1
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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2
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Sanderson BJ, Gambhir D, Feng G, Hu N, Cronk QC, Percy DM, Freaner FM, Johnson MG, Smart LB, Keefover-Ring K, Yin T, Ma T, DiFazio SP, Liu J, Olson MS. Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives. Syst Biol 2023; 72:1220-1232. [PMID: 37449764 DOI: 10.1093/sysbio/syad042] [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: 09/29/2021] [Revised: 06/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an fbranch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.
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Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Diksha Gambhir
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Nan Hu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Quentin C Cronk
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Diana M Percy
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York 14456, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tongming Yin
- Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
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3
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Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
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4
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Buck R, Ortega-Del Vecchyo D, Gehring C, Michelson R, Flores-Rentería D, Klein B, Whipple AV, Flores-Rentería L. Sequential hybridization may have facilitated ecological transitions in the Southwestern pinyon pine syngameon. THE NEW PHYTOLOGIST 2023; 237:2435-2449. [PMID: 36251538 DOI: 10.1111/nph.18543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Multispecies interbreeding networks, or syngameons, have been increasingly reported in natural systems. However, the formation, structure, and maintenance of syngameons have received little attention. Through gene flow, syngameons can increase genetic diversity, facilitate the colonization of new environments, and contribute to hybrid speciation. In this study, we evaluated the history, patterns, and consequences of hybridization in a pinyon pine syngameon using morphological and genomic data to assess genetic structure, demographic history, and geographic and climatic data to determine niche differentiation. We demonstrated that Pinus edulis, a dominant species in the Southwestern US and a barometer of climate change, is a core participant in the syngameon, involved in the formation of two drought-adapted hybrid lineages including the parapatric and taxonomically controversial fallax-type. We found that species remain morphologically and genetically distinct at range cores, maintaining species boundaries while undergoing extensive gene flow in areas of sympatry at range peripheries. Our study shows that sequential hybridization may have caused relatively rapid speciation and facilitated the colonization of different niches, resulting in the rapid formation of two new lineages. Participation in the syngameon may allow adaptive traits to be introgressed across species barriers and provide the changes needed to survive future climate scenarios.
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Affiliation(s)
- Ryan Buck
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Querétaro, 76230, Mexico
| | - Catherine Gehring
- Department of Biological Sciences and Center for Adaptive Western Landscapes, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Rhett Michelson
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, NV, 89146, USA
| | - Dulce Flores-Rentería
- CONACYT-CINVESTAV Unidad Saltillo, Grupo de Sustentabilidad de los Recursos Naturales y Energía, Av. Industria Metalúrgica 1062, Parque Industrial Ramos Arizpe, 25900, Ramos Arizpe, Coahuila, Mexico
| | - Barbara Klein
- Diné College, School of Science, Technology, Engineering and Mathematics, Tsaile, AZ, 86556, USA
| | - Amy V Whipple
- Department of Biological Sciences and Center for Adaptive Western Landscapes, Northern Arizona University, Flagstaff, AZ, 86011, USA
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5
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Eckert AJ, Neale DB. Probing the dark matter of environmental associations yields novel insights into the architecture of adaptation. THE NEW PHYTOLOGIST 2023; 237:1479-1482. [PMID: 36528858 DOI: 10.1111/nph.18639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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6
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Chaturvedi S, Gompert Z, Feder JL, Osborne OG, Muschick M, Riesch R, Soria-Carrasco V, Nosil P. Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects. Nat Ecol Evol 2022; 6:1952-1964. [PMID: 36280782 PMCID: PMC7613875 DOI: 10.1038/s41559-022-01909-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/13/2022] [Indexed: 12/15/2022]
Abstract
Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.
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Affiliation(s)
- Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA.
| | - Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, UK
| | - Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Rüdiger Riesch
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Patrik Nosil
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Univ. Paul Valéry Montpellier 3, Montpellier, France
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7
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Blanco Pastor JL. Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates. Genome Biol Evol 2022; 14:6647590. [PMID: 35859297 PMCID: PMC9348624 DOI: 10.1093/gbe/evac107] [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] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.
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8
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Hodel RGJ, Massatti R, Knowles LL. Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges. Mol Ecol 2022; 31:3722-3737. [PMID: 35560840 PMCID: PMC9327521 DOI: 10.1111/mec.16502] [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: 05/19/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.
