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Wang X, Heckel G. Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles. Genome Res 2024; 34:851-862. [PMID: 38955466 PMCID: PMC11293545 DOI: 10.1101/gr.278487.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
Island populations often experience different ecological and demographic conditions than their counterparts on the continent, resulting in divergent evolutionary forces affecting their genomes. Random genetic drift and selection both may leave their imprints on island populations, although the relative impact depends strongly on the specific conditions. Here we address their contributions to the island syndrome in a rodent with an unusually clear history of isolation. Common voles (Microtus arvalis) were introduced by humans on the Orkney archipelago north of Scotland >5000 years ago and rapidly evolved to exceptionally large size. Our analyses show that the genomes of Orkney voles were dominated by genetic drift, with extremely low diversity, variable Tajima's D, and very high divergence from continental conspecifics. Increased d N/d S ratios over a wide range of genes in Orkney voles indicated genome-wide relaxation of purifying selection. We found evidence of hard sweeps on key genes of the lipid metabolism pathway only in continental voles. The marked increase of body size in Orkney-a typical phenomenon of the island syndrome-may thus be associated to the relaxation of positive selection on genes related to this pathway. On the other hand, a hard sweep on immune genes of Orkney voles likely reflects the divergent ecological conditions and possibly the history of human introduction. The long-term isolated Orkney voles show that adaptive changes may still impact the evolutionary trajectories of such populations despite the pervasive consequences of genetic drift at the genome level.
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Affiliation(s)
- Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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2
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Srivastava K, Yin Q, Makuria AT, Rios M, Gebremedhin A, Flegel WA. CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities. Transfusion 2024; 64:1296-1305. [PMID: 38817044 PMCID: PMC11251854 DOI: 10.1111/trf.17869] [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: 11/18/2023] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND CD59 deficiency due to rare germline variants in the CD59 gene causes disabilities, ischemic strokes, neuropathy, and hemolysis. CD59 deficiency due to common somatic variants in the PIG-A gene in hematopoietic stem cells causes paroxysmal nocturnal hemoglobinuria. The ISBT database lists one nonsense and three missense germline variants that are associated with the CD59-null phenotype. To analyze the genetic diversity of the CD59 gene, we determined long-range CD59 haplotypes among individuals from different ethnicities. METHODS We determined a 22.7 kb genomic fragment of the CD59 gene in 113 individuals using next-generation sequencing (NGS), which covered the whole NM_203330.2 mRNA transcript of 7796 base pairs. Samples came from an FDA reference repository and our Ethiopia study cohorts. The raw genotype data were computationally phased into individual haplotype sequences. RESULTS Nucleotide sequencing of the CD59 gene of 226 chromosomes identified 216 positions with single nucleotide variants. Only three haplotypes were observed in homozygous form, which allowed us to assign them unambiguously as experimentally verified CD59 haplotypes. They were also the most frequent haplotypes among both cohorts. An additional 140 haplotypes were imputed computationally. DISCUSSION We provided a large set of haplotypes and proposed three verified long-range CD59 reference sequences, based on a population approach, using a generalizable rationale for our choice. Correct long-range haplotypes are useful as template sequences for allele calling in high-throughput NGS and precision medicine approaches, thus enhancing the reliability of clinical diagnostics. Long-range haplotypes can also be used to evaluate the influence of genetic variation on the risk of transfusion reactions or diseases.
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Affiliation(s)
- Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Qinan Yin
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Addisalem Taye Makuria
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
- Department of Pathology and Laboratory Services, ECU Health Medical Center, Greenville, NC, USA
| | - Maria Rios
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Amha Gebremedhin
- School of Medicine, College of Health Sciences, Addis Ababa University, Ethiopia
| | - Willy Albert Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
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3
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Laurent R, Gineau L, Utge J, Lafosse S, Phoeung CL, Hegay T, Olaso R, Boland A, Deleuze JF, Toupance B, Heyer E, Leutenegger AL, Chaix R. Measuring the Efficiency of Purging by non-random Mating in Human Populations. Mol Biol Evol 2024; 41:msae094. [PMID: 38839045 PMCID: PMC11184347 DOI: 10.1093/molbev/msae094] [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: 10/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.
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Affiliation(s)
- Romain Laurent
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Laure Gineau
- IRD, MERIT, Université Paris Cité, 75006 Paris, France
| | - José Utge
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Sophie Lafosse
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Tatyana Hegay
- Laboratory of Genome-cell technology, Institute of Immunology and Human genomics, Academy of Sciences, Tashkent, Uzbekistan
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Bruno Toupance
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
- Eco-Anthropologie, Université Paris Cité, 75006 Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Raphaëlle Chaix
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
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4
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Cheung K, Amos TG, Shine R, DeVore JL, Ducatez S, Edwards RJ, Rollins LA. Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory. Ecol Evol 2024; 14:e11115. [PMID: 38435005 PMCID: PMC10909579 DOI: 10.1002/ece3.11115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.
