [Indexed: 01/23/2023]
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39
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Staub K, Henneberg M, Galassi FM, Eppenberger P, Haeusler M, Morozova I, Rühli FJ, Bender N. Increasing variability of body mass and health correlates in Swiss conscripts, a possible role of relaxed natural selection? Evol Med Public Health 2018; 2018:116-126. [PMID: 29942512 PMCID: PMC6007356 DOI: 10.1093/emph/eoy012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 04/23/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND AND OBJECTIVES The body mass index (BMI) is an established anthropometric index for the development of obesity-related conditions. However, little is known about the distribution of BMI within a population, especially about this distribution's temporal change. Here, we analysed changes in the distribution of height, weight and BMI over the past 140 years based on data of Swiss conscripts and tested for correlations between anthropometric data and standard blood parameters. METHODS Height and weight were measured in 59 504 young Swiss males aged 18-19 years during conscription in 1875-79, 1932-36, 1994 and 2010-12. For 65% of conscripts in 2010-12, results of standard blood analysis were available. We calculated descriptive statistics of the distribution of height, weight and BMI over the four time periods and tested for associations between BMI and metabolic parameters. RESULTS Average and median body height, body weight and BMI increased over time. Height did no longer increase between 1994 and 2010-12, while weight and BMI still increased over these two decades. Variability ranges of weight and BMI increased over time, while variation of body height remained constant. Elevated levels of metabolic and inflammatory blood parameters were found at both ends of BMI distribution. CONCLUSIONS AND IMPLICATIONS Both overweight and underweight subgroups showed similar changes in inflammation parameters, pointing toward related metabolic deficiencies in both conditions. In addition to environmental influences, our results indicate a potential role of relaxed natural selection on genes affecting metabolism and body composition.
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Affiliation(s)
- Kaspar Staub
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Maciej Henneberg
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Francesco M Galassi
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Patrick Eppenberger
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Martin Haeusler
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Frank J Rühli
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Nicole Bender
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
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40
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Arslan RC, Willführ KP, Frans EM, Verweij KJH, Bürkner PC, Myrskylä M, Voland E, Almqvist C, Zietsch BP, Penke L. Relaxed selection and mutation accumulation are best studied empirically: reply to Woodley of Menie et al. Proc Biol Sci 2018; 285:rspb.2018.0092. [PMID: 29467268 PMCID: PMC5832716 DOI: 10.1098/rspb.2018.0092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/31/2018] [Indexed: 01/23/2023] Open
Affiliation(s)
- Ruben C Arslan
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Kai P Willführ
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
| | - Emma M Frans
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karin J H Verweij
- Department of Biological Psychology, VU University, 1081 BT Amsterdam, The Netherlands.,School of Psychology, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | | | - Mikko Myrskylä
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany.,Department of Social Policy, London School of Economics and Political Science, London WC2A 2AE, UK.,Population Research Unit, University of Helsinki, 00100 Helsinki, Finland
| | - Eckart Voland
- Department of Biophilosophy, Justus Liebig University Gießen, 35390 Gießen, Germany
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden.,Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Brendan P Zietsch
- School of Psychology, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.,Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Lars Penke
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, Georg August University Göttingen, 37073 Göttingen, Germany.,Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
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41
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Woodley Of Menie MA, Sarraf MA, Fernandes HBF. Mutation accumulation is still potentially problematic, despite declining paternal age: a comment on Arslan et al. (2017). Proc Biol Sci 2018; 285:rspb.2017.2511. [PMID: 29467263 PMCID: PMC5832703 DOI: 10.1098/rspb.2017.2511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- Michael A Woodley Of Menie
- Center Leo Apostel for Interdisciplinary Studies, Vrije Universiteit Brussel, Brussels, Belgium .,Unz Foundation Junior Fellow, Unz Foundation, Palo Alto, CA, USA
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42
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43
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Mutation, Eugenics, and the Boundaries of Science. Genetics 2017; 204:825-827. [PMID: 27729497 DOI: 10.1534/genetics.116.194621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/08/2016] [Indexed: 11/18/2022] Open
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44
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Chowell D, Napier J, Gupta R, Anderson KS, Maley CC, Sayres MAW. Modeling the Subclonal Evolution of Cancer Cell Populations. Cancer Res 2017; 78:830-839. [PMID: 29187407 DOI: 10.1158/0008-5472.can-17-1229] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/21/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022]
Abstract
Increasing evidence shows that tumor clonal architectures are often the consequence of a complex branching process, yet little is known about the expected dynamics and extent to which these divergent subclonal expansions occur. Here, we develop and implement more than 88,000 instances of a stochastic evolutionary model simulating genetic drift and neoplastic progression. Under different combinations of population genetic parameter values, including those estimated for colorectal cancer and glioblastoma multiforme, the distribution of sizes of subclones carrying driver mutations had a heavy right tail at the time of tumor detection, with only 1 to 4 dominant clones present at ≥10% frequency. In contrast, the vast majority of subclones were present at <10% frequency, many of which had higher fitness than currently dominant clones. The number of dominant clones (≥10% frequency) in a tumor correlated strongly with the number of subclones (<10% of the tumor). Overall, these subclones were frequently below current standard detection thresholds, frequently harbored treatment-resistant mutations, and were more common in slow-growing tumors.Significance: The model presented in this paper addresses tumor heterogeneity by framing expectations for the number of resistant subclones in a tumor, with implications for future studies of the evolution of therapeutic resistance. Cancer Res; 78(3); 830-9. ©2017 AACR.
