1
|
Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: The genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas. PLoS Genet 2024; 20:e1011036. [PMID: 38968323 PMCID: PMC11253941 DOI: 10.1371/journal.pgen.1011036] [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: 10/27/2023] [Revised: 07/17/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024] Open
Abstract
Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America.
Collapse
Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| |
Collapse
|
2
|
Wortel MT, Agashe D, Bailey SF, Bank C, Bisschop K, Blankers T, Cairns J, Colizzi ES, Cusseddu D, Desai MM, van Dijk B, Egas M, Ellers J, Groot AT, Heckel DG, Johnson ML, Kraaijeveld K, Krug J, Laan L, Lässig M, Lind PA, Meijer J, Noble LM, Okasha S, Rainey PB, Rozen DE, Shitut S, Tans SJ, Tenaillon O, Teotónio H, de Visser JAGM, Visser ME, Vroomans RMA, Werner GDA, Wertheim B, Pennings PS. Towards evolutionary predictions: Current promises and challenges. Evol Appl 2023; 16:3-21. [PMID: 36699126 PMCID: PMC9850016 DOI: 10.1111/eva.13513] [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: 02/09/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.
Collapse
Affiliation(s)
- Meike T. Wortel
- Swammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - Deepa Agashe
- National Centre for Biological SciencesBangaloreIndia
| | | | - Claudia Bank
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Gulbenkian Science InstituteOeirasPortugal
| | - Karen Bisschop
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Origins CenterGroningenThe Netherlands
- Laboratory of Aquatic Biology, KU Leuven KulakKortrijkBelgium
| | - Thomas Blankers
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Origins CenterGroningenThe Netherlands
| | | | - Enrico Sandro Colizzi
- Origins CenterGroningenThe Netherlands
- Mathematical InstituteLeiden UniversityLeidenThe Netherlands
| | | | | | - Bram van Dijk
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jacintha Ellers
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Astrid T. Groot
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | | | | | - Ken Kraaijeveld
- Leiden Centre for Applied BioscienceUniversity of Applied Sciences LeidenLeidenThe Netherlands
| | - Joachim Krug
- Institute for Biological PhysicsUniversity of CologneCologneGermany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of NanoscienceTU DelftDelftThe Netherlands
| | - Michael Lässig
- Institute for Biological PhysicsUniversity of CologneCologneGermany
| | - Peter A. Lind
- Department Molecular BiologyUmeå UniversityUmeåSweden
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Luke M. Noble
- Institute de Biologie, École Normale Supérieure, CNRS, InsermParisFrance
| | | | - Paul B. Rainey
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRSParisFrance
| | - Daniel E. Rozen
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Shraddha Shitut
- Origins CenterGroningenThe Netherlands
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | | | | | | | | | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Renske M. A. Vroomans
- Origins CenterGroningenThe Netherlands
- Informatics InstituteUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | | |
Collapse
|
3
|
Soni V, Vos M, Eyre-Walker A. A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection. PLoS Biol 2022; 20:e3001645. [PMID: 35653351 PMCID: PMC9162324 DOI: 10.1371/journal.pbio.3001645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.
Collapse
Affiliation(s)
- Vivak Soni
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, United Kingdom
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- * E-mail:
| |
Collapse
|
4
|
Pélissié B, Chen YH, Cohen ZP, Crossley MS, Hawthorne DJ, Izzo V, Schoville SD. Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle. Mol Biol Evol 2022; 39:6511499. [PMID: 35044459 PMCID: PMC8826761 DOI: 10.1093/molbev/msac016] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.