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Affiliation(s)
- Kelton Cheung
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Timothy G. Amos
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Rick Shine
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- Univ. Polynésie FrancaiseUMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Simon Ducatez
- Institut de Recherche pour le Développement (IRD)UMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Richard J. Edwards
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
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5
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Lucas-Sánchez M, Abdeli A, Bekada A, Calafell F, Benhassine T, Comas D. The Impact of Recent Demography on Functional Genetic Variation in North African Human Groups. Mol Biol Evol 2024; 41:msad283. [PMID: 38152862 PMCID: PMC10783648 DOI: 10.1093/molbev/msad283] [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: 05/22/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing is particularly relevant to determine the effects of these demographic events on current-day North Africans' genomes, since it allows to focus on those parts of the genome that are more likely to have direct biomedical consequences. Whole-exome sequencing can also be used to assess the effect of recent demography in functional genetic variation and the efficacy of natural selection, a long-lasting debate. In the present work, we use newly generated whole-exome sequencing and genome-wide array genotypes to investigate the effect of demography in functional variation in 7 North African populations, considering both cultural and demographic differences and with a special focus on Amazigh (plur. Imazighen) groups. We detect genetic differences among populations related to their degree of isolation and the presence of bottlenecks in their recent history. We find differences in the functional part of the genome that suggest a relaxation of purifying selection in the more isolated groups, allowing for an increase of putatively damaging variation. Our results also show a shift in mutational load coinciding with major demographic events in the region and reveal differences within and between cultural and geographic groups.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Amine Abdeli
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Asmahan Bekada
- Département de Biotechnologie, Faculté des Sciences de la Nature et de la Vie, Université Oran 1 (Ahmad Ben Bella), Oran, Algeria
| | - Francesc Calafell
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Traki Benhassine
- Faculté des Sciences Biologiques, Laboratoire de Biologie Cellulaire et Moléculaire, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - David Comas
- Departament de Medicina i Ciències de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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Irving MR, Goolsby EW, Stanford H, Lim-Hing S, Urrea M, Mason CM. Temperature alters the toxicological impacts of plant terpenoids on the polyphagous model herbivore Vanessa cardui. J Chem Ecol 2023; 49:666-680. [PMID: 37695522 PMCID: PMC10781811 DOI: 10.1007/s10886-023-01449-8] [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: 01/19/2023] [Revised: 07/30/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
Terpenes are a major class of secondary metabolites present in all plants, and long hypothesized to have diversified in response to specific plant-herbivore interactions. Herbivory is a major biotic interaction that plays out across broad temporal and spatial scales that vary dramatically in temperature regimes, both due to climatic variation across geographic locations as well as the effect of seasonality. In addition, there is an emerging understanding that global climate change will continue to alter the temperature regimes of nearly every habitat on Earth over the coming centuries. Regardless of source, variation in temperature may influence herbivory, in particular via changes in the efficacy and impacts of plant defensive chemistry. This study aims to characterize temperature-driven variation in toxicological effects across several structural classes of terpenes in the model herbivore Vanessa cardui, the painted lady butterfly. We observed a general increase in monoterpene toxicity to larvae, pupa, and adults at higher temperatures, as well as an increase in development time as terpene concentration increased. Results obtained from this study yield insights into possible drivers of seasonal variation in plant terpene production as well as inform effects of rising global temperatures on plant-insect interactions. In the context of other known effects of climate change on plant-herbivore interactions like carbon fertilization and compensatory feeding, temperature-driven changes in plant chemical defense efficacy may further complicate the prediction of climate change impacts on the fundamental ecological process of herbivory.
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Affiliation(s)
- Mari R Irving
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA.
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
| | - Eric W Goolsby
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Hannah Stanford
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Simone Lim-Hing
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Maria Urrea
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Chase M Mason
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
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7
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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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8
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Rougemont Q, Leroy T, Rondeau EB, Koop B, Bernatchez L. Allele surfing causes maladaptation in a Pacific salmon of conservation concern. PLoS Genet 2023; 19:e1010918. [PMID: 37683018 PMCID: PMC10545117 DOI: 10.1371/journal.pgen.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 10/02/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.
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Affiliation(s)
- Quentin Rougemont
- Centre d’Ecologie Fonctionnelle et Evolutive, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Auzeville- Tolosane, France
| | - Eric B. Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, Canada
| | - Ben Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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9
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Antinucci M, Comas D, Calafell F. Population history modulates the fitness effects of Copy Number Variation in the Roma. Hum Genet 2023; 142:1327-1343. [PMID: 37311904 PMCID: PMC10449987 DOI: 10.1007/s00439-023-02579-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
We provide the first whole genome Copy Number Variant (CNV) study addressing Roma, along with reference populations from South Asia, the Middle East and Europe. Using CNV calling software for short-read sequence data, we identified 3171 deletions and 489 duplications. Taking into account the known population history of the Roma, as inferred from whole genome nucleotide variation, we could discern how this history has shaped CNV variation. As expected, patterns of deletion variation, but not duplication, in the Roma followed those obtained from single nucleotide polymorphisms (SNPs). Reduced effective population size resulting in slightly relaxed natural selection may explain our observation of an increase in intronic (but not exonic) deletions within Loss of Function (LoF)-intolerant genes. Over-representation analysis for LoF-intolerant gene sets hosting intronic deletions highlights a substantial accumulation of shared biological processes in Roma, intriguingly related to signaling, nervous system and development features, which may be related to the known profile of private disease in the population. Finally, we show the link between deletions and known trait-related SNPs reported in the genome-wide association study (GWAS) catalog, which exhibited even frequency distributions among the studied populations. This suggests that, in general human populations, the strong association between deletions and SNPs associated to biomedical conditions and traits could be widespread across continental populations, reflecting a common background of potentially disease/trait-related CNVs.
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Affiliation(s)
- Marco Antinucci
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Comas
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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Shao C, Sun S, Liu K, Wang J, Li S, Liu Q, Deagle BE, Seim I, Biscontin A, Wang Q, Liu X, Kawaguchi S, Liu Y, Jarman S, Wang Y, Wang HY, Huang G, Hu J, Feng B, De Pittà C, Liu S, Wang R, Ma K, Ying Y, Sales G, Sun T, Wang X, Zhang Y, Zhao Y, Pan S, Hao X, Wang Y, Xu J, Yue B, Sun Y, Zhang H, Xu M, Liu Y, Jia X, Zhu J, Liu S, Ruan J, Zhang G, Yang H, Xu X, Wang J, Zhao X, Meyer B, Fan G. The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights. Cell 2023; 186:1279-1294.e19. [PMID: 36868220 DOI: 10.1016/j.cell.2023.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 03/05/2023]
Abstract
Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.
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Affiliation(s)
- Changwei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiqiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Jiahao Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Shuo Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian National Fish Collection, National Research Collections Australia, Hobart, TAS 7000, Australia; Australian Antarctic Division, Channel Highway, Kingston, TAS 7050, Australia
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | | | - Qian Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Beijing, Beijing 102601, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia
| | - So Kawaguchi
- Australian Antarctic Division, Channel Highway, Kingston, TAS 7050, Australia
| | - Yalin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6009, Australia
| | - Yue Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
| | - Hong-Yan Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | | | - Jiang Hu
- Nextomics Biosciences Institute, Wuhan, Hubei 430073, China
| | - Bo Feng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | | | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Rui Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Kailong Ma
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yiping Ying
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Gabrielle Sales
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Tao Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xinliang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yunxia Zhao
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xiancai Hao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yang Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jiakun Xu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Bowen Yue
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yanxu Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Mengyang Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yuyan Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong 252000, China
| | - Jiancheng Zhu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Shufang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; James D. Watson Institute of Genome Science, Hangzhou 310058, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jun Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xianyong Zhao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Bettina Meyer
- Section Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, Carlvon Ossietzky University of Oldenburg, 26111 Oldenburg, Germany; Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, 26129 Oldenburg, Germany.
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China; Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen 518120, China.
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11
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Carlberg C. Nutrigenomics in the context of evolution. Redox Biol 2023; 62:102656. [PMID: 36933390 PMCID: PMC10036735 DOI: 10.1016/j.redox.2023.102656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.
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Affiliation(s)
- Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Juliana Tuwima 10, PL-10748, Olsztyn, Poland; School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211, Kuopio, Finland.
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12
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Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annu Rev Anim Biosci 2023; 11:93-114. [PMID: 36332644 PMCID: PMC9933137 DOI: 10.1146/annurev-animal-080522-093311] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.
