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Nguyen TN, Repenning M, Suertegaray Fontana C, Campagna L. Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters. Evolution 2024:qpae051. [PMID: 38530643 DOI: 10.1093/evolut/qpae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Indexed: 03/28/2024]
Abstract
Incomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences between Sporophila plumbea and S. beltoni. S. beltoni has only recently been described based, most notably, on differences in bill coloration (yellow vs. black in S. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified three narrow peaks along the genome with highly differentiated SNPs. These regions harbor six genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation.
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Affiliation(s)
- Tram N Nguyen
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA
| | - Márcio Repenning
- Universidade Federal do Rio Grande (FURG), Laboratório de Aves Aquáticas e Tartarugas Marinhas (LAATM). Av. Itália km 8, Campus Carreiros, 96203-900, Rio Grande, Rio Grande do Sul, Brazil
| | - Carla Suertegaray Fontana
- Universidade Federal do Rio Grande do Sul (UFRGS). Laboratório de Ecologia de Comunidades e Populações, Instituto de Biociências, Avenida Bento Gonçalves, 9500, 91501-970, Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-graduação em Biodiversidade Animal, Universidade Federal de Santa Maria
| | - Leonardo Campagna
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
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2
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Soudi S, Crepeau M, Collier TC, Lee Y, Cornel AJ, Lanzaro GC. Genomic signatures of local adaptation in recent invasive Aedes aegypti populations in California. BMC Genomics 2023; 24:311. [PMID: 37301847 DOI: 10.1186/s12864-023-09402-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Rapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and spread of vector-borne disease, although they remain relatively unexplored. RESULTS Here, we integrate whole-genome sequencing data from 96 Aedes aegypti mosquitoes collected from various sites in southern and central California with 25 annual topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principal components and admixture analysis, were consistent with three genetic clusters. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic and environmental variation, we identified 112 genes showing strong signals of local environmental adaptation associated with one or more topo-climate factors. Some of them have known effects in climate adaptation, such as heat-shock proteins, which shows selective sweep and recent positive selection acting on these genomic regions. CONCLUSIONS Our results provide a genome wide perspective on the distribution of adaptive loci and lay the foundation for future work to understand how environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and how such adaptation could help or hinder efforts at population control.
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Affiliation(s)
- Shaghayegh Soudi
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Marc Crepeau
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Travis C Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
| | - Anthony J Cornel
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA
- Mosquito Control Research Laboratory, Department of Entomology and Nematology, University of California, Parlier, CA, USA
| | - Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California Davis, Davis, CA, USA.
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3
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Ahmadi N, Barry MB, Frouin J, de Navascués M, Toure MA. Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes' Selective Footprints in the Genes Network Regulating Flowering Time. Rice (N Y) 2023; 16:15. [PMID: 36947285 PMCID: PMC10033818 DOI: 10.1186/s12284-023-00633-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.
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Affiliation(s)
- Nourollah Ahmadi
- UMR AGAP, CIRAD, TA-A 108/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France.
