1
|
Rong S, Root E, Reilly SK. Massively parallel approaches for characterizing noncoding functional variation in human evolution. Curr Opin Genet Dev 2024; 88:102256. [PMID: 39217658 DOI: 10.1016/j.gde.2024.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
The genetic differences underlying unique phenotypes in humans compared to our closest primate relatives have long remained a mystery. Similarly, the genetic basis of adaptations between human groups during our expansion across the globe is poorly characterized. Uncovering the downstream phenotypic consequences of these genetic variants has been difficult, as a substantial portion lies in noncoding regions, such as cis-regulatory elements (CREs). Here, we review recent high-throughput approaches to measure the functions of CREs and the impact of variation within them. CRISPR screens can directly perturb CREs in the genome to understand downstream impacts on gene expression and phenotypes, while massively parallel reporter assays can decipher the regulatory impact of sequence variants. Machine learning has begun to be able to predict regulatory function from sequence alone, further scaling our ability to characterize genome function. Applying these tools across diverse phenotypes, model systems, and ancestries is beginning to revolutionize our understanding of noncoding variation underlying human evolution.
Collapse
Affiliation(s)
- Stephen Rong
- Department of Genetics, Yale University, New Haven, CT, USA.
| | - Elise Root
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Steven K Reilly
- Department of Genetics, Yale University, New Haven, CT, USA; Wu Tsai Institute, Yale University, New Haven, CT, USA.
| |
Collapse
|
2
|
Gao Z. Unveiling recent and ongoing adaptive selection in human populations. PLoS Biol 2024; 22:e3002469. [PMID: 38236800 PMCID: PMC10796035 DOI: 10.1371/journal.pbio.3002469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
Genome-wide scans for signals of selection have become a routine part of the analysis of population genomic variation datasets and have resulted in compelling evidence of selection during recent human evolution. This Essay spotlights methodological innovations that have enabled the detection of selection over very recent timescales, even in contemporary human populations. By harnessing large-scale genomic and phenotypic datasets, these new methods use different strategies to uncover connections between genotype, phenotype, and fitness. This Essay outlines the rationale and key findings of each strategy, discusses challenges in interpretation, and describes opportunities to improve detection and understanding of ongoing selection in human populations.
Collapse
Affiliation(s)
- Ziyue Gao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
3
|
Mathieson I. Human genetics: An extreme fitness landscape. Curr Biol 2023; 33:R1064-R1066. [PMID: 37875084 DOI: 10.1016/j.cub.2023.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
A new study aims to identify how genetic and physiological adaptations to altitude affect pregnancy, childbirth and neonatal health in one of the most extreme environments on Earth, the Tibetan Plateau.
Collapse
Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
4
|
Tobler R, Souilmi Y, Huber CD, Bean N, Turney CSM, Grey ST, Cooper A. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proc Natl Acad Sci U S A 2023; 120:e2213061120. [PMID: 37220274 PMCID: PMC10235988 DOI: 10.1073/pnas.2213061120] [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: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 05/25/2023] Open
Abstract
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
Collapse
Affiliation(s)
- Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Environment Institute, The University of Adelaide, Adelaide, SA5005, Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Nigel Bean
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA5005, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Chris S. M. Turney
- Division of Research, University of Technology Sydney, Ultimo, NSW2007, Australia
| | - Shane T. Grey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW2052, Australia
- Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW2010, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Blue Sky Genetics, Ashton, SA5137, Australia
| |
Collapse
|
5
|
Muktupavela RA, Petr M, Ségurel L, Korneliussen T, Novembre J, Racimo F. Modeling the spatiotemporal spread of beneficial alleles using ancient genomes. eLife 2022; 11:e73767. [PMID: 36537881 PMCID: PMC9767474 DOI: 10.7554/elife.73767] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.
Collapse
Affiliation(s)
- Rasa A Muktupavela
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| | - Martin Petr
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| | - Laure Ségurel
- UMR5558 Biométrie et Biologie Evolutive, CNRS - Université Lyon 1VilleurbanneFrance
| | | | - John Novembre
- Department of Human Genetics, University of ChicagoChicagoUnited States
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| |
Collapse
|
6
|
Souilmi Y, Tobler R, Johar A, Williams M, Grey ST, Schmidt J, Teixeira JC, Rohrlach A, Tuke J, Johnson O, Gower G, Turney C, Cox M, Cooper A, Huber CD. Admixture has obscured signals of historical hard sweeps in humans. Nat Ecol Evol 2022; 6:2003-2015. [PMID: 36316412 PMCID: PMC9715430 DOI: 10.1038/s41559-022-01914-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
Collapse
Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Angad Johar
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
| | - Matthew Williams
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Shane T Grey
- Transplantation Immunology Group, Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, New South Wales, Australia
| | - Joshua Schmidt
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - João C Teixeira
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Rohrlach
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jonathan Tuke
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Olivia Johnson
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia.
