1
|
Peláez P, Lorenzana GP, Baesen K, Montes JR, De La Torre AR. Spatially heterogeneous selection and inter-varietal differentiation maintain population structure and local adaptation in a widespread conifer. BMC Ecol Evol 2024; 24:117. [PMID: 39227766 PMCID: PMC11373507 DOI: 10.1186/s12862-024-02304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir's genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates. RESULTS Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas. CONCLUSIONS Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.
Collapse
Affiliation(s)
- Pablo Peláez
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Kailey Baesen
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Jose Ruben Montes
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | |
Collapse
|
2
|
Wesselkamp M, Roberts DR, Dormann CF. Identifying potential provenances for climate-change adaptation using spatially variable coefficient models. BMC Ecol Evol 2024; 24:70. [PMID: 38807083 DOI: 10.1186/s12862-024-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials can take decades, hence any approach that supports focussing on a likely set of candidates may save time and money. We use a non-stationary statistical analysis with spatially varying coefficients to identify ecotypes that indicate first regions of similarly adapted varieties of Douglas-fir (Pseudotsuga menziesii (Mirbel) Franco) in North America. For over 70,000 plot-level presence-absences, spatial differences in the survival response to climatic conditions are identified. RESULTS The spatially-variable coefficient model fits the data substantially better than a stationary, i.e. constant-effect analysis (as measured by AIC to account for differences in model complexity). Also, clustering the model terms identifies several potential ecotypes that could not be derived from clustering climatic conditions itself. Comparing these six identified ecotypes to known genetically diverging regions shows some congruence, as well as some mismatches. However, comparing ecotypes among each other, we find clear differences in their climate niches. CONCLUSION While our approach is data-demanding and computationally expensive, with the increasing availability of data on species distributions this may be a useful first screening step during the search for climate-change adapted varieties. With our unsupervised learning approach being explorative, finely resolved genotypic data would be helpful to improve its quantitative validation.
Collapse
Affiliation(s)
- Marieke Wesselkamp
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany.
| | - David R Roberts
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
- InnoTech Alberta, 3608 - 33 Street NW, Calgary, AB, T2L 2A6, Canada
- Alberta Biodiversity Monitoring Institute, 1-107 Centennial Centre for Interdisciplinary Studies (CCIS), University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Carsten F Dormann
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
| |
Collapse
|
3
|
Molecular Genetic Identification Explains Differences in Bud Burst Timing among Progenies of Selected Trees of the Swedish Douglas Fir Breeding Programme. FORESTS 2022. [DOI: 10.3390/f13060895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Douglas fir is expected to play an increasingly important role in Swedish forestry under a changing climate. Thus far, seed orchards with clones of phenotypically selected trees (plus trees) have been established to supply the market with highly qualitative reproductive material. Given the high genetic variation of the species, its growth properties are significantly affected by the provenance. Here, we applied microsatellite markers to identify the origin of clones selected within the Swedish breeding programme. Moreover, we analysed the timing of bud burst in open-pollinated families of these clones. In particular, we aimed to explain the provenance effect on phenology by using molecular identification as a proxy. A Bayesian clustering analysis with microsatellite data enabled the assignment of the clones to one of the two varieties and also resolved within-variety origins. The phenological observations indicated an earlier bud burst of the interior variety. Within the coastal variety, the northern provenances exhibited a later bud burst. We found a significant effect of the identified origin on bud burst timing. The results of this study will be used to support further breeding efforts.
Collapse
|
4
|
Non-Native Forest Tree Species in Europe: The Question of Seed Origin in Afforestation. FORESTS 2022. [DOI: 10.3390/f13020273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Non-native forest tree species have been introduced in Europe since the 16th century, but only in the second half of the 20th century the significance of the seed source origin for their economic use was recognized, resulting in the establishment of numerous provenance trials at a national, regional, European and International level, as those led by IUFRO. Breeding programs have also been launched in the continent for the most economically important species. Aim of this work is the formulation of provenance recommendations for planting of five non-native tree species in Europe (Douglas fir, grand fir, Sitka spruce, lodgepole pine and black locust), based on the information obtained from twenty countries, in the frame of the EU FP-1403 NNEXT Cost Action. The survey revealed that official and non-official national recommendations, based on provenance research results, have been elaborated and followed at a different level and extend for the above five species, but only for Douglas fir recommendations exist in almost all the participating to the survey countries. The compilation of provenance recommendations across Europe for each species is presented in the current work. Besides the recommended introduced seed sources, European seed sources are also preferred for planting, due to ease of access and high availability of forest reproductive material. European breeding programs yielding genetic material of high productivity and quality constitute currently the seed source of choice for several species and countries. Consolidation of trial data obtained across countries will allow the joint analysis that is urgently needed to draw solid conclusions, and will facilitate the development of ‘Universal-Response-Functions’ for the species of interest, rendering possible the identification of the genetic material suitable for global change. New provenance trial series that will test seed sources from the entire climatic range of the species, established in sites falling within and outside the environmental envelopes of their natural ranges, are urgently needed to pinpoint and understand the species-specific climate constraints, as well as to correlate functional traits to the seed origin and the environmental conditions of the test sites, so that the selection of suitable forest reproductive material of non-native tree species in the face of climate change can be feasible.