- AGAP, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | | | - Julien Frouin
- UMR AGAP, CIRAD, TA-A 108/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France
- AGAP, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Miguel de Navascués
- CBGP, CIRAD, INRAE, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Horimoto ARVR, Xue D, Thornton TA, Blue EE. Admixture mapping reveals the association between Native American ancestry at 3q13.11 and reduced risk of Alzheimer's disease in Caribbean Hispanics. Alzheimers Res Ther 2021; 13:122. [PMID: 34217363 PMCID: PMC8254995 DOI: 10.1186/s13195-021-00866-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/20/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Genetic studies have primarily been conducted in European ancestry populations, identifying dozens of loci associated with late-onset Alzheimer's disease (AD). However, much of AD's heritability remains unexplained; as the prevalence of AD varies across populations, the genetic architecture of the disease may also vary by population with the presence of novel variants or loci. METHODS We conducted genome-wide analyses of AD in a sample of 2565 Caribbean Hispanics to better understand the genetic contribution to AD in this population. Statistical analysis included both admixture mapping and association testing. Evidence for differential gene expression within regions of interest was collected from independent transcriptomic studies comparing AD cases and controls in samples with primarily European ancestry. RESULTS Our genome-wide association study of AD identified no loci reaching genome-wide significance. However, a genome-wide admixture mapping analysis that tests for association between a haplotype's ancestral origin and AD status detected a genome-wide significant association with chromosome 3q13.11 (103.7-107.7Mb, P = 8.76E-07), driven by a protective effect conferred by the Native American ancestry (OR = 0.58, 95%CI = 0.47-0.73). Within this region, two variants were significantly associated with AD after accounting for the number of independent tests (rs12494162, P = 2.33E-06; rs1731642, P = 6.36E-05). The significant admixture mapping signal is composed of 15 haplotype blocks spanning 5 protein-coding genes (ALCAM, BBX, CBLB, CCDC54, CD47) and four brain-derived topologically associated domains, and includes markers significantly associated with the expression of ALCAM, BBX, CBLB, and CD47 in the brain. ALCAM and BBX were also significantly differentially expressed in the brain between AD cases and controls with European ancestry. CONCLUSION These results provide multiethnic evidence for a relationship between AD and multiple genes at 3q13.11 and illustrate the utility of leveraging genetic ancestry diversity via admixture mapping for new insights into AD.
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Affiliation(s)
| | - Diane Xue
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Elizabeth E Blue
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA.
- Division of Medical Genetics, University of Washington, BOX 357720, Seattle, WA, 98195-7720, USA.
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6
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Grummer JA, Whitlock MC, Schulte PM, Taylor EB. Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss). BMC Ecol Evol 2021; 21:63. [PMID: 33888062 PMCID: PMC8063319 DOI: 10.1186/s12862-021-01795-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01795-9.
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Affiliation(s)
- Jared A Grummer
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Michael C Whitlock
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Eric B Taylor
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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El-Kurdi A, Khalil GA, Khazen G, Khoueiry P. fcScan: a versatile tool to cluster combinations of sites using genomic coordinates. BMC Bioinformatics 2020; 21:194. [PMID: 32429868 PMCID: PMC7236483 DOI: 10.1186/s12859-020-3536-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Finding combinations of homotypic or heterotypic genomic sites obeying a specific grammar in DNA sequences is a frequent task in bioinformatics. A typical case corresponds to the identification of cis-regulatory modules characterized by a combination of transcription factor binding sites in a defined window size. Although previous studies identified clusters of genomic sites in species with varying genome sizes, the availability of a dedicated and versatile tool to search for such clusters is lacking. RESULTS We present fcScan, an R/Bioconductor package to search for clusters of genomic sites based on user defined criteria including cluster size, inter-cluster distances and sites order and orientation allowing users to adapt their search criteria to specific biological questions. It supports GRanges, data frame and VCF/BED files as input and returns data in GRanges format. By performing clustering on vectorized data, fcScan is adapted to search for genomic clusters in millions of sites as input in short time and is thus ideal to scan data generated by high throughput methods including next generation sequencing. CONCLUSIONS fcScan is ideal for detecting cis-regulatory modules of transcription factor binding sites with a specific grammar as well as genomic loci enriched for mutations. The flexibility in input parameters allows users to perform searches targeting specific research questions. It is released under Artistic-2.0 License. The source code is freely available through Bioconductor (https://bioconductor.org/packages/fcScan) and GitHub (https://github.com/pkhoueiry/fcScan).