Collapse
Affiliation(s)
- Benjamin Pélissié
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael S Crossley
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Victor Izzo
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
5
|
Naik PP, Farrukh SN. Influence of Ethnicities and Skin Color Variations in Different Populations: A Review. Skin Pharmacol Physiol 2021; 35:65-76. [PMID: 34515229 DOI: 10.1159/000518826] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/30/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND In the world scientific tradition, skin color is the primary physical characteristic used to divide humans into groups. Human skin has a wide range of tones and colors, which can be seen in a wide range of demographic populations. Many factors influence the color of people's skin, but the pigment melanin is by far the most important. Melanin is produced by cells called melanocytes in the skin and is the primary determinant of skin color in people with darker skin. Indeed, >150 genes have now been identified as having a direct or indirect effect on skin color. Vitamin D has recently been discovered to regulate cellular proliferation and differentiation in a variety of tissues, including the skin. The mechanisms through which the active vitamin D metabolite 1,25 dihydroxyvitamin D3 (or calcitriol) affects keratinocyte development are numerous and overlap with the mechanisms by which calcium influences keratinocyte differentiation. Ultraviolet (UV) is the most major modifiable risk factor for skin cancer and many other environmental-influenced skin disorders when it is abundant in the environment. Although the UV component of sunlight is known to cause skin damage, few researches have looked at the impact of non-UV solar radiation on skin physiology in terms of inflammation, and there is less information on the role of visible light in pigmentation. SUMMARY The quantity and quality of melanin are regulating by the expression of genes. The enzyme tyrosinase is primarily responsible for the genetic mechanism that controls human skin color. Genetics determines constitutive skin color, which is reinforced by facultative melanogenesis and tanning reactions. High quantities of melanin and melanogenic substances are typically accepted in darker skin to protect against UV radiation-induced molecular damage. Previous research has proposed that skin color variation is caused by a dynamic genetic mechanism, contributing to our understanding of how population demographic history and natural selection shape human genetic and phenotypic diversity. However, the most significant ethnic skin color difference is determined by melanin content. This current review aimed to assess the influence of skin color variations in skin structure and functions as well as difference in dermatological disease patterns. Also, this article reviewed several cases of skin color adaptation in different populations. Key Messages: Skin color impacts the composition and activity. Therefore, the contrast of dermatological ailments between distinct race-related categories is remarkable. Skin color adaptation is a challenging procedure. Refinement of skin color is an age-old craving of humans with ever-evolving drifts.
Collapse
Affiliation(s)
- Piyu Parth Naik
- Department of Dermatology, Saudi-German Hospital & Clinic, Dubai, United Arab Emirates
| | - Syed Nadir Farrukh
- Department of Internal Medicine, Adam-Vital Hospital, Dubai, United Arab Emirates
| |
Collapse
|
6
|
Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
Collapse
|
7
|
Blankers T, Oh KP, Shaw KL. Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets. Proc Biol Sci 2019; 286:20191479. [PMID: 31594503 PMCID: PMC6790767 DOI: 10.1098/rspb.2019.1479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favoured over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and whether the likelihood of QTL sharing is related to QTL effect size. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more frequently than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.
Collapse
|
8
|
Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
Collapse
|
9
|
Positive selection in Europeans and East-Asians at the ABCA12 gene. Sci Rep 2019; 9:4843. [PMID: 30890716 PMCID: PMC6424970 DOI: 10.1038/s41598-019-40360-9] [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: 08/16/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022] Open
Abstract
Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation. We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation. We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons and the transcription starting site of ABCA12. We found no obvious effect of rs10180970 alleles on ABCA12 gene expression. We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and present in non-Africans 45,000 years ago.
Collapse
|
10
|
Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. Global genetic differentiation of complex traits shaped by natural selection in humans. Nat Commun 2018; 9:1865. [PMID: 29760457 PMCID: PMC5951811 DOI: 10.1038/s41467-018-04191-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height ([Formula: see text]), waist-to-hip ratio ([Formula: see text]), and schizophrenia ([Formula: see text]) are significantly more differentiated among populations than matched "control" SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height ([Formula: see text]) and schizophrenia ([Formula: see text]) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations.
Collapse
Affiliation(s)
- Jing Guo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, 325027, Zhejiang, China
| | - Maciej Trzaskowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew R Robinson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Department of Computational Biology, University of Lausanne, 1011, Lausanne, Switzerland
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
11
|
Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
Collapse
Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| |
Collapse
|
12
|
Berner D, Roesti M. Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate. Mol Ecol 2017; 26:6351-6369. [PMID: 28994152 DOI: 10.1111/mec.14373] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Genetic differentiation between divergent populations is often greater in chromosome centres than peripheries. Commonly overlooked, this broadscale differentiation pattern is sometimes ascribed to heterogeneity in crossover rate and hence linked selection within chromosomes, but the underlying mechanisms remain incompletely understood. A literature survey across 46 organisms reveals that most eukaryotes indeed exhibit a reduced crossover rate in chromosome centres relative to the peripheries. Using simulations of populations diverging into ecologically different habitats through sorting of standing genetic variation, we demonstrate that such chromosome-scale heterogeneity in crossover rate, combined with polygenic divergent selection, causes stronger hitchhiking and especially barriers to gene flow across chromosome centres. Without requiring selection on new mutations, this rapidly leads to elevated population differentiation in the low-crossover centres relative to the high-crossover peripheries of chromosomes ("Chromosome Centre-Biased Differentiation", CCBD). Using simulated and empirical data, we then show that strong CCBD between populations can provide evidence of polygenic adaptive divergence with a phase of gene flow. We further demonstrate that chromosome-scale heterogeneity in crossover rate impacts analyses beyond that of population differentiation, including the inference of phylogenies and parallel adaptive evolution among populations, the detection of genetic loci under selection, and the interpretation of the strength of selection on genomic regions. Overall, our results call for a greater appreciation of chromosome-scale heterogeneity in crossover rate in evolutionary genomics.