Collapse
|
5
|
George J, Schueler S, Grabner M, Karanitsch‐Ackerl S, Mayer K, Stierschneider M, Weissenbacher L, van Loo M. Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir ( Pseudotsuga menziesii). Ecol Evol 2021; 11:8238-8253. [PMID: 34188883 PMCID: PMC8216971 DOI: 10.1002/ece3.7654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 11/24/2022] Open
Abstract
Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.
Collapse
Affiliation(s)
- Jan‐Peter George
- Faculty of Science & TechnologyTartu ObservatoryUniversity of TartuTartuEstonia
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Silvio Schueler
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsViennaAustria
| | - Michael Grabner
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Sandra Karanitsch‐Ackerl
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Konrad Mayer
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | | | - Lambert Weissenbacher
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| |
Collapse
|
6
|
North American Douglas-fir ( P. menziesii) in Europe: establishment and reproduction within new geographic space without consequences for its genetic diversity. Biol Invasions 2019; 21:3249-3267. [PMID: 31929722 PMCID: PMC6936651 DOI: 10.1007/s10530-019-02045-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 06/25/2019] [Indexed: 01/02/2023]
Abstract
Genetic admixture and plasticity along with propagule pressure, large seed dispersal distances and fast adaptation support successful establishment and spread of introduced species outside their native range. Consequently, introductions may display climatic niche shifts in the introduced range. Douglas-fir, a controversial forest and ornamental conifer represented by two ecologically different and hybridising varieties, was transferred multiple times outside the native range in North America. Here, we compare climatic and genetic patterns of 38 native populations from North America with six old Pseudotsuga menziesii populations with natural regeneration in the introduced range in Central Europe. Following variety and geographic origin assessment of introduced populations, genotypic and climatic data were examined for signatures of inter-varietal gene flow, reduced genetic diversity, presence of fine-scale spatial genetic structure (SGS), dispersal patterns, and climate similarities between native and introduced range. In the introduced range, dominating coastal variety originated from a restricted area in the US, whereas the interior variety, with limited presence in the European sites, displayed wider geographic origin. Variety hybrids with contributing coastal, but not the interior parent were identified. Differences in genetic diversity between both ranges, but also among the parent and their respective offspring populations in Europe were not found. Old populations in general lacked any SGS, whereas natural regeneration revealed different patterns of SGS. Distances of propagule dispersal ranged between 2.5 and 92 m. The climate of the studied European introduced range was most similar to the climate of the coastal variety from the western Cascade range from which the majority of the analysed coastal European Douglas-fir, but not the European interior variety, was assigned to originate. The results we present here shed not only light on dynamics of invasive species in the introduced range in general, but also allow for refinement of climatic niche modeling when using lower than species level.
Collapse
|
7
|
Aubriot X, Knapp S, Syfert MM, Poczai P, Buerki S. Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongena L.) and its wild relatives. AMERICAN JOURNAL OF BOTANY 2018; 105:1175-1187. [PMID: 30091787 DOI: 10.1002/ajb2.1133] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/04/2018] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY While brinjal eggplant (Solanum melongena L.) is the second most important solanaceous fruit crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step-wise expansion of the eggplant group from Africa to Asia. METHODS We use museum collections to generate nuclear and full-plastome data for all species of the Eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade. KEY RESULTS The Eggplant clade has Pleistocene origins in northern Africa. Dispersals to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to African distinct lineages of widespread and southern African species. Results suggest that spread of the species to southern Africa has been recent and likely facilitated by large mammalian herbivores, such as the African elephant and impala feeding on Solanum fruit. CONCLUSIONS Rather than a linear 'Out Of Africa' sequence, our results are more consistent with an initial dispersal event into Asia, and subsequent wide dispersal and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will affect future work on eggplant domestication and affect the use of wild relatives in breeding of this increasingly important solanaceous crop.
Collapse
Affiliation(s)
- Xavier Aubriot
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
- Unité Mixte de Recherche 6553 Écosystèmes, Biodiversité, Évolution (ECOBIO), Observatoire des Sciences de l'Univers de Rennes, Centre National de la Recherche Scientifique, Université de Rennes 1, Rennes CEDEX, France
| | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
| | - Mindy M Syfert
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland
| | - Sven Buerki
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, U.S.A
| |
Collapse
|
8
|
Hrivnák M, Paule L, Krajmerová D, Kulaç Ş, Şevik H, Turna İ, Tvauri I, Gömöry D. Genetic variation in Tertiary relics: The case of eastern-Mediterranean Abies (Pinaceae). Ecol Evol 2017; 7:10018-10030. [PMID: 29238533 PMCID: PMC5723589 DOI: 10.1002/ece3.3519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/11/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023] Open
Abstract
The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.
Collapse
Affiliation(s)
| | | | | | | | - Hakan Şevik
- Faculty of Engineering and Architecture Kastamonu University Kastamonu Turkey
| | - İbrahim Turna
- Faculty of Forestry Karadeniz Technical University Trabzon Turkey
| | - Irina Tvauri
- Scientific-Research Center of Agriculture Tbilisi Georgia.,Vasil Gulisashvili Forest Institute Agricultural University of Georgia Tbilisi Georgia
| | | |
Collapse
|