- BlueSky Genetics, Ashton, South Australia, Australia.
| | - Christian D Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Biology, Penn State University, University Park, PA, USA.
| |
Collapse
|
7
|
Abondio P, Cilli E, Luiselli D. Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods. Genes (Basel) 2022; 13:genes13050926. [PMID: 35627311 PMCID: PMC9141518 DOI: 10.3390/genes13050926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework.
Collapse
Affiliation(s)
- Paolo Abondio
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (E.C.); (D.L.)
- Laboratory of Molecular Anthropology and Center for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
- Correspondence:
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (E.C.); (D.L.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (E.C.); (D.L.)
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies (FMC), Viale Adriatico 1/N, 61032 Fano, Italy
| |
Collapse
|
8
|
The challenge of detecting recent natural selection in human populations. Proc Natl Acad Sci U S A 2022; 119:e2203237119. [PMID: 35353603 PMCID: PMC9169803 DOI: 10.1073/pnas.2203237119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
9
|
Wahyudi F, Aghakhanian F, Rahman S, Teo YY, Szpak M, Dhaliwal J, Ayub Q. Prioritising positively selected variants in whole-genome sequencing data using FineMAV. BMC Bioinformatics 2021; 22:604. [PMID: 34922440 PMCID: PMC8684245 DOI: 10.1186/s12859-021-04506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Background In population genomics, polymorphisms that are highly differentiated between geographically separated populations are often suggestive of Darwinian positive selection. Genomic scans have highlighted several such regions in African and non-African populations, but only a handful of these have functional data that clearly associates candidate variations driving the selection process. Fine-Mapping of Adaptive Variation (FineMAV) was developed to address this in a high-throughput manner using population based whole-genome sequences generated by the 1000 Genomes Project. It pinpoints positively selected genetic variants in sequencing data by prioritizing high frequency, population-specific and functional derived alleles. Results We developed a stand-alone software that implements the FineMAV statistic. To graphically visualise the FineMAV scores, it outputs the statistics as bigWig files, which is a common file format supported by many genome browsers. It is available as a command-line and graphical user interface. The software was tested by replicating the FineMAV scores obtained using 1000 Genomes Project African, European, East and South Asian populations and subsequently applied to whole-genome sequencing datasets from Singapore and China to highlight population specific variants that can be subsequently modelled. The software tool is publicly available at https://github.com/fadilla-wahyudi/finemav. Conclusions The software tool described here determines genome-wide FineMAV scores, using low or high-coverage whole-genome sequencing datasets, that can be used to prioritize a list of population specific, highly differentiated candidate variants for in vitro or in vivo functional screens. The tool displays these scores on the human genome browsers for easy visualisation, annotation and comparison between different genomic regions in worldwide human populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04506-9.
Collapse
Affiliation(s)
- Fadilla Wahyudi
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Farhang Aghakhanian
- Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Genes and Human Disease Research Program, Oklahoma Medical Research Foundation,, Oklahoma City, OK, 73104, USA
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Michał Szpak
- European Bioinformatics Institute, Hinxton, CB10 1SA, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jasbir Dhaliwal
- School of Information Technology, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Qasim Ayub
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
10
|
Szpak M, Collins SC, Li Y, Liu X, Ayub Q, Fischer MC, Vancollie VE, Lelliott CJ, Xue Y, Yalcin B, Yang H, Tyler-Smith C. A Positively Selected MAGEE2 LoF Allele Is Associated with Sexual Dimorphism in Human Brain Size and Shows Similar Phenotypes in Magee2 Null Mice. Mol Biol Evol 2021; 38:5655-5663. [PMID: 34464968 PMCID: PMC8662591 DOI: 10.1093/molbev/msab243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A nonsense allele at rs1343879 in human MAGEE2 on chromosome X has previously been reported as a strong candidate for positive selection in East Asia. This premature stop codon causing ∼80% protein truncation is characterized by a striking geographical pattern of high population differentiation: common in Asia and the Americas (up to 84% in the 1000 Genomes Project East Asians) but rare elsewhere. Here, we generated a Magee2 mouse knockout mimicking the human loss-of-function mutation to study its functional consequences. The Magee2 null mice did not exhibit gross abnormalities apart from enlarged brain structures (13% increased total brain area, P = 0.0022) in hemizygous males. The area of the granular retrosplenial cortex responsible for memory, navigation, and spatial information processing was the most severely affected, exhibiting an enlargement of 34% (P = 3.4×10-6). The brain size in homozygous females showed the opposite trend of reduced brain size, although this did not reach statistical significance. With these insights, we performed human association analyses between brain size measurements and rs1343879 genotypes in 141 Chinese volunteers with brain MRI scans, replicating the sexual dimorphism seen in the knockout mouse model. The derived stop gain allele was significantly associated with a larger volume of gray matter in males (P = 0.00094), and smaller volumes of gray (P = 0.00021) and white (P = 0.0015) matter in females. It is unclear whether or not the observed neuroanatomical phenotypes affect behavior or cognition, but it might have been the driving force underlying the positive selection in humans.
