1
|
Laetsch DR, Bisschop G, Martin SH, Aeschbacher S, Setter D, Lohse K. Demographically explicit scans for barriers to gene flow using gIMble. PLoS Genet 2023; 19:e1010999. [PMID: 37816069 PMCID: PMC10610087 DOI: 10.1371/journal.pgen.1010999] [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: 06/06/2023] [Revised: 10/27/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Progress has been impeded by a conceptual and methodological divide between analyses that infer the demographic history of speciation and genome scans aimed at identifying locally maladaptive alleles i.e. genomic barriers to gene flow. Here we implement genomewide IM blockwise likelihood estimation (gIMble), a composite likelihood approach for the quantification of barriers, that bridges this divide. This analytic framework captures background selection and selection against barriers in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. gIMble includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied pair of sister species of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analyses uncover both large-effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of a polygenic barrier architecture.
Collapse
Affiliation(s)
- Dominik R. Laetsch
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Gertjan Bisschop
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon H. Martin
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Derek Setter
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Konrad Lohse
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
2
|
Yoshida N, Morinaga SI, Wakamiya T, Ishii Y, Kubota S, Hikosaka K. Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient. JOURNAL OF PLANT RESEARCH 2023; 136:183-199. [PMID: 36547771 DOI: 10.1007/s10265-022-01429-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Adaptive divergence occurs even between insufficiently isolated populations when there is a great difference in environments between their habitats. Individuals present in an intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene flow. A selective pressure that acts on the genetically admixed individuals may limit the gene flow and maintain the adaptive divergence. Here, we addressed a question whether selection occurs in the genetically admixed individuals between two divergent populations. Arabidopsis halleri is a perennial montane plant, which has clear phenotypic dimorphisms between highland and lowland habitats in Mt. Ibuki, central Japan. We obtained the whole-genome sequences of Arabidopsis halleri plants along an altitudinal gradient of 359-1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found a zone where the highland and lowland genes were mixing (intermediate subpopulation). In the intermediate subpopulation, we identified 5 and 13 genome regions, which included 3 and 8 genes, that had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively. In addition, we also found that the frequency of highland alleles of these selected genome regions was smaller in the lowland subpopulation compared with that of the non-selected regions. These results suggest that the selection in the intermediate subpopulation might limit the gene flow and contribute to the adaptive divergence between altitudes. We also identified 7 genome regions that had low heterozygote frequencies in the intermediate subpopulation. We conclude that different types of selection in addition to gene flow occur at the intermediate altitude and shape the genetic structure across altitudes.
Collapse
Affiliation(s)
- Naofumi Yoshida
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan.
| | - Shin-Ichi Morinaga
- Faculty of Life and Environmental Sciences, Teikyo University of Science, 120-0045, Adachi, Tokyo, Japan
| | - Takeshi Wakamiya
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Kagamiyama, Hiroshima, Higashi, Japan
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan
| | | | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan
| |
Collapse
|
3
|
Eriksson M, Kinnby A, De Wit P, Rafajlović M. Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms. Evol Appl 2023; 16:486-503. [PMID: 36793703 PMCID: PMC9923493 DOI: 10.1111/eva.13482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies nonzero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral, or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments or correlated to fitness.
Collapse
Affiliation(s)
- Martin Eriksson
- Department of Marine Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Gothenburg Sweden.,Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden
| | - Alexandra Kinnby
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Gothenburg Sweden.,Department of Marine Sciences University of Gothenburg Strömstad-Tjärnö Sweden
| | - Pierre De Wit
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Gothenburg Sweden.,Department of Marine Sciences University of Gothenburg Strömstad-Tjärnö Sweden
| | - Marina Rafajlović
- Department of Marine Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Gothenburg Sweden
| |
Collapse
|
4
|
White NJ, Beckerman AP, Snook RR, Brockhurst MA, Butlin RK, Eyres I. Experimental evolution of local adaptation under unidimensional and multidimensional selection. Curr Biol 2022; 32:1310-1318.e4. [DOI: 10.1016/j.cub.2022.01.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 01/17/2023]
|
5
|
Fraïsse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes. Genetics 2021; 217:6042694. [PMID: 33724409 DOI: 10.1093/genetics/iyaa025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
Collapse
Affiliation(s)
- Christelle Fraïsse
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Himani Sachdeva
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,Mathematics and BioSciences Group, Faculty of Mathematics, University of Vienna, A-1090 Vienna, Austria
| |
Collapse
|
6
|
Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190528. [PMID: 32654637 PMCID: PMC7423269 DOI: 10.1098/rstb.2019.0528] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Collapse
Affiliation(s)
- Jonna Kulmuni
- Organismal and Evolutionary Biology, University of Helsinki, Finland
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | | |
Collapse
|
7
|
|