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Affiliation(s)
- Diego Chowell
- Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, Arizona.,Biodesign Institute, Tempe, Arizona
| | | | | | - Karen S Anderson
- Biodesign Institute, Tempe, Arizona.,School of Life Sciences, Tempe, Arizona
| | - Carlo C Maley
- Biodesign Institute, Tempe, Arizona. .,School of Life Sciences, Tempe, Arizona.,Center for Evolution and Cancer, University of California San Francisco, San Francisco, California.,Centre for Evolution and Cancer, Institute of Cancer Research, Sutton, United Kingdom
| | - Melissa A Wilson Sayres
- Biodesign Institute, Tempe, Arizona. .,School of Life Sciences, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
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45
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46
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Arslan RC, Willführ KP, Frans EM, Verweij KJH, Bürkner PC, Myrskylä M, Voland E, Almqvist C, Zietsch BP, Penke L. Older fathers' children have lower evolutionary fitness across four centuries and in four populations. Proc Biol Sci 2017; 284:rspb.2017.1562. [PMID: 28904145 DOI: 10.1101/042788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/07/2017] [Indexed: 05/25/2023] Open
Abstract
Higher paternal age at offspring conception increases de novo genetic mutations. Based on evolutionary genetic theory we predicted older fathers' children, all else equal, would be less likely to survive and reproduce, i.e. have lower fitness. In sibling control studies, we find support for negative paternal age effects on offspring survival and reproductive success across four large populations with an aggregate N > 1.4 million. Three populations were pre-industrial (1670-1850) Western populations and showed negative paternal age effects on infant survival and offspring reproductive success. In twentieth-century Sweden, we found minuscule paternal age effects on survival, but found negative effects on reproductive success. Effects survived tests for key competing explanations, including maternal age and parental loss, but effects varied widely over different plausible model specifications and some competing explanations such as diminishing paternal investment and epigenetic mutations could not be tested. We can use our findings to aid in predicting the effect increasingly older parents in today's society will have on their children's survival and reproductive success. To the extent that we succeeded in isolating a mutation-driven effect of paternal age, our results can be understood to show that de novo mutations reduce offspring fitness across populations and time periods.
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Affiliation(s)
- Ruben C Arslan
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
| | - Kai P Willführ
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
| | - Emma M Frans
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karin J H Verweij
- Department of Biological Psychology, VU University, 1081 BT Amsterdam, The Netherlands
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | - Mikko Myrskylä
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
- Department of Social Policy, London School of Economics and Political Science, London WC2A 2AE, UK
- Population Research Unit, University of Helsinki, 00100 Helsinki, Finland
| | - Eckart Voland
- Department of Biophilosophy, Justus Liebig University Gießen, 35390 Gießen, Germany
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Brendan P Zietsch
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Lars Penke
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
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47
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Arslan RC, Willführ KP, Frans EM, Verweij KJH, Bürkner PC, Myrskylä M, Voland E, Almqvist C, Zietsch BP, Penke L. Older fathers' children have lower evolutionary fitness across four centuries and in four populations. Proc Biol Sci 2017; 284:20171562. [PMID: 28904145 PMCID: PMC5597845 DOI: 10.1098/rspb.2017.1562] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022] Open
Abstract
Higher paternal age at offspring conception increases de novo genetic mutations. Based on evolutionary genetic theory we predicted older fathers' children, all else equal, would be less likely to survive and reproduce, i.e. have lower fitness. In sibling control studies, we find support for negative paternal age effects on offspring survival and reproductive success across four large populations with an aggregate N > 1.4 million. Three populations were pre-industrial (1670-1850) Western populations and showed negative paternal age effects on infant survival and offspring reproductive success. In twentieth-century Sweden, we found minuscule paternal age effects on survival, but found negative effects on reproductive success. Effects survived tests for key competing explanations, including maternal age and parental loss, but effects varied widely over different plausible model specifications and some competing explanations such as diminishing paternal investment and epigenetic mutations could not be tested. We can use our findings to aid in predicting the effect increasingly older parents in today's society will have on their children's survival and reproductive success. To the extent that we succeeded in isolating a mutation-driven effect of paternal age, our results can be understood to show that de novo mutations reduce offspring fitness across populations and time periods.
