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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [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: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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Béliveau C, Gagné P, Picq S, Vernygora O, Keeling CI, Pinkney K, Doucet D, Wen F, Spencer Johnston J, Maaroufi H, Boyle B, Laroche J, Dewar K, Juretic N, Blackburn G, Nisole A, Brunet B, Brandão M, Lumley L, Duan J, Quan G, Lucarotti CJ, Roe AD, Sperling FAH, Levesque RC, Cusson M. The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins. Genome Biol Evol 2022; 14:evac087. [PMID: 35668612 PMCID: PMC9210311 DOI: 10.1093/gbe/evac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.
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Affiliation(s)
- Catherine Béliveau
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Patrick Gagné
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Sandrine Picq
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Oksana Vernygora
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Christopher I Keeling
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Quebec, Canada
| | - Kristine Pinkney
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Daniel Doucet
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Fayuan Wen
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington DC, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, 2475 College Station, Texas, USA
| | - Halim Maaroufi
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Brian Boyle
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Jérôme Laroche
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Ken Dewar
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - Nikoleta Juretic
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gwylim Blackburn
- Pacific Forestry Centre, Natural Resources Canada, Victoria, British Columbia, Canada
| | - Audrey Nisole
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
| | - Bryan Brunet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Marcelo Brandão
- Laboratório de Biologia Integrativa e Sistêmica - CBMEG/UNICAMP, Campinas, Brazil
| | - Lisa Lumley
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jun Duan
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Guoxing Quan
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | | | - Amanda D Roe
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Michel Cusson
- Laurentian Forestry Centre, Natural Resources Canada, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Quebec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
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Nelson TD, MacDonald ZG, Sperling FAH. Moths passing in the night: Phenological and genomic divergences within a forest pest complex. Evol Appl 2022; 15:166-180. [PMID: 35126654 PMCID: PMC8792478 DOI: 10.1111/eva.13338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Temporal separation of reproductive timing can contribute to species diversification both through allochronic speciation and later reinforcement of species boundaries. Such phenological differences are an enigmatic component of evolutionary divergence between two major forest defoliator species of the spruce budworm complex: Choristoneura fumiferana and C. occidentalis. While these species interbreed freely in laboratory settings, natural hybridization rates have not been reliably quantified due to their indistinguishable morphology. To assess whether temporal isolation is contributing to reproductive isolation, we collected adult individuals throughout their expected zone of sympatry in western Canada at 10-day intervals over two successive years, assigning taxonomic identities using thousands of single nucleotide polymorphisms. We found unexpectedly broad sympatry between C. fumiferana and C. occidentalis biennis and substantial overlap of regional flight periods. However, flight period divergence was much more apparent on a location-by-location basis, highlighting the importance of considering spatial scale in these analyses. Phenological comparisons were further complicated by the biennial life cycle of C. o. biennis, the main subspecies of C. occidentalis in the region, and the occasional occurrence of the annually breeding subspecies C. o. occidentalis. Nonetheless, we demonstrate that biennialism is not a likely contributor to reproductive isolation within the species complex. Overall, interspecific F1 hybrids comprised 2.9% of sequenced individuals, confirming the genomic distinctiveness of C. fumiferana and C. occidentalis, while also showing incomplete reproductive isolation of lineages. Finally, we used F ST-based outlier and genotype-environment association analyses to identify several genomic regions under putative divergent selection. These regions were disproportionately located on the Z linkage region of C. fumiferana, and contained genes, particularly antifreeze proteins, that are likely to be associated with overwintering success and diapause. In addition to temporal isolation, we conclude that other mechanisms, including ecologically mediated selection, are contributing to evolutionary divergence within the spruce budworm species complex.
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Affiliation(s)
- Tyler D. Nelson
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Summerland Research and Development CentreAgriculture and Agri‐Food CanadaSummerlandBritish ColumbiaCanada
| | - Zachary G. MacDonald
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Department of Renewable ResourcesUniversity of AlbertaEdmontonAlbertaCanada
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Wen G, Fu J. Isolation and reconnection: Demographic history and multiple contact zones of the green odorous frog (Odorrana margaretae) around the Sichuan Basin. Mol Ecol 2021; 30:4103-4117. [PMID: 34145663 DOI: 10.1111/mec.16021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 01/25/2023]
Abstract
The green odorous frog (Odorrana margaretae) displays a circular distribution around the Sichuan Basin of western China and possesses multiple replicate hybrid zones between lineages with high levels of divergence. To gain an understanding of the speciation process, we obtained 1540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: the West, North & South, and East groups. Demographic inference showed that they were initially isolated at ~2 million years ago, and subsequent post-glacial expansion produced the current circular distribution with four secondary contact zones. Hybridization in those zones involved lineages with various levels of divergence and produced greatly different patterns of introgression. Contact zones between the East and North & South groups (E-S and E-N) had contrast admixture levels but both showed a general lack of potential barrier loci. Meanwhile, the reconnection of the West and North & South groups produced two contact zones along the rim of the Basin. The S-W zone had extensive admixture while the N-W zone had limited admixture within a narrow geographic distance. Both showed substantial barrier effects, and a large number of potential barrier loci were shared. We also detected strong coupling among these loci. The N-W hybrid zone involved two highly-diverged lineages (FST = 0.704) and many loci have reached fixation around the hybrid zone. This study system offers a unique opportunity to understand the dynamics of introgression in contact zones and the architecture of reproductive isolation at different stages of speciation.
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Affiliation(s)
- Guannan Wen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Lumley LM, Pouliot E, Laroche J, Boyle B, Brunet BMT, Levesque RC, Sperling FAH, Cusson M. Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm ( Choristoneura fumiferana). Ecol Evol 2020; 10:914-927. [PMID: 32015854 PMCID: PMC6988549 DOI: 10.1002/ece3.5950] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.
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Affiliation(s)
- Lisa M. Lumley
- Royal Alberta MuseumEdmontonABCanada
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Esther Pouliot
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
| | | | | | | | | | | | - Michel Cusson
- Laurentian Forestry CentreNatural Resources CanadaQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
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