Collapse
Affiliation(s)
- Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Marius Roesti
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
13
|
Deng L, Xu S. Adaptation of human skin color in various populations. Hereditas 2017; 155:1. [PMID: 28701907 PMCID: PMC5502412 DOI: 10.1186/s41065-017-0036-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/02/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine. DISCUSSION Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies. CONCLUSION Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.
Collapse
Affiliation(s)
- Lian Deng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China.,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438 China
| |
Collapse
|
14
|
Abstract
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based "Population Branch Excess" statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ∼4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to "soft sweeps". One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. Another codirectional outlier SNP, at senseless-2, had a strong association with our cold trait measurements, but in the opposite direction as predicted. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation.
Collapse
Affiliation(s)
- John E. Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| | | | - Justin B. Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| |
Collapse
|
15
|
Shu L, Laurila A, Suter MJF, Räsänen K. Molecular phenotyping of maternally mediated parallel adaptive divergence withinRana arvalisandRana temporaria. Mol Ecol 2016; 25:4564-79. [DOI: 10.1111/mec.13786] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/20/2016] [Accepted: 07/26/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Longfei Shu
- Department of Aquatic Ecology; Eawag; Duebendorf 8600 Switzerland
- Institute of Integrative Biology; ETH Zürich; Zürich 8092 Switzerland
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics; Evolutionary Biology Center; Uppsala University; Uppsala 75236 Sweden
| | - Marc J.-F. Suter
- Department of Environmental Toxicology; Eawag; Duebendorf 8600 Switzerland
- Department of Environmental Systems Science; ETH Zürich; Zürich 8092 Switzerland
| | - Katja Räsänen
- Department of Aquatic Ecology; Eawag; Duebendorf 8600 Switzerland
- Institute of Integrative Biology; ETH Zürich; Zürich 8092 Switzerland
| |
Collapse
|
16
|
The genomics of ecological vicariance in threespine stickleback fish. Nat Commun 2015; 6:8767. [PMID: 26556609 PMCID: PMC4659939 DOI: 10.1038/ncomms9767] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/29/2015] [Indexed: 12/19/2022] Open
Abstract
Populations occurring in similar habitats and displaying similar phenotypes are increasingly used to explore parallel evolution at the molecular level. This generally ignores the possibility that parallel evolution can be mimicked by the fragmentation of an ancestral population followed by genetic exchange with ecologically different populations. Here we demonstrate such an ecological vicariance scenario in multiple stream populations of threespine stickleback fish divergent from a single adjacent lake population. On the basis of demographic and population genomic analyses, we infer the initial spread of a stream-adapted ancestor followed by the emergence of a lake-adapted population, that selective sweeps have occurred mainly in the lake population, that adaptive lake–stream divergence is maintained in the face of gene flow from the lake into the streams, and that this divergence involves major inversion polymorphisms also important to marine-freshwater stickleback divergence. Overall, our study highlights the need for a robust understanding of the demographic and selective history in evolutionary investigations. Threespine stickleback fish are adapted to lake and stream habitats in Central Europe. Here, the authors show colonization of a lake basin by a stream-adapted ancestor, followed by the emergence of a lake-adapted population in the face of gene flow across lake–stream boundaries.
Collapse
|
17
|
Gautam P, Chaurasia A, Bhattacharya A, Grover R, Mukerji M, Natarajan VT. Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes. Mol Biol Evol 2014; 32:555-73. [PMID: 25534032 DOI: 10.1093/molbev/msu342] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.