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Affiliation(s)
- Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, California, USA;
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Stella C Yuan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , , .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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13
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Kreger J, Brown D, Komarova NL, Wodarz D, Pritchard J. The role of migration in mutant dynamics in fragmented populations. J Evol Biol 2023; 36:444-460. [PMID: 36514852 PMCID: PMC10108075 DOI: 10.1111/jeb.14131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/16/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022]
Abstract
Mutant dynamics in fragmented populations have been studied extensively in evolutionary biology. Yet, open questions remain, both experimentally and theoretically. Some of the fundamental properties predicted by models still need to be addressed experimentally. We contribute to this by using a combination of experiments and theory to investigate the role of migration in mutant distribution. In the case of neutral mutants, while the mean frequency of mutants is not influenced by migration, the probability distribution is. To address this empirically, we performed in vitro experiments, where mixtures of GFP-labelled ("mutant") and non-labelled ("wid-type") murine cells were grown in wells (demes), and migration was mimicked via cell transfer from well to well. In the presence of migration, we observed a change in the skewedness of the distribution of the mutant frequencies in the wells, consistent with previous and our own model predictions. In the presence of de novo mutant production, we used modelling to investigate the level at which disadvantageous mutants are predicted to exist, which has implications for the adaptive potential of the population in case of an environmental change. In panmictic populations, disadvantageous mutants can persist around a steady state, determined by the rate of mutant production and the selective disadvantage (selection-mutation balance). In a fragmented system that consists of demes connected by migration, a steady-state persistence of disadvantageous mutants is also observed, which, however, is fundamentally different from the mutation-selection balance and characterized by higher mutant levels. The increase in mutant frequencies above the selection-mutation balance can be maintained in small ( N < N c ) demes as long as the migration rate is sufficiently small. The migration rate above which the mutants approach the selection-mutation balance decays exponentially with N / N c . The observed increase in the mutant numbers is not explained by the change in the effective population size. Implications for evolutionary processes in diseases are discussed, where the pre-existence of disadvantageous drug-resistant mutant cells or pathogens drives the response of the disease to treatments.
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Affiliation(s)
- Jesse Kreger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA.,Department of Mathematics, University of California Irvine, Irvine, California, USA
| | - Donovan Brown
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institute for the Life Sciences, University Park, Pennsylvania, USA
| | - Natalia L Komarova
- Department of Mathematics, University of California Irvine, Irvine, California, USA
| | - Dominik Wodarz
- Department of Mathematics, University of California Irvine, Irvine, California, USA.,Department of Population Health and Disease Prevention Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, California, USA
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institute for the Life Sciences, University Park, Pennsylvania, USA
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14
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Maier PA, Vandergast AG, Bohonak AJ. Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad ( Anaxyrus canorus). Evol Appl 2023; 16:74-97. [PMID: 36699123 PMCID: PMC9850018 DOI: 10.1111/eva.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/05/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future "Geminate Evolutionary Units" (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo-genomic simulations. Using this process, we delineated conservation units for the Yosemite toad (Anaxyrus canorus), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome-wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection (R 2 ranging from 0.09 to 0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF-North (high winter snowpack with moderate summer rainfall), YF-East (low to moderate snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF-East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, and (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non-model species with genomic data alone and has wide applicability to other declining species.
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Affiliation(s)
- Paul A. Maier
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
- FamilyTreeDNAGene by GeneHoustonTexasUSA
| | - Amy G. Vandergast
- Western Ecological Research CenterU.S. Geological SurveySan DiegoCaliforniaUSA
| | - Andrew J. Bohonak
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
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15
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Jain K, Kaushik S. Joint effect of changing selection and demography on the site frequency spectrum. Theor Popul Biol 2022; 146:46-60. [PMID: 35809866 DOI: 10.1016/j.tpb.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/14/2022] [Accepted: 07/03/2022] [Indexed: 10/17/2022]
Abstract
The site frequency spectrum (SFS) is an important statistic that summarizes the molecular variation in a population, and is used to estimate population-genetic parameters and detect natural selection. Here, we study the SFS in a randomly mating, diploid population in which both the population size and selection coefficient vary periodically with time using a diffusion theory approach, and derive simple analytical expressions for the time-averaged SFS in slowly and rapidly changing environments. We show that for strong selection and in slowly changing environments where the population experiences both positive and negative cycles of the selection coefficient, the time-averaged SFS differs significantly from the equilibrium SFS in a constant environment. The deviation is found to depend on the time spent by the population in the deleterious part of the selection cycle and the phase difference between the selection coefficient and population size, and can be captured by an effective population size.
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Affiliation(s)
- Kavita Jain
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
| | - Sachin Kaushik
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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16
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Labuda D, Harding T, Milot E, Vézina H. The effective family size of immigrant founders predicts their long-term demographic outcome: From Québec settlers to their 20th-century descendants. PLoS One 2022; 17:e0266079. [PMID: 35507549 PMCID: PMC9067642 DOI: 10.1371/journal.pone.0266079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
Population history reconstruction, using extant genetic diversity data, routinely relies on simple demographic models to project the past through ascending genealogical-tree branches. Because genealogy and genetics are intimately related, we traced descending genealogies of the Québec founders to pursue their fate and to assess their contribution to the present-day population. Focusing on the female and male founder lines, we observed important sex-biased immigration in the early colony years and documented a remarkable impact of these early immigrants on the genetic make-up of 20th-century Québec. We estimated the immigrants’ survival ratio as a proportion of lineages found in the 1931–60 Québec to their number introduced within the immigration period. We assessed the effective family size, EFS, of all immigrant parents and their Québec-born descendants. The survival ratio of the earliest immigrants was the highest and declined over centuries in association with the immigrants’ EFS. Parents with high EFS left plentiful married descendants, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. EFS of immigrant founders appears to predict their long-term demographic and, consequently, their genetic outcome. Genealogically inferred immigrants’ "autosomal" genetic contribution to 1931–60 Québec from consecutive immigration periods follow the same yearly pattern as the corresponding maternal and paternal lines. Québec genealogical data offer much broader information on the ancestral diversity distribution than genetic scrutiny of a limited population sample. Genealogically inferred population history could assist studies of evolutionary factors shaping population structure and provide tools to target specific health interventions.
