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Publications (10 of 72) Show all publications
Zhao, W., Gao, J., Hall, D., Andersson, B., Bruxaux, J., Tomlinson, K. W., . . . Wang, X.-R. (2024). Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. New Phytologist
Open this publication in new window or tab >>Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow
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2024 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed) Epub ahead of print
Abstract [en]

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with (Formula presented.) 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

Place, publisher, year, edition, pages
Wiley-Blackwell Publishing Inc., 2024
Keywords
demographic history, divergent adaptation, ecological gradients, introgression, phylogeny, Pinus evolution, selection
National Category
Botany Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-222889 (URN)10.1111/nph.19694 (DOI)001188798500001 ()2-s2.0-85188811775 (Scopus ID)
Funder
Swedish Research Council, 2017-04686Swedish Research Council Formas, 2021-02155
Available from: 2024-04-08 Created: 2024-04-08 Last updated: 2024-04-08
Bruxaux, J., Zhao, W., Hall, D., Curtu, A. L., Androsiuk, P., Drouzas, A. D., . . . Wang, X.-R. (2024). Scots pine – panmixia and the elusive signal of genetic adaptation. New Phytologist
Open this publication in new window or tab >>Scots pine – panmixia and the elusive signal of genetic adaptation
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2024 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed) Epub ahead of print
Abstract [en]

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them.

To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.

We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients.

The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
conifer, demography, gene flow, genetic diversity, genetic-environmental association, Pinus sylvestris, population structure
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-221025 (URN)10.1111/nph.19563 (DOI)001155409000001 ()2-s2.0-85184157884 (Scopus ID)
Funder
Swedish Research Council Formas, 2018-00842Swedish Research Council Formas, 2021-02155Carl Tryggers foundation
Available from: 2024-03-06 Created: 2024-03-06 Last updated: 2024-03-06
He, L., Guo, F.-Y., Cai, X.-J., Chen, H.-P., Lian, C.-L., Wang, Y., . . . Wang, X.-R. (2023). Evolutionary origin and establishment of a dioecious diploid-tetraploid complex. Molecular Ecology, 32(11), 2732-2749
Open this publication in new window or tab >>Evolutionary origin and establishment of a dioecious diploid-tetraploid complex
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2023 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 11, p. 2732-2749Article in journal (Refereed) Published
Abstract [en]

Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
dioecious plants, mountain biodiversity, polyploidization, population history, sex determination system
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-206352 (URN)10.1111/mec.16902 (DOI)000946777300001 ()36843569 (PubMedID)2-s2.0-85150602020 (Scopus ID)
Available from: 2023-04-26 Created: 2023-04-26 Last updated: 2023-07-12Bibliographically approved
Qu, C., Kao, H.-N., Xu, H., Wang, B.-S., Yang, Z.-L., Yang, Q., . . . Zeng, Q.-Y. (2023). Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex. Journal of Systematics and Evolution
Open this publication in new window or tab >>Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex
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2023 (English)In: Journal of Systematics and Evolution, ISSN 1674-4918, E-ISSN 1759-6831Article in journal (Refereed) Epub ahead of print
Abstract [en]

Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
enzymatic function, functional divergence, gene expression, glutathione S-transferases, homoploid hybrid species
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-206957 (URN)10.1111/jse.12953 (DOI)000970443700001 ()2-s2.0-85152362299 (Scopus ID)
Available from: 2023-04-26 Created: 2023-04-26 Last updated: 2023-09-05
Guo, J.-F., Zhao, W., Andersson, B., Mao, J.-F. & Wang, X.-R. (2023). Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau. Plant Communications, 4(4), Article ID 100574.
Open this publication in new window or tab >>Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau
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2023 (English)In: Plant Communications, E-ISSN 2590-3462, Vol. 4, no 4, article id 100574Article in journal (Refereed) Published
Abstract [en]

Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.