Collapse
Affiliation(s)
- Michał Szpak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Stephan C Collins
- Inserm UMR1231, Genetics of Developmental Disorders Laboratory, University of Bourgogne Franche-Comté, Dijon, France.,IGBMC, UMR7104, Illkirch, Inserm, France
| | - Yan Li
- BGI-Shenzhen, Shenzhen, China
| | - Xiao Liu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Qasim Ayub
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | | | | | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Binnaz Yalcin
- Inserm UMR1231, Genetics of Developmental Disorders Laboratory, University of Bourgogne Franche-Comté, Dijon, France.,IGBMC, UMR7104, Illkirch, Inserm, France
| | | | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| |
Collapse
|
11
|
Nguembang Fadja A, Riguzzi F, Bertorelle G, Trucchi E. Identification of natural selection in genomic data with deep convolutional neural network. BioData Min 2021; 14:51. [PMID: 34863217 PMCID: PMC8642854 DOI: 10.1186/s13040-021-00280-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background With the increase in the size of genomic datasets describing variability in populations, extracting relevant information becomes increasingly useful as well as complex. Recently, computational methodologies such as Supervised Machine Learning and specifically Convolutional Neural Networks have been proposed to make inferences on demographic and adaptive processes using genomic data. Even though it was already shown to be powerful and efficient in different fields of investigation, Supervised Machine Learning has still to be explored as to unfold its enormous potential in evolutionary genomics. Results The paper proposes a method based on Supervised Machine Learning for classifying genomic data, represented as windows of genomic sequences from a sample of individuals belonging to the same population. A Convolutional Neural Network is used to test whether a genomic window shows the signature of natural selection. Training performed on simulated data show that the proposed model can accurately predict neutral and selection processes on portions of genomes taken from real populations with almost 90% accuracy.
Collapse
Affiliation(s)
- Arnaud Nguembang Fadja
- Dipartimento di Matematica e Informatica, University of Ferrara, Via Saragat 1, Ferrara, I-44122, Italy.
| | - Fabrizio Riguzzi
- Dipartimento di Matematica e Informatica, University of Ferrara, Via Saragat 1, Ferrara, I-44122, Italy
| | - Giorgio Bertorelle
- Dipartimento di Scienze della Vita e Biotecnologie, University of Ferrara, Via Luigi Borsari 46, Ferrara, I-44121, Italy
| | - Emiliano Trucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Marche Polytechnic University, Via Brecce Bianche, Ancona, I-60131, Italy
| |
Collapse
|
12
|
Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
Collapse
Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| |
Collapse
|
13
|
Hernandez M, Perry GH. Scanning the human genome for "signatures" of positive selection: Transformative opportunities and ethical obligations. Evol Anthropol 2021; 30:113-121. [PMID: 33788352 DOI: 10.1002/evan.21893] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/25/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over-assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying "signatures" of past positive selection from haplotype-based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome-wide "scans" for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome-wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross-application of the genome-wide scan approach to existing datasets, which we also discuss.
Collapse
Affiliation(s)
- Margarita Hernandez
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
14
|
A Selective Sweep Conceals a MicroRNA with Broad Metabolic Effects. Cell Metab 2020; 32:697-698. [PMID: 33147481 DOI: 10.1016/j.cmet.2020.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The need for discovering new genes driving metabolic disease susceptibility is clear; even clearer is the need for their subsequent functional characterization. A new paper reports a role for miR-128-1 in metabolic control through a series of elegant mouse studies, and an intriguing hypothesis about its "thrifty" role in metabolism.
Collapse
|
15
|
Mathieson I. Human adaptation over the past 40,000 years. Curr Opin Genet Dev 2020; 62:97-104. [PMID: 32745952 PMCID: PMC7484260 DOI: 10.1016/j.gde.2020.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/10/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.
Collapse
Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States.
| |
Collapse
|
16
|
Wieland F. The 44th FEBS Congress in Krakow: celebrating the multidisciplinarity of biological research. FEBS Lett 2019; 593:1413-1414. [PMID: 31222735 DOI: 10.1002/1873-3468.13503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|