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Affiliation(s)
- Ruben C Arslan
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
| | - Kai P Willführ
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
| | - Emma M Frans
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karin J H Verweij
- Department of Biological Psychology, VU University, 1081 BT Amsterdam, The Netherlands
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | - Mikko Myrskylä
- Max Planck Institute for Demographic Research, 18057 Rostock, Germany
- Department of Social Policy, London School of Economics and Political Science, London WC2A 2AE, UK
- Population Research Unit, University of Helsinki, 00100 Helsinki, Finland
| | - Eckart Voland
- Department of Biophilosophy, Justus Liebig University Gießen, 35390 Gießen, Germany
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Brendan P Zietsch
- School of Psychology, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Lars Penke
- Biological Personality Psychology, Georg Elias Müller Institute of Psychology, University of Göttingen, 37073 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37073 Göttingen, Germany
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48
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You W, Henneberg M. Cancer incidence increasing globally: The role of relaxed natural selection. Evol Appl 2017; 11:140-152. [PMID: 29387151 PMCID: PMC5775494 DOI: 10.1111/eva.12523] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/20/2017] [Indexed: 12/21/2022] Open
Abstract
Cancer incidence increase has multiple aetiologies. Mutant alleles accumulation in populations may be one of them due to strong heritability of many cancers. The opportunity for the operation of natural selection has decreased in the past ~150 years because of reduction in mortality and fertility. Mutation‐selection balance may have been disturbed in this process and genes providing background for some cancers may have been accumulating in human gene pools. Worldwide, based on the WHO statistics for 173 countries the index of the opportunity for selection is strongly inversely correlated with cancer incidence in peoples aged 0–49 years and in people of all ages. This relationship remains significant when gross domestic product per capita (GDP), life expectancy of older people (e50), obesity, physical inactivity, smoking and urbanization are kept statistically constant for fifteen (15) of twenty‐seven (27) individual cancers incidence rates. Twelve (12) cancers which are not correlated with relaxed natural selection after considering the six potential confounders are largely attributable to external causes like viruses and toxins. Ratios of the average cancer incidence rates of the 10 countries with lowest opportunities for selection to the average cancer incidence rates of the 10 countries with highest opportunities for selection are 2.3 (all cancers at all ages), 2.4 (all cancers in 0–49 years age group), 5.7 (average ratios of strongly genetically based cancers) and 2.1 (average ratios of cancers with less genetic background).
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Affiliation(s)
- Wenpeng You
- Biological Anthropology and Comparative Anatomy Unit Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Maciej Henneberg
- Biological Anthropology and Comparative Anatomy Unit Adelaide Medical School The University of Adelaide Adelaide SA Australia.,Institute of Evolutionary Medicine University of Zurich Zurich Switzerland
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49
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Riordan JD, Nadeau JH. From Peas to Disease: Modifier Genes, Network Resilience, and the Genetics of Health. Am J Hum Genet 2017; 101:177-191. [PMID: 28777930 PMCID: PMC5544383 DOI: 10.1016/j.ajhg.2017.06.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Phenotypes are rarely consistent across genetic backgrounds and environments, but instead vary in many ways depending on allelic variants, unlinked genes, epigenetic factors, and environmental exposures. In the extreme, individuals carrying the same causal DNA sequence variant but on different backgrounds can be classified as having distinct conditions. Similarly, some individuals that carry disease alleles are nevertheless healthy despite affected family members in the same environment. These genetic background effects often result from the action of so-called "modifier genes" that modulate the phenotypic manifestation of target genes in an epistatic manner. While complicating the prospects for gene discovery and the feasibility of mechanistic studies, such effects are opportunities to gain a deeper understanding of gene interaction networks that provide organismal form and function as well as resilience to perturbation. Here, we review the principles of modifier genetics and assess progress in studies of modifier genes and their targets in both simple and complex traits. We propose that modifier effects emerge from gene interaction networks whose structure and function vary with genetic background and argue that these effects can be exploited as safe and effective ways to prevent, stabilize, and reverse disease and dysfunction.
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Affiliation(s)
- Jesse D Riordan
- Pacific Northwest Research Institute, Seattle, WA 98122, USA.
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA 98122, USA.
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50
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Lynch M, Ackerman MS, Gout JF, Long H, Sung W, Thomas WK, Foster PL. Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet 2017; 17:704-714. [PMID: 27739533 DOI: 10.1038/nrg.2016.104] [Citation(s) in RCA: 438] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Matthew S Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Hongan Long
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
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