Place, publisher, year, edition, pages
Cell Press, 2023
Keywords
demographic history, ecological selection, genomic cline, introgression outliers, reproductive isolation, species boundary
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-208078 (URN)10.1016/j.xplc.2023.100574 (DOI)2-s2.0-85153500172 (Scopus ID)
Funder
Swedish Research Council, 2017-04686
Available from: 2023-05-17 Created: 2023-05-17 Last updated: 2024-01-10Bibliographically approved
Andersson, B., Zhao, W., Haller, B. C., Brännström, Å. & Wang, X.-R. (2023). Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure. Molecular Ecology Resources, 23(7), 1589-1603
Open this publication in new window or tab >>Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure
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2023 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 23, no 7, p. 1589-1603Article in journal (Refereed) Published
Abstract [en]

The distribution of fitness effects (DFE) of new mutations has been of interest to evolutionary biologists since the concept of mutations arose. Modern population genomic data enable us to quantify the DFE empirically, but few studies have examined how data processing, sample size and cryptic population structure might affect the accuracy of DFE inference. We used simulated and empirical data (from Arabidopsis lyrata) to show the effects of missing data filtering, sample size, number of single nucleotide polymorphisms (SNPs) and population structure on the accuracy and variance of DFE estimates. Our analyses focus on three filtering methods—downsampling, imputation and subsampling—with sample sizes of 4–100 individuals. We show that (1) the choice of missing-data treatment directly affects the estimated DFE, with downsampling performing better than imputation and subsampling; (2) the estimated DFE is less reliable in small samples (<8 individuals), and becomes unpredictable with too few SNPs (<5000, the sum of 0- and 4-fold SNPs); and (3) population structure may skew the inferred DFE towards more strongly deleterious mutations. We suggest that future studies should consider downsampling for small data sets, and use samples larger than 4 (ideally larger than 8) individuals, with more than 5000 SNPs in order to improve the robustness of DFE inference and enable comparative analyses.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
DFE, missing-data treatment, population structure, sample size, SLiM simulation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-211803 (URN)10.1111/1755-0998.13825 (DOI)001015493200001 ()37340611 (PubMedID)2-s2.0-85162975600 (Scopus ID)
Funder
Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC)
Available from: 2023-07-11 Created: 2023-07-11 Last updated: 2024-01-10Bibliographically approved
Guo, J.-F., Wang, B., Liu, Z.-L., Mao, J.-F., Wang, X.-R. & Zhao, W. (2023). Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana. Journal of Systematics and Evolution, 61(1), 143-156
Open this publication in new window or tab >>Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana
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2023 (English)In: Journal of Systematics and Evolution, ISSN 1674-4918, E-ISSN 1759-6831, Vol. 61, no 1, p. 143-156Article in journal (Refereed) Published
Abstract [en]

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
climate relict, genetic diversity, genomic offset, migration barrier, Pinus bungeana, population bottleneck
National Category
Botany Genetics
Identifiers
urn:nbn:se:umu:diva-192657 (URN)10.1111/jse.12821 (DOI)000755100500001 ()2-s2.0-85124608048 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC)Swedish Research Council
Available from: 2022-02-21 Created: 2022-02-21 Last updated: 2023-07-13Bibliographically approved
Gao, J., Tomlinson, K. W., Zhao, W., Wang, B., Lapuz, R. S., Liu, J.-X., . . . Wang, X.-R. (2023). Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia. Journal of Systematics and Evolution
Open this publication in new window or tab >>Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia
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2023 (English)In: Journal of Systematics and Evolution, ISSN 1674-4918, E-ISSN 1759-6831Article in journal (Refereed) Epub ahead of print
Abstract [en]

Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
cpDNA, introgression, mtDNA capture, phylogeography, Pinus kesiya, Pinus yunnanensis
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-206205 (URN)10.1111/jse.12949 (DOI)000945788000001 ()2-s2.0-85150507847 (Scopus ID)
Available from: 2023-04-03 Created: 2023-04-03 Last updated: 2023-04-03
Hall, D., Zhao, W., Heuchel, A., Gao, J., Wennström, U. & Wang, X.-R. (2023). The effect of gene flow on frost tolerance in Scots pine – Latitudinal translocation of genetic material. Forest Ecology and Management, 544, Article ID 121215.
Open this publication in new window or tab >>The effect of gene flow on frost tolerance in Scots pine – Latitudinal translocation of genetic material
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2023 (English)In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 544, article id 121215Article in journal (Refereed) Published
Abstract [en]

Extensive gene flow can be detrimental to local adaptation and similarly, forestry seed sources such as seed orchards can be heavily influenced by external pollination, especially if the orchard material has been translocated a great distance. Here we conducted a coordinated genotyping-phenotyping study to examine how external pollination events and fecundity variation in a Pinus sylvestris seed orchard influence the genetic composition and the seed-lots’ autumn frost hardiness when genetic material had been translocated 630 km south. The results were then compared to those of a in situ established seed orchard. We genotyped and phenotype >1000 seedlings from these orchards, and constructed their pedigrees and scored their autumn frost tolerance in a controlled climate chamber environment. The hardiness scores were compared with a reference of nine natural stands along a latitudinal cline. We find substantial variation in fecundity and external pollination over crop years, thus unpredictable genetic composition because the contribution of some orchard clones is high in one crop but low in another. We observed that seedlings produced by mating among orchard genotypes were less hardy than expected (corresponding to an origin of −0.6°N) but the opposite in externally pollinated seedlings (+0.3 to +0.7°N). The freeze damage levels reflect the origin of parental genotypes, but to a smaller degree than expected (13% lower than expected damage levels for externally pollinate seedlings and 21% greater damage levels for internally pollinates seedlings). These results suggest that orchard parents’ origins, mating composition and orchard local environment could all affect the seed crops’ quality and their climate adaptation. Seed orchard crops are the key to realize the gain in forestry from breeding efforts. However, genetic monitoring of seed crops is necessary to improve the performance of seed orchards further and adjust deployment areas of seed crops in a timely manner for a more dynamic forestry, considering climate change and biodiversity demands.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
Cold hardiness, External pollination, Genetic composition, Pollen contamination, Scots pine, Seed orchard crops
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-211147 (URN)10.1016/j.foreco.2023.121215 (DOI)2-s2.0-85162203117 (Scopus ID)
Funder
Swedish Research Council, 2018-05973Swedish National Infrastructure for Computing (SNIC)Swedish Research Council Formas, 2018-00842Swedish Research Council Formas, 2021-02155
Available from: 2023-07-06 Created: 2023-07-06 Last updated: 2023-10-31Bibliographically approved
Borthakur, D., Busov, V., Cao, X. H., Du, Q., Gailing, O., Isik, F., . . . Wei, H. (2022). Current status and trends in forest genomics. Forestry Research, 2, Article ID 11.
Open this publication in new window or tab >>Current status and trends in forest genomics
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2022 (English)In: Forestry Research, E-ISSN 2767-3812, Vol. 2, article id 11Article, review/survey (Refereed) Published
Abstract [en]

Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

Place, publisher, year, edition, pages
Maximum Academic Press, 2022
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-216632 (URN)10.48130/FR-2022-0011 (DOI)2-s2.0-85144615227 (Scopus ID)
Available from: 2023-11-17 Created: 2023-11-17 Last updated: 2023-11-17Bibliographically approved
Projects
Importance of allelic variation in homoploid hybrid speciation in plants [2008-05709_VR]; Umeå UniversityIn-depth evaluation of the function of an advanced Scots pine seed orchard [2010-591_Formas]; Umeå UniversityEcological and genetic dynamics in species boundaries [2011-03195_VR]; Umeå UniversityLong-term sustainable forest production: knowledge-based strategies in seed orchard and reforestation operations [2015-67_Formas]; Umeå UniversityDynamics of hybrid speciation and adaptation to extreme habitats [2017-04686_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-6150-7046

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