Collapse
Affiliation(s)
- Pramod Gautam
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Amit Chaurasia
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | - Aniket Bhattacharya
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research, Delhi, India
| | - Ritika Grover
- Academy of Scientific and Innovative Research, Delhi, India Systems Biology Group, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Mitali Mukerji
- Genomics and Molecular Medicine, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research, Delhi, India
| | - Vivek T Natarajan
- Academy of Scientific and Innovative Research, Delhi, India Systems Biology Group, Council for Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Delhi, India
| |
Collapse
|
18
|
Xu L, Bickhart DM, Cole JB, Schroeder SG, Song J, Tassell CPV, Sonstegard TS, Liu GE. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Mol Biol Evol 2014; 32:711-25. [PMID: 25431480 DOI: 10.1093/molbev/msu333] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.
Collapse
Affiliation(s)
- Lingyang Xu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| |
Collapse
|
19
|
Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P. Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl 2014; 7:1008-25. [PMID: 25553064 PMCID: PMC4231592 DOI: 10.1111/eva.12149] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.
Collapse
Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| | | | - Paul Sunnucks
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| |
Collapse
|
20
|
Foll M, Gaggiotti O, Daub J, Vatsiou A, Excoffier L. Widespread signals of convergent adaptation to high altitude in Asia and america. Am J Hum Genet 2014; 95:394-407. [PMID: 25262650 DOI: 10.1016/j.ajhg.2014.09.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023] Open
Abstract
Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low- and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia.
Collapse
|
21
|
Seeb LW, Waples RK, Limborg MT, Warheit KI, Pascal CE, Seeb JE. Parallel signatures of selection in temporally isolated lineages of pink salmon. Mol Ecol 2014; 23:2473-85. [PMID: 24762204 DOI: 10.1111/mec.12769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 12/12/2022]
Abstract
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly abundant and widely ranging salmonid, provide a naturally occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life history. The species is composed of two reproductively isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction-site-associated DNA (RAD) sequencing to discover and genotype approximately 8000 SNP loci in three population pairs of even- and odd-year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd-year than within the even-year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation-based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment.
Collapse
Affiliation(s)
- L W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | | | | | | | | | | |
Collapse
|
22
|
Choudhury A, Hazelhurst S, Meintjes A, Achinike-Oduaran O, Aron S, Gamieldien J, Jalali Sefid Dashti M, Mulder N, Tiffin N, Ramsay M. Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. BMC Genomics 2014; 15:437. [PMID: 24906912 PMCID: PMC4092225 DOI: 10.1186/1471-2164-15-437] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/19/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have important consequences for health and wellbeing. Their interpretation is contextualised by currently available genome data. RESULTS The identification of common population-specific (CPS) variants (SNPs and SSV) is influenced by admixture and the sample size under investigation. Nine of the populations in the 1000 Genomes Project (2 African, 2 Asian (including a merged Chinese group) and 5 European) revealed that the African populations (LWK and YRI), followed by the Japanese (JPT) have the highest number of CPS SNPs, in concordance with their histories and given the populations studied. Using two methods, sliding 50-SNP and 5-kb windows, the CPS SNPs showed distinct clustering across large genome segments and little overlap of clusters between populations. iHS enrichment score and the population branch statistic (PBS) analyses suggest that selective sweeps are unlikely to account for the clustering and population specificity. Of interest is the association of clusters close to recombination hotspots. Functional analysis of genes associated with the CPS SNPs revealed over-representation of genes in pathways associated with neuronal development, including axonal guidance signalling and CREB signalling in neurones. CONCLUSIONS Common population-specific SNPs are non-randomly distributed throughout the genome and are significantly associated with recombination hotspots. Since the variant alleles of most CPS SNPs are the derived allele, they likely arose in the specific population after a split from a common ancestor. Their proximity to genes involved in specific pathways, including neuronal development, suggests evolutionary plasticity of selected genomic regions. Contrary to expectation, selective sweeps did not play a large role in the persistence of population-specific variation. This suggests a stochastic process towards population-specific variation which reflects demographic histories and may have some interesting implications for health and susceptibility to disease.