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Affiliation(s)
- Damian Labuda
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, Québec, Canada
- * E-mail:
| | - Tommy Harding
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Emmanuel Milot
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Hélène Vézina
- Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada
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17
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Acosta-Uribe J, Aguillón D, Cochran JN, Giraldo M, Madrigal L, Killingsworth BW, Singhal R, Labib S, Alzate D, Velilla L, Moreno S, García GP, Saldarriaga A, Piedrahita F, Hincapié L, López HE, Perumal N, Morelo L, Vallejo D, Solano JM, Reiman EM, Surace EI, Itzcovich T, Allegri R, Sánchez-Valle R, Villegas-Lanau A, White CL, Matallana D, Myers RM, Browning SR, Lopera F, Kosik KS. A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects. Genome Med 2022; 14:27. [PMID: 35260199 PMCID: PMC8902761 DOI: 10.1186/s13073-022-01035-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders, and enslaved Africans, all of whom passed through a population bottleneck due to widespread infectious diseases that left small isolated local settlements. As a result, the current population reflects multiple founder effects derived from diverse ancestries. METHODS We characterized the role of admixture and founder effects on the origination of the mutational landscape that led to neurodegenerative disorders under these historical circumstances. Genomes from 900 Colombian individuals with Alzheimer's disease (AD) [n = 376], frontotemporal lobar degeneration-motor neuron disease continuum (FTLD-MND) [n = 197], early-onset dementia not otherwise specified (EOD) [n = 73], and healthy participants [n = 254] were analyzed. We examined their global and local ancestry proportions and screened this cohort for deleterious variants in disease-causing and risk-conferring genes. RESULTS We identified 21 pathogenic variants in AD-FTLD related genes, and PSEN1 harbored the majority (11 pathogenic variants). Variants were identified from all three continental ancestries. TREM2 heterozygous and homozygous variants were the most common among AD risk genes (102 carriers), a point of interest because the disease risk conferred by these variants differed according to ancestry. Several gene variants that have a known association with MND in European populations had FTLD phenotypes on a Native American haplotype. Consistent with founder effects, identity by descent among carriers of the same variant was frequent. CONCLUSIONS Colombian demography with multiple mini-bottlenecks probably enhanced the detection of founder events and left a proportionally higher frequency of rare variants derived from the ancestral populations. These findings demonstrate the role of genomically defined ancestry in phenotypic disease expression, a phenotypic range of different rare mutations in the same gene, and further emphasize the importance of inclusiveness in genetic studies.
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Affiliation(s)
- Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - David Aguillón
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Margarita Giraldo
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
- Instituto Neurológico de Colombia (INDEC), Medellín, Colombia
| | - Lucía Madrigal
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Bradley W Killingsworth
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Rijul Singhal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sarah Labib
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Diana Alzate
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Lina Velilla
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Sonia Moreno
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Gloria P García
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Amanda Saldarriaga
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Piedrahita
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Liliana Hincapié
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Hugo E López
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Nithesh Perumal
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Leonilde Morelo
- Department of Internal Medicine, School of Medicine, Universidad del Sinú, Montería, Colombia
| | - Dionis Vallejo
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Juan Marcos Solano
- Department of Neurology, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Ezequiel I Surace
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Tatiana Itzcovich
- Laboratorio de Enfermedades Neurodegenerativas (Fleni-CONICET), Buenos Aires, Argentina
| | - Ricardo Allegri
- Centro de Memoria y Envejecimiento (Fleni-CONICET), Buenos Aires, Argentina
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Andrés Villegas-Lanau
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Charles L White
- Neuropathology Section, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana Matallana
- Instituto de Envejecimiento, Department of Psychiatry, School of Medicine, Pontifical Xaverian University, Bogotá, Colombia
- Department of Mental Health, Hospital Universitario Santa Fe de Bogotá, Bogotá, Colombia
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
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18
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Vecchyo DOD, Lohmueller KE, Novembre J. Haplotype-based inference of the distribution of fitness effects. Genetics 2022; 220:6501446. [PMID: 35100400 PMCID: PMC8982047 DOI: 10.1093/genetics/iyac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/18/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Recent genome sequencing studies with large sample sizes in humans have discovered a vast quantity of low-frequency variants, providing an important source of information to analyze how selection is acting on human genetic variation. In order to estimate the strength of natural selection acting on low-frequency variants, we have developed a likelihood-based method that uses the lengths of pairwise identity-by-state between haplotypes carrying low-frequency variants. We show that in some non-equilibrium populations (such as those that have had recent population expansions) it is possible to distinguish between positive or negative selection acting on a set of variants. With our new framework, one can infer a fixed selection intensity acting on a set of variants at a particular frequency, or a distribution of selection coefficients for standing variants and new mutations. We show an application of our method to the UK10K phased haplotype dataset of individuals.
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Affiliation(s)
- Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, 76230, México
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
| | - Kirk E Lohmueller
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637, United States of America
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19
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Bemmels JB, Mikkelsen EK, Haddrath O, Colbourne RM, Robertson HA, Weir JT. Demographic decline and lineage-specific adaptations characterize New Zealand kiwi. Proc Biol Sci 2021; 288:20212362. [PMID: 34905706 PMCID: PMC8670953 DOI: 10.1098/rspb.2021.2362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/19/2021] [Indexed: 12/24/2022] Open
Abstract
Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi (Apteryx), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation (FST), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.
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Affiliation(s)
- Jordan B. Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada ON M1C 1A4
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
| | - Else K. Mikkelsen
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada ON M1C 1A4
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
| | - Oliver Haddrath
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
- Department of Natural History, Royal Ontario Museum, Toronto, Canada ON M5S 2C6
| | | | | | - Jason T. Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada ON M1C 1A4
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada ON M5S 3B2
- Department of Natural History, Royal Ontario Museum, Toronto, Canada ON M5S 2C6
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20
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A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS One 2021; 16:e0259685. [PMID: 34882683 PMCID: PMC8659316 DOI: 10.1371/journal.pone.0259685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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21
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Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. Sci Rep 2021; 11:21125. [PMID: 34702931 PMCID: PMC8548440 DOI: 10.1038/s41598-021-00576-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
Human populations are genetically affected by their demographic history, which shapes the distribution of their functional genomic variation. However, the genetic impact of recent demography is debated. This issue has been studied in different populations, but never in North Africans, despite their relevant cultural and demographic diversity. In this study we address the question by analyzing new whole-exome sequences from two culturally different Tunisian populations, an isolated Amazigh population and a close non-isolated Arab-speaking population, focusing on the distribution of functional variation. Both populations present clear differences in their variant frequency distribution, in general and for putatively damaging variation. This suggests a relevant effect in the Amazigh population of genetic isolation, drift, and inbreeding, pointing to relaxed purifying selection. We also discover the enrichment in Imazighen of variation associated to specific diseases or phenotypic traits, but the scarce genetic and biomedical data in the region limits further interpretation. Our results show the genomic impact of recent demography and reveal a clear genetic differentiation probably related to culture. These findings highlight the importance of considering cultural and demographic heterogeneity within North Africa when defining population groups, and the need for more data to improve knowledge on the region's health and disease landscape.