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Affiliation(s)
- Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghiwa Ali Khalil
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Georges Khazen
- Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon. .,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
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Lobréaux S, Miquel C. Identification of Arabis alpina genomic regions associated with climatic variables along an elevation gradient through whole genome scan. Genomics 2020; 112:729-35. [PMID: 31085222 DOI: 10.1016/j.ygeno.2019.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/24/2019] [Accepted: 05/08/2019] [Indexed: 01/23/2023]
Abstract
We performed a pooled whole-genome sequencing on samples of the alpine plant Arabis alpina, harvested in ten populations along an elevation gradient in the French Alps. A large dataset of genetic variations was produced as single nucleotide polymorphisms (SNPs). A combined genome scan approach enabled detecting genomic regions associated with a synthetic environmental variable characterizing the climate at each sampling location. Positive loci detected by two methods were retained and belong to 19 regions in the Arabis alpina genome. The most significant region harbors an ortholog of the AtNAC062 gene, encoding a membrane-bound transcription factor described as linking the cold response and pathogen resistance that may confer protection to plants under extended snow coverage at high elevations. Other genes involved in the stress response or in flowering regulation were also detected. Altogether, our results indicated that Arabis alpina represent a suitable model for studying genomic adaptation in alpine perennial plants.
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Buckley J, Holub EB, Koch MA, Vergeer P, Mable BK. Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection. BMC Genomics 2018; 19:496. [PMID: 29945543 PMCID: PMC6020377 DOI: 10.1186/s12864-018-4806-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 05/18/2018] [Indexed: 11/22/2022] Open
Abstract
Background Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima’s D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts. Electronic supplementary material The online version of this article (10.1186/s12864-018-4806-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. .,Adaptation to a Changing Environment, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Eric B Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, D69120, Heidelberg, Germany
| | - Philippine Vergeer
- Plant Ecology and Nature Conservation Group, Wageningen University, P.O.Box 47, 6700, AA, Wageningen, The Netherlands
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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10
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Dalongeville A, Benestan L, Mouillot D, Lobreaux S, Manel S. Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus). BMC Genomics 2018; 19:217. [PMID: 29580201 PMCID: PMC5870821 DOI: 10.1186/s12864-018-4579-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/02/2018] [Indexed: 12/24/2022] Open
Abstract
Background Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species. Results Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method. Conclusion The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment. Electronic supplementary material The online version of this article (10.1186/s12864-018-4579-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alicia Dalongeville
- CEFE UMR 5175, EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, 34293, Montpellier, France. .,MARBEC UMR 9190, CNRS - IRD - Université Montpellier - Ifremer, 34095, Montpellier, France.
| | - Laura Benestan
- Departement de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - David Mouillot
- MARBEC UMR 9190, CNRS - IRD - Université Montpellier - Ifremer, 34095, Montpellier, France
| | - Stephane Lobreaux
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, BP53 38041, Grenoble, France
| | - Stéphanie Manel
- CEFE UMR 5175, EPHE, PSL Research University, CNRS, UM, SupAgro, IRD, INRA, 34293, Montpellier, France
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Croze M, Wollstein A, Božičević V, Živković D, Stephan W, Hutter S. A genome-wide scan for genes under balancing selection in Drosophila melanogaster. BMC Evol Biol 2017; 17:15. [PMID: 28086750 PMCID: PMC5237213 DOI: 10.1186/s12862-016-0857-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/17/2016] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population. We screened a total of 34 genomes searching for regions of high genetic diversity and an excess of SNPs with intermediate frequency. RESULTS In total, we found 183 candidate genes: 141 in the European population and 45 in the African one, with only three genes shared between both populations. Most differences between both populations were observed on the X chromosome, though this might be partly due to false positives. Functionally, we find an overrepresentation of genes involved in neuronal development and circadian rhythm. Furthermore, some of the top genes we identified are involved in innate immunity. CONCLUSION Our results revealed evidence of genes under balancing selection in European and African populations. More candidate genes have been found in the European population. They are involved in several different functions.
