1
|
Burban E, Tenaillon MI, Glémin S. RIDGE, a tool tailored to detect gene flow barriers across species pairs. Mol Ecol Resour 2024; 24:e13944. [PMID: 38419376 DOI: 10.1111/1755-0998.13944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE-Reproductive Isolation Detection using Genomic polymorphisms-a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model-averaging approach to accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along the genome while accounting for variation in linked selection and recombination. The barrier detection test relies on numerous summary statistics to compute a Bayes factor, offering a robust statistical framework that facilitates cross-species comparisons. Simulations revealed RIDGE's efficiency in capturing signals of ongoing migration. Model averaging proved particularly valuable in scenarios of high model uncertainty where no migration or migration homogeneity can be wrongly assumed, typically for recent divergence times <0.1 2Ne generations. Applying RIDGE to four published crow data sets, we first validated our tool by identifying a well-known large genomic region associated with mate choice patterns. Second, while we identified a significant overlap of outlier loci using RIDGE and traditional genomic scans, our results suggest that a substantial portion of previously identified outliers are likely false positives. Outlier detection relies on allele differentiation, relative measures of divergence and the count of shared polymorphisms and fixed differences. Our analyses also highlight the value of incorporating multiple summary statistics including our newly developed outlier ones that can be useful in challenging detection conditions.
Collapse
Affiliation(s)
- Ewen Burban
- University of Rennes, CNRS, ECOBIO-UMR 6553, Rennes, France
| | - Maud I Tenaillon
- University Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Sylvain Glémin
- University of Rennes, CNRS, ECOBIO-UMR 6553, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| |
Collapse
|
2
|
Li LF, Pusadee T, Wedger MJ, Li YL, Li MR, Lau YL, Yap SJ, Jamjod S, Rerkasem B, Hao Y, Song BK, Olsen KM. Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia. Nat Commun 2024; 15:1182. [PMID: 38383554 PMCID: PMC10881511 DOI: 10.1038/s41467-024-45447-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.
Collapse
Affiliation(s)
- Lin-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Tonapha Pusadee
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Marshall J Wedger
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Ya-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ming-Rui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - Sansanee Jamjod
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Benjavan Rerkasem
- Plant Genetic Resources and Nutrition Laboratory, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Yan Hao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Beng-Kah Song
- School of Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA.
| |
Collapse
|
3
|
González GE, Poggio L. Polyploid speciation in Zea (Poaceae): cytogenetic insights. PLANTA 2024; 259:67. [PMID: 38332313 DOI: 10.1007/s00425-024-04345-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024]
Abstract
MAIN CONCLUSION The analysis of meiotic pairing affinities and genomic formulae in species and hybrids of Zea allowed us to speculate an evolutionary model to recreate the ancient polyploidization of maize and allied species. The meiotic pairing affinities and the genomic formulae analysis in Zea species and hybrids obtained in new and previous crosses, together with the molecular data known in the genus, allowed us to speculate an evolutionary model to attempt to recreate the ancient polyploidization process of Zea species. We propose that x = 5 semispecies are the ancestors of all modern species of the genus. The complex evolutionary process that originated the different taxa could be included hybridization between sympatric diploid ancestral semispecies (2n = 10) and recurrent duplication of the hybrid chromosome number, resulting in distinct auto- and allopolyploids. After the merger and doubling of independent genomes would have undergone cytological and genetical diploidization, implying revolutionary changes in genome organization and genic balance processes. Based on the meiotic behaviour of the 2n = 30 hybrids, that showed homoeology between the A subgenomes of all parental species, we propose that this subgenome A would be pivotal in all the species and would have conserved the rDNA sequences and the pairing regulator locus (PrZ). In the hypothetical model postulated here, the ancestral semispecies with the pivotal subgenome A would have had a wide geographic distribution, co-occurring and hybridizing with the semispecies harbouring B subgenomes, thus enabling sympatric speciation.
Collapse
Affiliation(s)
- Graciela Esther González
- Instituto de Ecología, Genética y Evolución (IEGEBA, Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Lidia Poggio
- Instituto de Ecología, Genética y Evolución (IEGEBA, Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
4
|
Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
Collapse
Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| |
Collapse
|