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22
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Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo-Mesa A, Bosch E, Calafell F, Quintana-Murci L, Comas D. The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. Mol Biol Evol 2021; 38:2804-2817. [PMID: 33713133 PMCID: PMC8233508 DOI: 10.1093/molbev/msab070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modeled in human populations.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rocio Caro-Consuegra
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Elena Bosch
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Human Genomics and Evolution, Collège de France, Paris, France
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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23
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de Pedro M, Riba M, González-Martínez SC, Seoane P, Bautista R, Claros MG, Mayol M. Demography, genetic diversity and expansion load in the colonizing species Leontodon longirostris (Asteraceae) throughout its native range. Mol Ecol 2021; 30:1190-1205. [PMID: 33452714 DOI: 10.1111/mec.15802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022]
Abstract
Unravelling the evolutionary processes underlying range expansions is fundamental to understand the distribution of organisms, as well as to predict their future responses to environmental change. Predictions for range expansions include a loss of genetic diversity and an accumulation of deleterious alleles along the expansion axis, which can decrease fitness at the range-front (expansion load). In plants, empirical studies supporting expansion load are scarce, and its effects remain to be tested outside a few model species. Leontodon longirostris is a colonizing Asteraceae with a widespread distribution in the Western Mediterranean, providing a particularly interesting system to gain insight into the factors that can enhance or mitigate expansion load. In this study, we produced a first genome draft for the species, covering 418 Mbp (~53% of the genome). Although incomplete, this draft was suitable to design a targeted sequencing of ~1.5 Mbp in 238 L. longirostris plants from 21 populations distributed along putative colonization routes in the Iberian Peninsula. Inferred demographic history supports a range expansion from southern Iberia around 40,000 years ago, reaching northern Iberia around 25,000 years ago. The expansion was accompanied by a loss of genetic diversity and a significant increase in the proportion of putatively deleterious mutations. However, levels of expansion load in L. longirostris were smaller than those found in other plant species, which can be explained, at least partially, by its high dispersal ability, the self-incompatible mating system, and the fact that the expansion occurred along a strong environmental cline.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, Spain.,Univ. Autònoma Barcelona, Cerdanyola del Vallès, Spain
| | | | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, and Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Málaga, Spain.,CIBER de Enfermedades Raras (CIBERER), Málaga, Spain.,Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain
| | - Rocío Bautista
- Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain
| | - Manuel Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, and Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Málaga, Spain.,CIBER de Enfermedades Raras (CIBERER), Málaga, Spain.,Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Málaga, Spain
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24
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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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25
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Galtier N, Rousselle M. How Much Does Ne Vary Among Species? Genetics 2020; 216:559-572. [PMID: 32839240 PMCID: PMC7536855 DOI: 10.1534/genetics.120.303622] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic drift is an important evolutionary force of strength inversely proportional to Ne , the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load - which implies also inferring the distribution of fitness effects of deleterious mutations. To this aim, we analyze the nonsynonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the distribution of fitness effects is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of nonsynonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin's paradox while further questioning the meaning of the Ne parameter in population genomics.
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Affiliation(s)
- Nicolas Galtier
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
| | - Marjolaine Rousselle
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
- Bioinformatics Research Centre, Aarhus University, DK Aarhus, Denmark
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26
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Dauphin B, Wüest RO, Brodbeck S, Zoller S, Fischer MC, Holderegger R, Gugerli F, Rellstab C. Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine. Mol Ecol 2020; 29:1972-1989. [PMID: 32395881 DOI: 10.1111/mec.15467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 01/27/2023]
Abstract
It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, FST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (He ) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.
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Affiliation(s)
| | - Rafael O Wüest
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Sabine Brodbeck
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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27
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Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, Gauthier LD, Brand H, Solomonson M, Watts NA, Rhodes D, Singer-Berk M, England EM, Seaby EG, Kosmicki JA, Walters RK, Tashman K, Farjoun Y, Banks E, Poterba T, Wang A, Seed C, Whiffin N, Chong JX, Samocha KE, Pierce-Hoffman E, Zappala Z, O'Donnell-Luria AH, Minikel EV, Weisburd B, Lek M, Ware JS, Vittal C, Armean IM, Bergelson L, Cibulskis K, Connolly KM, Covarrubias M, Donnelly S, Ferriera S, Gabriel S, Gentry J, Gupta N, Jeandet T, Kaplan D, Llanwarne C, Munshi R, Novod S, Petrillo N, Roazen D, Ruano-Rubio V, Saltzman A, Schleicher M, Soto J, Tibbetts K, Tolonen C, Wade G, Talkowski ME, Neale BM, Daly MJ, MacArthur DG. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 2020; 581:434-443. [PMID: 32461654 PMCID: PMC7334197 DOI: 10.1038/s41586-020-2308-7] [Citation(s) in RCA: 5341] [Impact Index Per Article: 1335.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/26/2020] [Indexed: 12/04/2022]
Abstract
Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes1. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.