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Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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9
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Liu JJ, Schoettle AW, Sniezko RA, Waring KM, Williams H, Zamany A, Johnson JS, Kegley A. Comparative Association Mapping Reveals Conservation of Major Gene Resistance to White Pine Blister Rust in Southwestern White Pine ( Pinus strobiformis) and Limber Pine ( P. flexilis). PHYTOPATHOLOGY 2022; 112:1093-1102. [PMID: 34732078 DOI: 10.1094/phyto-09-21-0382-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All native North American white pines are highly susceptible to white pine blister rust (WPBR) caused by Cronartium ribicola. Understanding genomic diversity and molecular mechanisms underlying genetic resistance to WPBR remains one of the great challenges in improvement of white pines. To compare major gene resistance (MGR) present in two species, southwestern white pine (Pinus strobiformis) Cr3 and limber pine (P. flexilis) Cr4, we performed association analyses of Cr3-controlled resistant traits using single nucleotide polymorphism (SNP) assays designed with Cr4-linked polymorphic genes. We found that ∼70% of P. flexilis SNPs were transferable to P. strobiformis. Furthermore, several Cr4-linked SNPs were significantly associated with the Cr3-controlled traits in P. strobiformis families. The most significantly associated SNP (M326511_1126R) almost colocalized with Cr4 on the Pinus consensus linkage group 8, suggesting that Cr3 and Cr4 might be the same R locus, or have localizations very close to each other in the syntenic region of the P. strobiformis and P. flexilis genomes. M326511_1126R was identified as a nonsynonymous SNP, causing amino acid change (Val376Ile) in a putative pectin acetylesterase, with coding sequences identical between the two species. Moreover, top Cr3-associated SNPs were further developed as TaqMan genotyping assays, suggesting their usefulness as marker-assisted selection (MAS) tools to distinguish genotypes between quantitative resistance and MGR. This work demonstrates the successful transferability of SNP markers between two closely related white pine species in the hybrid zone, and the possibility for deployment of MAS tools to facilitate long-term WPBR management in P. strobiformis breeding and conservation.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Anna W Schoettle
- Rocky Mountain Research Station, Forest Service, U.S. Department of Agriculture, Fort Collins, CO 80526, U.S.A
| | - Richard A Sniezko
- Dorena Genetic Resource Center, Forest Service, U.S. Department of Agriculture, Cottage Grove, OR 97424, U.S.A
| | - Kristen M Waring
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011-5018, U.S.A
| | - Holly Williams
- Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Jeremy S Johnson
- Dorena Genetic Resource Center, Forest Service, U.S. Department of Agriculture, Cottage Grove, OR 97424, U.S.A
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011-5018, U.S.A
| | - Angelia Kegley
- Dorena Genetic Resource Center, Forest Service, U.S. Department of Agriculture, Cottage Grove, OR 97424, U.S.A
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10
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Abstract
Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.
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Affiliation(s)
- Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Current affiliation: Yale Institute for Biospheric Studies and Yale School of the Environment, Yale University, New Haven, Connecticut 06511, USA;
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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11
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Menon M, Bagley JC, Page GFM, Whipple AV, Schoettle AW, Still CJ, Wehenkel C, Waring KM, Flores-Renteria L, Cushman SA, Eckert AJ. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 2021; 4:160. [PMID: 33547394 PMCID: PMC7864969 DOI: 10.1038/s42003-020-01632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/18/2020] [Indexed: 01/30/2023] Open
Abstract
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.
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Affiliation(s)
- Mitra Menon
- grid.27860.3b0000 0004 1936 9684Department of Evolution and Ecology, University of California, Davis, CA USA
| | - Justin C. Bagley
- grid.257992.20000 0001 0019 1845Department of Biology, Jacksonville State University, Jacksonville, AL USA
| | - Gerald F. M. Page
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Amy V. Whipple
- grid.261120.60000 0004 1936 8040Department of Biological Sciences and Merriam Powel Center for Environmental Research, Northern Arizona University, Flagstaff, AZ USA
| | - Anna W. Schoettle
- grid.497401.f0000 0001 2286 5230Rocky Mountain Research Station, USDA Forest Service, Fort Collins, CO USA
| | - Christopher J. Still
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Christian Wehenkel
- grid.412198.70000 0000 8724 8383Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango, Mexico
| | - Kristen M. Waring
- grid.261120.60000 0004 1936 8040School of Forestry, Northern Arizona University, Flagstaff, AZ USA
| | - Lluvia Flores-Renteria
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA
| | - Samuel A. Cushman
- grid.472551.00000 0004 0404 3120Rocky Mountain Research Station, USDA Forest Service, Flagstaff, AZ USA
| | - Andrew J. Eckert
- grid.224260.00000 0004 0458 8737Department of Biology, Virginia Commonwealth University, Richmond, VA USA
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