Collapse
Affiliation(s)
- Ananyo Choudhury
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Ayton Meintjes
- />Department Clinical Laboratory Sciences, Computational Biology Group, IDM, University of Cape Town, Cape Town, South Africa
| | - Ovokeraye Achinike-Oduaran
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Junaid Gamieldien
- />South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Mahjoubeh Jalali Sefid Dashti
- />South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Nicola Mulder
- />Department Clinical Laboratory Sciences, Computational Biology Group, IDM, University of Cape Town, Cape Town, South Africa
| | - Nicki Tiffin
- />South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Michèle Ramsay
- />Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- />Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
23
|
Frazier TW, Youngstrom EA, Frankel BA, Zunta-Soares GB, Sanches M, Escamilla M, Nielsen DA, Soares JC. Candidate gene associations with mood disorder, cognitive vulnerability, and fronto-limbic volumes. Brain Behav 2014; 4:418-30. [PMID: 24944871 PMCID: PMC4055192 DOI: 10.1002/brb3.226] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 02/03/2014] [Accepted: 02/13/2014] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Four of the most consistently replicated variants associated with mood disorder occur in genes important for synaptic function: ANK3 (rs10994336), BDNF (rs6265), CACNA1C (rs1006737), and DGKH (rs1170191). AIMS The present study examined associations between these candidates, mood disorder diagnoses, cognition, and fronto-limbic regions implicated in affect regulation. METHODS AND MATERIALS Participants included 128 individuals with bipolar disorder (33% male, Mean age = 38.5), 48 with major depressive disorder (29% male, Mean age = 40.4), and 149 healthy controls (35% male, Mean age = 36.5). Genotypes were determined by 5'-fluorogenic exonuclease assays (TaqMan®). Fronto-limbic volumes were obtained from high resolution brain images using Freesurfer. Chi-square analyses, bivariate correlations, and mediational models examined relationships between genetic variants, mood diagnoses, cognitive measures, and brain volumes. RESULTS Carriers of the minor BDNF and ANK3 alleles showed nonsignificant trends toward protective association in controls relative to mood disorder patients (P = 0.047). CACNA1C minor allele carriers had larger bilateral caudate, insula, globus pallidus, frontal pole, and nucleus accumbens volumes (smallest r = 0.13, P = 0.043), and increased IQ (r = 0.18, P < 0.001). CACNA1C associations with brain volumes and IQ were independent; larger fronto-limbic volumes did not mediate increased IQ. Other candidate variants were not significantly associated with diagnoses, cognition, or fronto-limbic volumes. DISCUSSION AND CONCLUSIONS CACNA1C may be associated with biological systems altered in mood disorder. Increases in fronto-limbic volumes and cognitive ability associated with CACNA1C minor allele genotypes are congruent with findings in healthy samples and may be a marker for increased risk for neuropsychiatric phenotypes. Even larger multimodal studies are needed to quantify the magnitude and specificity of genetic-imaging-cognition-symptom relationships.
Collapse
Affiliation(s)
- Thomas W Frazier
- Centers for Autism and Pediatric Behavioral Health, Cleveland Clinic Cleveland, Ohio
| | - Eric A Youngstrom
- Departments of Psychology and Psychiatry, University of North Carolina at Chapel Hill Chapel Hill, North Carolina
| | - Brian A Frankel
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine and Michael E. DeBakey VA Medical Center Houston, Texas
| | - Giovana B Zunta-Soares
- Department of Psychiatry and Behavioral Sciences, UT Center of Excellence on Mood Disorders, University of Texas Medical School at Houston Houston, Texas
| | - Marsal Sanches
- Department of Psychiatry and Behavioral Sciences, UT Center of Excellence on Mood Disorders, University of Texas Medical School at Houston Houston, Texas
| | - Michael Escamilla
- Center of Excellence in Neurosciences, Texas Tech University Health Science Center El Paso, Texas
| | - David A Nielsen
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine and Michael E. DeBakey VA Medical Center Houston, Texas
| | - Jair C Soares
- Department of Psychiatry and Behavioral Sciences, UT Center of Excellence on Mood Disorders, University of Texas Medical School at Houston Houston, Texas
| |
Collapse
|
24
|
Roesti M, Gavrilets S, Hendry AP, Salzburger W, Berner D. The genomic signature of parallel adaptation from shared genetic variation. Mol Ecol 2014; 23:3944-56. [PMID: 24635356 DOI: 10.1111/mec.12720] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/12/2014] [Accepted: 03/12/2014] [Indexed: 12/19/2022]
Abstract
Parallel adaptation is common and may often occur from shared genetic variation, but the genomic consequences of this process remain poorly understood. We first use individual-based simulations to demonstrate that comparisons between populations adapted in parallel to similar environments from shared variation reveal a characteristic genomic signature around a selected locus: a low-divergence valley centred at the locus and flanked by twin peaks of high divergence. This signature is initiated by the hitchhiking of haplotype tracts differing between derived populations in the broader neighbourhood of the selected locus (driving the high-divergence twin peaks) and shared haplotype tracts in the tight neighbourhood of the locus (driving the low-divergence valley). This initial hitchhiking signature is reinforced over time because the selected locus acts as a barrier to gene flow from the source to the derived populations, thus promoting divergence by drift in its close neighbourhood. We next empirically confirm the peak-valley-peak signature by combining targeted and RAD sequence data at three candidate adaptation genes in multiple marine (source) and freshwater (derived) populations of threespine stickleback. Finally, we use a genome-wide screen for the peak-valley-peak signature to discover additional genome regions involved in parallel marine-freshwater divergence. Our findings offer a new explanation for heterogeneous genomic divergence and thus challenge the standard view that peaks in population divergence harbour divergently selected loci and that low-divergence regions result from balancing selection or localized introgression. We anticipate that genome scans for peak-valley-peak divergence signatures will promote the discovery of adaptation genes in other organisms.