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Affiliation(s)
- Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
| | - Laurent C Francioli
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Beryl B Cummings
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica Alföldi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Qingbo Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Ryan L Collins
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Ganna
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Daniel P Birnbaum
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel Rhodes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London and Barts Health NHS Trust, London, UK
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina M England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jack A Kosmicki
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Raymond K Walters
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine Tashman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yossi Farjoun
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arcturus Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Whiffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London, UK
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kaitlin E Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Zachary Zappala
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Vertex Pharmaceuticals Inc, Boston, MA, USA
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Eric Vallabh Minikel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - James S Ware
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London, UK
| | - Christopher Vittal
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Irina M Armean
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Louis Bergelson
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristian Cibulskis
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Miguel Covarrubias
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey Donnelly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Ferriera
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey Gabriel
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeff Gentry
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault Jeandet
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Kaplan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Ruchi Munshi
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sam Novod
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikelle Petrillo
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Roazen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Andrea Saltzman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Molly Schleicher
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose Soto
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Tibbetts
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gordon Wade
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
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28
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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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29
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [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: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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30
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Chen J, Li L, Milesi P, Jansson G, Berlin M, Karlsson B, Aleksic J, Vendramin GG, Lascoux M. Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce. Evol Appl 2019; 12:1539-1551. [PMID: 31462913 PMCID: PMC6708423 DOI: 10.1111/eva.12801] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
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Affiliation(s)
- Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Lili Li
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gunnar Jansson
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Mats Berlin
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk)EkeboSweden
| | - Jelena Aleksic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Giovanni G. Vendramin
- Division of Florence, Institute of Biosciences and BioResourcesNational Research Council (IBBR‐CNR)Sesto FiorentinoItaly
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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31
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Evolution and Genetic Diversity of the k13 Gene Associated with Artemisinin Delayed Parasite Clearance in Plasmodium falciparum. Antimicrob Agents Chemother 2019; 63:AAC.02550-18. [PMID: 31085516 DOI: 10.1128/aac.02550-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/28/2019] [Indexed: 01/19/2023] Open
Abstract
Mutations in the Plasmodium falciparum k13 (Pfk13) gene are linked to delayed parasite clearance in response to artemisinin-based combination therapies (ACTs) in Southeast Asia. To explore the evolutionary rate and constraints acting on this gene, k13 orthologs from species sharing a recent common ancestor with P. falciparum and Plasmodium vivax were analyzed. These comparative studies were followed by genetic polymorphism analyses within P. falciparum using 982 complete Pfk13 sequences from public databases and new data obtained by next-generation sequencing from African and Haitian isolates. Although k13 orthologs evolve at heterogeneous rates, the gene was conserved across the genus, with only synonymous substitutions being found at residues where mutations linked to the delayed parasite clearance phenotype have been reported. This suggests that those residues were under constraint from undergoing nonsynonymous changes during evolution of the genus. No fixed nonsynonymous differences were found between Pfk13 and its orthologs in closely related species found in African apes. This indicates that all nonsynonymous substitutions currently found in Pfk13 are younger than the time of divergence between P. falciparum and its closely related species. At the population level, no mutations linked to delayed parasite clearance were found in our samples from Africa and Haiti. However, there is a high number of single Pfk13 mutations segregating in P. falciparum populations, and two predominant alleles are distributed worldwide. This pattern is discussed in terms of how changes in the efficacy of natural selection, affected by population expansion, may have allowed for the emergence of mutations tolerant to ACTs.
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32
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Kim BY, Huber CD, Lohmueller KE. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet 2018; 14:e1007741. [PMID: 30346959 PMCID: PMC6233928 DOI: 10.1371/journal.pgen.1007741] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/13/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30–75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation. Individuals from distinct populations sometimes will produce fertile offspring and will exchange genetic material in a process called hybridization. Genomes of hybrid individuals often show non-random patterns of hybrid ancestry across the genome, where some regions have a high frequency of ancestry from the second population and other regions have less. Typically, this pattern has been attributed to adaptive introgression, where beneficial genetic variants are passed from one population to the other, or to genomic incompatibilities between these distinct species. However, other mechanisms could lead to these heterogeneous patterns of ancestry in hybrids. Here we use simulations to investigate whether deleterious mutations affect the patterns of introgressed ancestry across genomes. We show that when ancestry from a larger population is added to a smaller population, the ancestry from the larger population dramatically increases in frequency because it carries fewer deleterious mutations. This occurs even in the absence of beneficial mutations in either population. Additionally, we show that differences in sex chromosome evolution relative to autosomes, or differences in mating system, can affect patterns of introgression in similar ways. Our study argues that deleterious mutations should be included in population genetic models used to identify unusual regions of the genome that appear to be under selection in hybrids.
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Affiliation(s)
- Bernard Y. Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Christian D. Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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33
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Morin A, Madore AM, Kwan T, Ban M, Partanen J, Rönnblom L, Syvänen AC, Sawcer S, Stunnenberg H, Lathrop M, Pastinen T, Laprise C. Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits. Eur J Hum Genet 2018; 27:90-101. [PMID: 30206357 PMCID: PMC6303288 DOI: 10.1038/s41431-018-0266-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022] Open
Abstract
The Saguenay–Lac-Saint-Jean (SLSJ) region is located in northeastern Quebec and is known for its unique demographic history and founder effect. As founder populations are enriched with population-specific variants, we characterized the variants distribution in SLSJ and compared it with four European populations (Finnish, Sweden, United Kingdom and France), of which the Finnish population is another founder population. Targeted sequencing of the coding and non-coding immune regulatory regions of the SLSJ asthma familial cohort and the four European populations were performed. Rare and low-frequency coding and non-coding regulatory variants identified in the SLSJ population were then investigated for variant- and gene-level associations with asthma and allergy-related traits (eosinophil percentage, immunoglobulin (Ig) E levels and lung function). Our data showed that (1) rare or deleterious variants were not enriched in the two founder populations as compared with the three non-founder European populations; (2) a larger proportion of founder population-specific variants occurred with higher frequencies; and (3) low-frequency variants appeared to be more deleterious. Furthermore, a rare variant, rs1386931, located in the 3ʹ-UTR of CXCR6 and intron of FYCO1 was found to be associated with eosinophil percentage. Gene-based analyses identified NRP2, MRPL44 and SERPINE2 to be associated with various asthma and allergy-related traits. Our study demonstrated the usefulness of using a founder population to identify new genes associated with asthma and allergy-related traits; thus better understand the genes and pathways implicated in pathophysiology.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Anne-Marie Madore
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jukka Partanen
- Research & Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Lars Rönnblom
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Hendrik Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada.,Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada. .,Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada.
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34
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Torres R, Szpiech ZA, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet 2018; 14:e1007387. [PMID: 29912945 PMCID: PMC6056204 DOI: 10.1371/journal.pgen.1007387] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/23/2018] [Accepted: 04/30/2018] [Indexed: 01/22/2023] Open
Abstract
Natural populations often grow, shrink, and migrate over time. Such demographic processes can affect genome-wide levels of genetic diversity. Additionally, genetic variation in functional regions of the genome can be altered by natural selection, which drives adaptive mutations to higher frequencies or purges deleterious ones. Such selective processes affect not only the sites directly under selection but also nearby neutral variation through genetic linkage via processes referred to as genetic hitchhiking in the context of positive selection and background selection (BGS) in the context of purifying selection. While there is extensive literature examining the consequences of selection at linked sites at demographic equilibrium, less is known about how non-equilibrium demographic processes influence the effects of hitchhiking and BGS. Utilizing a global sample of human whole-genome sequences from the Thousand Genomes Project and extensive simulations, we investigate how non-equilibrium demographic processes magnify and dampen the consequences of selection at linked sites across the human genome. When binning the genome by inferred strength of BGS, we observe that, compared to Africans, non-African populations have experienced larger proportional decreases in neutral genetic diversity in strong BGS regions. We replicate these findings in admixed populations by showing that non-African ancestral components of the genome have also been affected more severely in these regions. We attribute these differences to the strong, sustained/recurrent population bottlenecks that non-Africans experienced as they migrated out of Africa and throughout the globe. Furthermore, we observe a strong correlation between FST and the inferred strength of BGS, suggesting a stronger rate of genetic drift. Forward simulations of human demographic history with a model of BGS support these observations. Our results show that non-equilibrium demography significantly alters the consequences of selection at linked sites and support the need for more work investigating the dynamic process of multiple evolutionary forces operating in concert.
