1
|
Yang CH, Scarpino SV. The ensemble of gene regulatory networks at mutation-selection balance. J R Soc Interface 2023; 20:20220075. [PMID: 36596452 PMCID: PMC9810427 DOI: 10.1098/rsif.2022.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The evolution of diverse phenotypes both involves and is constrained by molecular interaction networks. When these networks influence patterns of expression, we refer to them as gene regulatory networks (GRNs). Here, we develop a model of GRN evolution analogous to work from quasi-species theory, which is itself essentially the mutation-selection balance model from classical population genetics extended to multiple loci. With this GRN model, we prove that-across a broad spectrum of selection pressures-the dynamics converge to a stationary distribution over GRNs. Next, we show from first principles how the frequency of GRNs at equilibrium is related to the topology of the genotype network, in particular, via a specific network centrality measure termed the eigenvector centrality. Finally, we determine the structural characteristics of GRNs that are favoured in response to a range of selective environments and mutational constraints. Our work connects GRN evolution to quasi-species theory-and thus to classical populations genetics-providing a mechanistic explanation for the observed distribution of GRNs evolving in response to various evolutionary forces, and shows how complex fitness landscapes can emerge from simple evolutionary rules.
Collapse
Affiliation(s)
- Chia-Hung Yang
- Network Science Institute, Northeastern University, Boston, MA, USA
| | - Samuel V. Scarpino
- Network Science Institute, Northeastern University, Boston, MA, USA,Institute for Experiential AI, Northeastern University, Boston, MA, USA,Department of Health Sciences, Northeastern University, Boston, MA, USA,Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA,Roux Institute, Northeastern University, Boston, MA, USA,Santa Fe Institute, Santa Fe, NM, USA,Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA
| |
Collapse
|
2
|
Bogaerts‐Márquez M, Guirao‐Rico S, Gautier M, González J. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Mol Ecol 2021; 30:938-954. [PMID: 33350518 PMCID: PMC7986194 DOI: 10.1111/mec.15783] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well-annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%-51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome-environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.
Collapse
Affiliation(s)
- María Bogaerts‐Márquez
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| |
Collapse
|
3
|
Jones MR, Mills LS, Jensen JD, Good JM. The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares. Am Nat 2020; 196:316-332. [DOI: 10.1086/710022] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
4
|
Jones MR, Mills LS, Jensen JD, Good JM. Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range*. Evolution 2020; 74:2033-2045. [DOI: 10.1111/evo.13976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew R. Jones
- Division of Biological Sciences University of Montana Missoula Montana 59812
| | - L. Scott Mills
- Wildlife Biology Program University of Montana Missoula Montana 59812
- Office of Research and Creative Scholarship University of Montana Missoula Montana 59812
| | - Jeffrey D. Jensen
- School of Life Sciences Arizona State University Tempe Arizona 85281
| | - Jeffrey M. Good
- Division of Biological Sciences University of Montana Missoula Montana 59812
- Wildlife Biology Program University of Montana Missoula Montana 59812
| |
Collapse
|
5
|
Abstract
Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established “de novo” from marine colonists. Independently evolved freshwater populations exhibit similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels of gene flow leads to significant mutation load – but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.
Collapse
|
6
|
Schweizer RM, Velotta JP, Ivy CM, Jones MR, Muir SM, Bradburd GS, Storz JF, Scott GR, Cheviron ZA. Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice. PLoS Genet 2019; 15:e1008420. [PMID: 31697676 PMCID: PMC6837288 DOI: 10.1371/journal.pgen.1008420] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/13/2019] [Indexed: 11/19/2022] Open
Abstract
Evolutionary adaptation to extreme environments often requires coordinated changes in multiple intersecting physiological pathways, but how such multi-trait adaptation occurs remains unresolved. Transcription factors, which regulate the expression of many genes and can simultaneously alter multiple phenotypes, may be common targets of selection if the benefits of induced changes outweigh the costs of negative pleiotropic effects. We combined complimentary population genetic analyses and physiological experiments in North American deer mice (Peromyscus maniculatus) to examine links between genetic variation in transcription factors that coordinate physiological responses to hypoxia (hypoxia-inducible factors, HIFs) and multiple physiological traits that potentially contribute to high-altitude adaptation. First, we sequenced the exomes of 100 mice sampled from different elevations and discovered that several SNPs in the gene Epas1, which encodes the oxygen sensitive subunit of HIF-2α, exhibited extreme allele frequency differences between highland and lowland populations. Broader geographic sampling confirmed that Epas1 genotype varied predictably with altitude throughout the western US. We then discovered that Epas1 genotype influences heart rate in hypoxia, and the transcriptomic responses to hypoxia (including HIF targets and genes involved in catecholamine signaling) in the heart and adrenal gland. Finally, we used a demographically-informed selection scan to show that Epas1 variants have experienced a history of spatially varying selection, suggesting that differences in cardiovascular function and gene regulation contribute to high-altitude adaptation. Our results suggest a mechanism by which Epas1 may aid long-term survival of high-altitude deer mice and provide general insights into the role that highly pleiotropic transcription factors may play in the process of environmental adaptation.
Collapse
Affiliation(s)
- Rena M. Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- * E-mail:
| | - Jonathan P. Velotta
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Catherine M. Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Matthew R. Jones
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Sarah M. Muir
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Gideon S. Bradburd
- Ecology, Evolutionary Biology, and Behavior Graduate Group, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Zachary A. Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| |
Collapse
|