Collapse
Affiliation(s)
- Marius Roesti
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | | | | | | | | |
Collapse
|
25
|
Wray GA. Genomics and the Evolution of Phenotypic Traits. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135828] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of model organisms in lab settings to identify the genetic basis for evolutionarily interesting traits in many organisms in natural settings. Other benefits are the abilities to identify causal mutations and validate their phenotypic consequences more readily and in many more species. Genomic technologies have reinvigorated interest in some of the most fundamental and persistent questions in evolutionary genetics, revealed previously unsuspected evolutionary phenomena, and opened the door to a wide range of new questions.
Collapse
Affiliation(s)
- Gregory A. Wray
- Department of Biology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27701
| |
Collapse
|
26
|
Geographical, environmental and pathophysiological influences on the human blood transcriptome. CURRENT GENETIC MEDICINE REPORTS 2013; 1:203-211. [PMID: 25830076 DOI: 10.1007/s40142-013-0028-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Gene expression variation provides a read-out of both genetic and environmental influences on gene activity. Geographical, genomic and sociogenomic studies have highlighted how life circumstances of an individual modify the expression of hundreds and in some cases thousands of genes in a co-ordinated manner. This review places such results in the context of a conserved set of 90 transcripts known as Blood Informative Transcripts (BIT) that capture the major conserved components of variation in the peripheral blood transcriptome. Pathophysiological states are also shown to associate with the perturbation of transcript abundance along the major axes. Discussion of false negative rates leads us to argue that simple significance thresholds provide a biased perspective on assessment of differential expression that may cloud the interpretation of studies with small sample sizes.
Collapse
|
27
|
Abstract
An enduring goal of evolutionary biology is to understand how natural selection has shaped patterns of polymorphism and divergence within and between species and to map the genetic basis of adaptations. The rapid maturation of next-generation sequencing technology has generated a deluge of genomics data from nonhuman primates, extinct hominins, and diverse human populations. These emerging genome data sets have simultaneously broadened our understanding of human evolution and sharply defined existing gaps in knowledge about the mechanistic basis of evolutionary change. In this review, we summarize recent insights into how natural selection has influenced the human genome across different timescales. Although the path to a more comprehensive understanding of selection and adaptation in humans remains arduous, some general insights are beginning to emerge, such as the importance of adaptive regulatory evolution, the absence of pervasive classic selective sweeps, and the potential roles that selection from standing variation and polygenic adaptation have likely played in recent human evolutionary history.
Collapse
Affiliation(s)
- Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065;
| | | |
Collapse
|
28
|
Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet 2013; 9:e1003447. [PMID: 23717210 PMCID: PMC3662561 DOI: 10.1371/journal.pgen.1003447] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 02/28/2013] [Indexed: 12/21/2022] Open
Abstract
Genetic diversity across different human populations can enhance understanding of the genetic basis of disease. We calculated the genetic risk of 102 diseases in 1,043 unrelated individuals across 51 populations of the Human Genome Diversity Panel. We found that genetic risk for type 2 diabetes and pancreatic cancer decreased as humans migrated toward East Asia. In addition, biliary liver cirrhosis, alopecia areata, bladder cancer, inflammatory bowel disease, membranous nephropathy, systemic lupus erythematosus, systemic sclerosis, ulcerative colitis, and vitiligo have undergone genetic risk differentiation. This analysis represents a large-scale attempt to characterize genetic risk differentiation in the context of migration. We anticipate that our findings will enable detailed analysis pertaining to the driving forces behind genetic risk differentiation. The environment humans inhabit has changed many times in the last 100,000 years. Migration and dynamic local environments can lead to genetic adaptations favoring beneficial traits. Many genes responsible for these adaptations can alter disease susceptibility. Genes can also affect disease susceptibility by varying randomly across different populations. We have studied genetic variants that are known to modify disease susceptibility in the context of worldwide migration. We found that variants associated with 11 diseases have been affected to an extent that is not explained by random variation. We also found that the genetic risk of type 2 diabetes has steadily decreased along the worldwide human migration trajectory from Africa to America.