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Affiliation(s)
- Raul Torres
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Zachary A. Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, United States of America
- * E-mail:
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35
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36
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Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina. Proc Natl Acad Sci U S A 2018; 115:816-821. [PMID: 29301967 DOI: 10.1073/pnas.1707492115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.
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37
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Baharian S, Gravel S. On the decidability of population size histories from finite allele frequency spectra. Theor Popul Biol 2018; 120:42-51. [PMID: 29305873 DOI: 10.1016/j.tpb.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/15/2017] [Accepted: 12/20/2017] [Indexed: 10/18/2022]
Abstract
Understanding the historical events that shaped current genomic diversity has applications in historical, biological, and medical research. However, the amount of historical information that can be inferred from genetic data is finite, which leads to an identifiability problem. For example, different historical processes can lead to identical distribution of allele frequencies. This identifiability issue casts a shadow of uncertainty over the results of any study which uses the frequency spectrum to infer past demography. It has been argued that imposing mild 'reasonableness' constraints on demographic histories can enable unique reconstruction, at least in an idealized setting where the length of the genome is nearly infinite. Here, we discuss this problem for finite sample size and genome length. Using the diffusion approximation, we obtain bounds on likelihood differences between similar demographic histories, and use them to construct pairs of very different reasonable histories that produce almost-identical frequency distributions. The finite-genome problem therefore remains poorly determined even among reasonable histories. Where fits to few-parameter models produce narrow parameter confidence intervals, large uncertainties lurk hidden by model assumption.
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Affiliation(s)
- Soheil Baharian
- Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
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38
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Relaxed Selection During a Recent Human Expansion. Genetics 2017; 208:763-777. [PMID: 29187508 DOI: 10.1534/genetics.117.300551] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/22/2017] [Indexed: 01/15/2023] Open
Abstract
Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that: (i) both new and low-frequency variants are significantly more deleterious in front than in core individuals, (ii) equally deleterious mutations are at higher frequencies in front individuals, and (iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past six to nine generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection mainly due to higher rates of genetic drift on the wave front. Demographic inference and modeling of the evolution of rare variants suggest lower effective size on the front, and lead to an estimation of selection coefficients that increase with conservation scores. Even though range expansions have had a relatively limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions of Quebec.
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39
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Range Expansion Compromises Adaptive Evolution in an Outcrossing Plant. Curr Biol 2017; 27:2544-2551.e4. [DOI: 10.1016/j.cub.2017.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/22/2017] [Accepted: 07/04/2017] [Indexed: 01/04/2023]
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40
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Sullivan AP, de Manuel M, Marques-Bonet T, Perry GH. An evolutionary medicine perspective on Neandertal extinction. J Hum Evol 2017. [PMID: 28622932 DOI: 10.1016/j.jhevol.2017.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Eurasian sympatry of Neandertals and anatomically modern humans - beginning at least 45,000 years ago and possibly lasting for more than 5000 years - has sparked immense anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the "differential pathogen resistance" extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture - and thus direct contact - between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (three individuals, or six chromosomes, per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates, those genes with the highest 1% genetic diversity genome-wide in non-human hominoids (apes). In contrast, Neandertals had similar or higher levels of genetic diversity than humans in 12 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, the expectations of this model are not universally met.
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Affiliation(s)
- Alexis P Sullivan
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - George H Perry
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
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Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nat Genet 2017; 49:806-810. [PMID: 28369035 PMCID: PMC5618255 DOI: 10.1038/ng.3831] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/07/2017] [Indexed: 12/14/2022]
Abstract
The dispensability of individual genes for viability has interested generations of geneticists. For some genes it is essential to maintain two functional chromosomal copies, while others may tolerate the loss of one or both copies. Exome sequence data from 60,706 individuals provide sufficient observations of rare protein truncating variants (PTVs) to make genome-wide estimates of selection against heterozygous loss of gene function. The cumulative frequency of rare deleterious PTVs is primarily determined by the balance between incoming mutations and purifying selection rather than genetic drift. This enables the estimation of the genome-wide distribution of selection coefficients for heterozygous PTVs and corresponding Bayesian estimates for individual genes. The strength of selection can discriminate the severity, age of onset, and mode of inheritance in Mendelian exome sequencing cases. We find that genes under the strongest selection are enriched in embryonic lethal mouse knockouts, putatively cell-essential genes, Mendelian disease genes, and regulators of transcription. Screening by essentiality, we find a large set of genes under strong selection that likely have critical function but have not yet been extensively annotated in published literature.
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42
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A Temporal Perspective on the Interplay of Demography and Selection on Deleterious Variation in Humans. G3-GENES GENOMES GENETICS 2017; 7:1027-1037. [PMID: 28159863 PMCID: PMC5345704 DOI: 10.1534/g3.117.039651] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When mutations have small effects on fitness, population size plays an important role in determining the amount and nature of deleterious genetic variation. The extent to which recent population size changes have impacted deleterious variation in humans has been a question of considerable interest and debate. An emerging consensus is that the Out-of-Africa bottleneck and subsequent growth events have been too short to cause meaningful differences in genetic load between populations; though changes in the number and average frequencies of deleterious variants have taken place. To provide more support for this view and to offer additional insight into the divergent evolution of deleterious variation across populations, we numerically solve time-inhomogeneous diffusion equations and study the temporal dynamics of the frequency spectra in models of population size change for modern humans. We observe how the response to demographic change differs by the strength of selection, and we then assess whether similar patterns are observed in exome sequence data from 33,370 and 5203 individuals of non-Finnish European and West African ancestry, respectively. Our theoretical results highlight how even simple summaries of the frequency spectrum can have complex responses to demographic change. These results support the finding that some apparent discrepancies between previous results have been driven by the behaviors of the precise summaries of deleterious variation. Further, our empirical results make clear the difficulty of inferring slight differences in frequency spectra using recent next-generation sequence data.