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Affiliation(s)
- Myriam Croze
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Vedran Božičević
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Daniel Živković
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Center of Food and Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Natural History Museum Berlin, 10115, Berlin, Germany
| | - Stephan Hutter
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
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12
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Balao F, García-Castaño JL. AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations. Plant Methods 2014; 10:40. [PMID: 25926861 PMCID: PMC4413549 DOI: 10.1186/1746-4811-10-40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/24/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND In spite of a large diversity of approaches to investigate loci under selection from a population genetic perspective, very few programs have been specifically designed to date to test selection in hybrids using dominant markers. In addition, simulators of dominant markers are very scarce and they do not usually take into account hybridization. RESULTS Here, we present a new, multifunctional, R package for dominant genetic markers, AFLPsim. This package can simulate dominant markers in hybridizing populations and implements genome scan methods for detecting outlier dominant loci in hybrids. In addition, it includes tools for further manipulating the results, plotting them and other tasks. We describe and tabulate the major functions implemented in AFLPsim. In addition, we provide some demonstration of its use and we perform a comparative study with other software. Finally, we conclude by briefly describing the input and output formats. CONCLUSIONS The R package AFLPsim application provides several useful tools in the context of hybridization studies. It can simulate dominant markers in hybridizing populations and predict their demographic evolution. In addition, we implement a new genome scan method for detecting outlier dominant loci in hybrids, which shows a rather high sensitivity and is very conservative in comparison with Gagnaire et al.'s, Bayescan and introgress. The application is downloadable at http://cran.r-project.org/web/packages/AFLPsim/.
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Affiliation(s)
- Francisco Balao
- />Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap-1095, 41080 Sevilla, Spain
- />Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, 1030 Austria
| | - Juan Luis García-Castaño
- />Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap-1095, 41080 Sevilla, Spain
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Lobréaux S, Melodelima C. Detection of genomic loci associated with environmental variables using generalized linear mixed models. Genomics 2015; 105:69-75. [PMID: 25499197 DOI: 10.1016/j.ygeno.2014.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 11/27/2014] [Accepted: 12/05/2014] [Indexed: 11/21/2022]
Abstract
We tested the use of Generalized Linear Mixed Models to detect associations between genetic loci and environmental variables, taking into account the population structure of sampled individuals. We used a simulation approach to generate datasets under demographically and selectively explicit models. These datasets were used to analyze and optimize GLMM capacity to detect the association between markers and selective coefficients as environmental data in terms of false and true positive rates. Different sampling strategies were tested, maximizing the number of populations sampled, sites sampled per population, or individuals sampled per site, and the effect of different selective intensities on the efficiency of the method was determined. Finally, we apply these models to an Arabidopsis thaliana SNP dataset from different accessions, looking for loci associated with spring minimal temperature. We identified 25 regions that exhibit unusual correlations with the climatic variable and contain genes with functions related to temperature stress.
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Leroy T, Le Cam B, Lemaire C. When virulence originates from non-agricultural hosts: new insights into plant breeding. Infect Genet Evol 2014; 27:521-9. [PMID: 24412509 DOI: 10.1016/j.meegid.2013.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/11/2013] [Accepted: 12/30/2013] [Indexed: 12/27/2022]
Abstract
Monogenic plant resistance breakdown is a model for testing evolution in action in pathogens. As a rule, plant pathologists argue that virulence - the allele that allows pathogens to overcome resistance - is due to a new mutation at the avirulence locus within the native/endemic population that infects susceptible crops. In this article, we develop an alternative and neglected scenario where a given virulence pre-exists in a non-agricultural host and might be accidentally released or introduced on the matching resistant cultivar in the field. The main difference between the two scenarios is the divergence time expected between the avirulent and the virulent populations. As a consequence, population genetic approaches such as genome scans and Approximate Bayesian Computation methods allow explicit testing of the two scenarios by timing the divergence. This review then explores the fundamental implications of this alternative scenario for plant breeding, including the invasion of virulence or the evolution of more aggressive hybrids, and proposes concrete solutions to achieve a sustainable resistance.
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Affiliation(s)
- Thibault Leroy
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France
| | - Bruno Le Cam
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France
| | - Christophe Lemaire
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France.
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