Collapse
Affiliation(s)
- Erik Corona
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Rong Chen
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Martin Sikora
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alexander A. Morgan
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Chirag J. Patel
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Aditya Ramesh
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Atul J. Butte
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children's Hospital, Palo Alto, California, United States of America
- * E-mail:
| |
Collapse
|
29
|
Qian W, Deng L, Lu D, Xu S. Genome-wide landscapes of human local adaptation in Asia. PLoS One 2013; 8:e54224. [PMID: 23349834 PMCID: PMC3551950 DOI: 10.1371/journal.pone.0054224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 12/11/2012] [Indexed: 01/30/2023] Open
Abstract
Genetic studies of human local adaptation have been facilitated greatly by recent advances in high-throughput genotyping and sequencing technologies. However, few studies have investigated local adaptation in Asian populations on a genome-wide scale and with a high geographic resolution. In this study, taking advantage of the dense population coverage in Southeast Asia, which is the part of the world least studied in term of natural selection, we depicted genome-wide landscapes of local adaptations in 63 Asian populations representing the majority of linguistic and ethnic groups in Asia. Using genome-wide data analysis, we discovered many genes showing signs of local adaptation or natural selection. Notable examples, such as FOXQ1, MAST2, and CDH4, were found to play a role in hair follicle development and human cancer, signal transduction, and tumor repression, respectively. These showed strong indications of natural selection in Philippine Negritos, a group of aboriginal hunter-gatherers living in the Philippines. MTTP, which has associations with metabolic syndrome, body mass index, and insulin regulation, showed a strong signature of selection in Southeast Asians, including Indonesians. Functional annotation analysis revealed that genes and genetic variants underlying natural selections were generally enriched in the functional category of alternative splicing. Specifically, many genes showing significant difference with respect to allele frequency between northern and southern Asian populations were found to be associated with human height and growth and various immune pathways. In summary, this study contributes to the overall understanding of human local adaptation in Asia and has identified both known and novel signatures of natural selection in the human genome.
Collapse
Affiliation(s)
- Wei Qian
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lian Deng
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
30
|
Olson-Manning CF, Wagner MR, Mitchell-Olds T. Adaptive evolution: evaluating empirical support for theoretical predictions. Nat Rev Genet 2012; 13:867-77. [PMID: 23154809 PMCID: PMC3748133 DOI: 10.1038/nrg3322] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adaptive evolution is shaped by the interaction of population genetics, natural selection and underlying network and biochemical constraints. Variation created by mutation, the raw material for evolutionary change, is translated into phenotypes by flux through metabolic pathways and by the topography and dynamics of molecular networks. Finally, the retention of genetic variation and the efficacy of selection depend on population genetics and demographic history. Emergent high-throughput experimental methods and sequencing technologies allow us to gather more evidence and to move beyond the theory in different systems and populations. Here we review the extent to which recent evidence supports long-established theoretical principles of adaptation.