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43
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Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples. Genetics 2017; 206:345-361. [PMID: 28249985 PMCID: PMC5419480 DOI: 10.1534/genetics.116.197145] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/14/2017] [Indexed: 12/23/2022] Open
Abstract
The distribution of fitness effects (DFE) has considerable importance in population genetics. To date, estimates of the DFE come from studies using a small number of individuals. Thus, estimates of the proportion of moderately to strongly deleterious new mutations may be unreliable because such variants are unlikely to be segregating in the data. Additionally, the true functional form of the DFE is unknown, and estimates of the DFE differ significantly between studies. Here we present a flexible and computationally tractable method, called Fit∂a∂i, to estimate the DFE of new mutations using the site frequency spectrum from a large number of individuals. We apply our approach to the frequency spectrum of 1300 Europeans from the Exome Sequencing Project ESP6400 data set, 1298 Danes from the LuCamp data set, and 432 Europeans from the 1000 Genomes Project to estimate the DFE of deleterious nonsynonymous mutations. We infer significantly fewer (0.38-0.84 fold) strongly deleterious mutations with selection coefficient |s| > 0.01 and more (1.24-1.43 fold) weakly deleterious mutations with selection coefficient |s| < 0.001 compared to previous estimates. Furthermore, a DFE that is a mixture distribution of a point mass at neutrality plus a gamma distribution fits better than a gamma distribution in two of the three data sets. Our results suggest that nearly neutral forces play a larger role in human evolution than previously thought.
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Chen J, Glémin S, Lascoux M. Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species. Mol Biol Evol 2017; 34:1417-1428. [DOI: 10.1093/molbev/msx088] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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45
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Gilbert KJ, Sharp NP, Angert AL, Conte GL, Draghi JA, Guillaume F, Hargreaves AL, Matthey-Doret R, Whitlock MC. Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load. Am Nat 2017; 189:368-380. [PMID: 28350500 DOI: 10.1086/690673] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The biotic and abiotic factors that facilitate or hinder species range expansions are many and complex. We examine the impact of two genetic processes and their interaction on fitness at expanding range edges: local maladaptation resulting from the presence of an environmental gradient and expansion load resulting from increased genetic drift at the range edge. Results from spatially explicit simulations indicate that the presence of an environmental gradient during range expansion reduces expansion load; conversely, increasing expansion load allows only locally adapted populations to persist at the range edge. Increased maladaptation reduces the speed of range expansion, resulting in less genetic drift at the expanding front and more immigration from the range center, therefore reducing expansion load at the range edge. These results may have ramifications for species being forced to shift their ranges because of climate change or other anthropogenic changes. If rapidly changing climate leads to faster expansion as populations track their shifting climatic optima, populations may suffer increased expansion load beyond previous expectations.
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A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets. PLoS Genet 2017; 13:e1006573. [PMID: 28103232 PMCID: PMC5289629 DOI: 10.1371/journal.pgen.1006573] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 02/02/2017] [Accepted: 01/05/2017] [Indexed: 12/17/2022] Open
Abstract
The genetic component of complex disease risk in humans remains largely unexplained. A corollary is that the allelic spectrum of genetic variants contributing to complex disease risk is unknown. Theoretical models that relate population genetic processes to the maintenance of genetic variation for quantitative traits may suggest profitable avenues for future experimental design. Here we use forward simulation to model a genomic region evolving under a balance between recurrent deleterious mutation and Gaussian stabilizing selection. We consider multiple genetic and demographic models, and several different methods for identifying genomic regions harboring variants associated with complex disease risk. We demonstrate that the model of gene action, relating genotype to phenotype, has a qualitative effect on several relevant aspects of the population genetic architecture of a complex trait. In particular, the genetic model impacts genetic variance component partitioning across the allele frequency spectrum and the power of statistical tests. Models with partial recessivity closely match the minor allele frequency distribution of significant hits from empirical genome-wide association studies without requiring homozygous effect sizes to be small. We highlight a particular gene-based model of incomplete recessivity that is appealing from first principles. Under that model, deleterious mutations in a genomic region partially fail to complement one another. This model of gene-based recessivity predicts the empirically observed inconsistency between twin and SNP based estimated of dominance heritability. Furthermore, this model predicts considerable levels of unexplained variance associated with intralocus epistasis. Our results suggest a need for improved statistical tools for region based genetic association and heritability estimation. Gene action determines how mutations affect phenotype. When placed in an evolutionary context, the details of the genotype-to-phenotype model can impact the maintenance of genetic variation for complex traits. Likewise, non-equilibrium demographic history may affect patterns of genetic variation. Here, we explore the impact of genetic model and population growth on distribution of genetic variance across the allele frequency spectrum underlying risk for a complex disease. Using forward-in-time population genetic simulations, we show that the genetic model has important impacts on the composition of variation for complex disease risk in a population. We explicitly simulate genome-wide association studies (GWAS) and perform heritability estimation on population samples. A particular model of gene-based partial recessivity, based on allelic non-complementation, aligns well with empirical results. This model is congruent with the dominance variance estimates from both SNPs and twins, and the minor allele frequency distribution of GWAS hits.
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Genetic surfing in human populations: from genes to genomes. Curr Opin Genet Dev 2016; 41:53-61. [DOI: 10.1016/j.gde.2016.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 12/20/2022]
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The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit. Genetics 2016; 205:787-801. [PMID: 27903613 DOI: 10.1534/genetics.116.193821] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/11/2016] [Indexed: 11/18/2022] Open
Abstract
The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect of deleterious alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe <4% increase in the number of derived deleterious alleles in the Inuit. In contrast, proxies for genetic load under a recessive model suggest that the Inuit have a significantly higher load (20% increase or more) compared to other less bottlenecked human populations. Forward simulations under realistic models of demography support our empirical findings, showing up to a 6% increase in the genetic load for the Inuit population across all models of dominance. Further, the Inuit population carries fewer deleterious variants than other human populations, but those that are present tend to be at higher frequency than in other populations. Overall, our results show how recent demographic history has affected patterns of deleterious variants in human populations.
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49
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Freedman AH, Lohmueller KE, Wayne RK. Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dog is our oldest domesticate and has experienced a wide variety of demographic histories, including a bottleneck associated with domestication and individual bottlenecks associated with the formation of modern breeds. Admixture with gray wolves, and among dog breeds and populations, has also occurred throughout its history. Likewise, the intensity and focus of selection have varied, from an initial focus on traits enhancing cohabitation with humans, to more directed selection on specific phenotypic characteristics and behaviors. In this review, we summarize and synthesize genetic findings from genome-wide and complete genome studies that document the genomic consequences of demography and selection, including the effects on adaptive and deleterious variation. Consistent with the evolutionary history of the dog, signals of natural and artificial selection are evident in the dog genome. However, conclusions from studies of positive selection are fraught with the problem of false positives given that demographic history is often not taken into account.
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Affiliation(s)
- Adam H. Freedman
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
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50
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Simons YB, Sella G. The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr Opin Genet Dev 2016; 41:150-158. [PMID: 27744216 DOI: 10.1016/j.gde.2016.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 01/22/2023]
Abstract
Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.
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Affiliation(s)
- Yuval B Simons
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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