Collapse
Affiliation(s)
- Carrie F. Olson-Manning
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| | - Maggie R. Wagner
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| | - Thomas Mitchell-Olds
- Department of Biology, Box 90338, Program in Genetics and Genomics, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708
| |
Collapse
|
31
|
Schoville SD, Bonin A, François O, Lobreaux S, Melodelima C, Manel S. Adaptive Genetic Variation on the Landscape: Methods and Cases. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-110411-160248] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sean D. Schoville
- Laboratoire TIMC-IMAG, UMR-CNRS 5525, Université Joseph Fourier, 38041 Grenoble, France; ,
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Olivier François
- Laboratoire TIMC-IMAG, UMR-CNRS 5525, Université Joseph Fourier, 38041 Grenoble, France; ,
| | - Stéphane Lobreaux
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Christelle Melodelima
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Stéphanie Manel
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
- Laboratoire Population Environnement et Développement, UMR-IRD 151, Université Aix-Marseille, 13331 Marseille, France
| |
Collapse
|
32
|
Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
Collapse
Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
| | | |
Collapse
|
33
|
Abstract
While hundreds of loci have been identified as reflecting strong-positive selection in human populations, connections between candidate loci and specific selective pressures often remain obscure. This study investigates broader patterns of selection in African populations, which are underrepresented despite their potential to offer key insights into human adaptation. We scan for hard selective sweeps using several haplotype and allele-frequency statistics with a data set of nearly 500,000 genome-wide single-nucleotide polymorphisms in 12 highly diverged African populations that span a range of environments and subsistence strategies. We find that positive selection does not appear to be a strong determinant of allele-frequency differentiation among these African populations. Haplotype statistics do identify putatively selected regions that are shared across African populations. However, as assessed by extensive simulations, patterns of haplotype sharing between African populations follow neutral expectations and suggest that tails of the empirical distributions contain false-positive signals. After highlighting several genomic regions where positive selection can be inferred with higher confidence, we use a novel method to identify biological functions enriched among populations' empirical tail genomic windows, such as immune response in agricultural groups. In general, however, it seems that current methods for selection scans are poorly suited to populations that, like the African populations in this study, are affected by ascertainment bias and have low levels of linkage disequilibrium, possibly old selective sweeps, and potentially reduced phasing accuracy. Additionally, population history can confound the interpretation of selection statistics, suggesting that greater care is needed in attributing broad genetic patterns to human adaptation.
Collapse
|
34
|
Novembre J, Han E. Human population structure and the adaptive response to pathogen-induced selection pressures. Philos Trans R Soc Lond B Biol Sci 2012; 367:878-86. [PMID: 22312055 DOI: 10.1098/rstb.2011.0305] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The past few years of research in human evolutionary genetics have provided novel insights and questions regarding how human adaptations to recent selective pressures have taken place. Here, we review the advances most relevant to understanding human evolution in response to pathogen-induced selective pressures. Key insights come from theoretical models of adaptive evolution, particularly those that consider spatially structured populations, and from empirical population genomic studies of adaptive evolution in humans. We also review the CCR5-Δ32 HIV resistance allele as a case study of pathogen resistance in humans. Taken together, the results make clear that the human response to pathogen-induced selection pressures depends on a complex interplay between the age of the pathogen, the genetic basis of potential resistance phenotypes, and how population structure impacts the adaptive process in humans.
Collapse
Affiliation(s)
- John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
| | | |
Collapse
|
35
|
|
36
|
Martínez-Abadías N, Esparza M, Sjøvold T, González-José R, Santos M, Hernández M, Klingenberg CP. Pervasive genetic integration directs the evolution of human skull shape. Evolution 2011; 66:1010-23. [PMID: 22486686 DOI: 10.1111/j.1558-5646.2011.01496.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It has long been unclear whether the different derived cranial traits of modern humans evolved independently in response to separate selection pressures or whether they resulted from the inherent morphological integration throughout the skull. In a novel approach to this issue, we combine evolutionary quantitative genetics and geometric morphometrics to analyze genetic and phenotypic integration in human skull shape. We measured human skulls in the ossuary of Hallstatt (Austria), which offer a unique opportunity because they are associated with genealogical data. Our results indicate pronounced covariation of traits throughout the skull. Separate simulations of selection for localized shape changes corresponding to some of the principal derived characters of modern human skulls produced outcomes that were similar to each other and involved a joint response in all of these traits. The data for both genetic and phenotypic shape variation were not consistent with the hypothesis that the face, cranial base, and cranial vault are completely independent modules but relatively strongly integrated structures. These results indicate pervasive integration in the human skull and suggest a reinterpretation of the selective scenario for human evolution where the origin of any one of the derived characters may have facilitated the evolution of the others.
Collapse
|
37
|
Tennessen JA, O'Connor TD, Bamshad MJ, Akey JM. The promise and limitations of population exomics for human evolution studies. Genome Biol 2011; 12:127. [PMID: 21920050 PMCID: PMC3308040 DOI: 10.1186/gb-2011-12-9-127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality.
Collapse
Affiliation(s)
- Jacob A Tennessen
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Box 355065, Seattle, WA 98195-5065, USA
| | | | | | | |
Collapse
|