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Dean LL, Whiting JR, Jones FC, MacColl ADC. Reproductive isolation in a three-way contact zone. Mol Ecol 2024; 33:e17275. [PMID: 38235507 DOI: 10.1111/mec.17275] [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: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - James R Whiting
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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Qi M, Du FK, Guo F, Yin K, Tang J. Species identification through deep learning and geometrical morphology in oaks ( Quercus spp.): Pros and cons. Ecol Evol 2024; 14:e11032. [PMID: 38357593 PMCID: PMC10864717 DOI: 10.1002/ece3.11032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Plant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf-scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost-efficient method in terms of time-consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.
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Affiliation(s)
- Min Qi
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Fang K. Du
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Fei Guo
- School of Computer Science and EngineeringCentral South UniversityChangshaHunanChina
| | - Kangquan Yin
- School of Grassland ScienceBeijing Forestry UniversityBeijingChina
| | - Jijun Tang
- Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
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Indira Cervantes-Díaz C, Patiño-Conde V, González-Rodríguez A, Quesada M, Cuevas E. Molecular and morphological evidence of hybridization between two dimorphic sympatric species of Fuchsia (Onagraceae). AOB PLANTS 2024; 16:plad089. [PMID: 38213511 PMCID: PMC10783250 DOI: 10.1093/aobpla/plad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/16/2023] [Indexed: 01/13/2024]
Abstract
Hybridization is commonly reported in angiosperms, generally based on morphology, and in few cases confirmed by molecular markers. Fuchsia has a long tradition of ornamental cultivars with different hybrids produced by artificial crosses, so natural hybridization between sympatric Fuchsia species could be common. Natural hybridization between F. microphylla and F. thymifolia was tested using six newly developed microsatellites for F. microphylla in addition to other molecular markers with codominant and maternal inheritance. Geometric morphometrics of leaves and floral structures were also used to identify putative hybrids. Hybrids showed a different degree of genetic admixture between both parental species. Chloroplast DNA (cpDNA) sequences indicated that hybridization occurs in both directions, in fact, some of the hybrids showed new haplotypes for cpDNA and ITS (internal transcriber spacer of nuclear ribosomal RNA genes) sequences. The morphology of hybrid individuals varied between the two parental species, but they could be better identified by their leaves and floral tubes. Our study is the first to confirm the hybridization in natural populations of Fuchsia species and suggests that hybridization has probably occurred repeatedly throughout the entire distribution of the species. Phylogeographic analysis of both species will be essential to understanding the impact of hybridization throughout their complete distribution.
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Affiliation(s)
- Cinthya Indira Cervantes-Díaz
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo 58000, Morelia, Michoacán, México
| | - Violeta Patiño-Conde
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
| | - Mauricio Quesada
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
| | - Eduardo Cuevas
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo 58000, Morelia, Michoacán, México
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Rauschendorfer J, Rooney R, Külheim C. Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a changing climate. TREE PHYSIOLOGY 2022; 42:2383-2400. [PMID: 35867476 DOI: 10.1093/treephys/tpac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Red oaks (Quercus sect. Lobatae) are a taxonomic group of hardwood trees, which occur in swamp forests, subtropical chaparral and savannahs from Columbia to Canada. They cover a wide range of ecological niches, and many species are thought to be able to cope with current trends in climate change. Genus Quercus encompasses ca. 500 species, of which ca. 80 make up sect. Lobatae. Species diversity is greatest within the southeastern USA and within the northern and eastern regions of Mexico. This review discusses the weak reproductive barriers between species of red oaks and the effects this has on speciation and niche range. Distribution and diversity have been shaped by drought adaptations common to the species of sect. Lobatae, which enable them to fill various xeric niches across the continent. Drought adaptive traits of this taxonomic group include deciduousness, deep tap roots, ring-porous xylem, regenerative stump sprouting, greater leaf thickness and smaller stomata. The complex interplay between these anatomical and morphological traits has given red oaks features of drought tolerance and avoidance. Here, we discuss physiological and genetic components of these adaptations to address how many species of sect. Lobatae reside within xeric sites and/or sustain normal metabolic function during drought. Although extensive drought adaptation appears to give sect. Lobatae a resilience to climate change, aging tree stands, oak life history traits and the current genetic structures place many red oak species at risk. Furthermore, oak decline, a complex interaction between abiotic and biotic agents, has severe effects on red oaks and is likely to accelerate species decline and fragmentation. We suggest that assisted migration can be used to avoid species fragmentation and increase climate change resilience of sect. Lobatae.
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Affiliation(s)
- James Rauschendorfer
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rebecca Rooney
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Carsten Külheim
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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Du FK, Qi M, Zhang YY, Petit RJ. Asymmetric character displacement in mixed oak stands. THE NEW PHYTOLOGIST 2022; 236:1212-1224. [PMID: 35706383 DOI: 10.1111/nph.18311] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Ecological character displacement (ECD) refers to a pattern of increased divergence at sites where species ranges overlap caused by competition for resources. Although ECD is believed to be common, there are few in-depth studies that clearly establish its existence, especially in plants. Thus, we have compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks: Quercus dentata and Quercus aliena. In contrast to previous studies, we define sympatry and allopatry at a local scale, thereby comparing populations that can or cannot directly interact. Using genetic markers, we found greater genetic divergence between the two oak species growing in mixed stands and inferred that long-term gene flow has predominantly occurred asymmetrically from the cold-tolerant species (Q. dentata) to the warm-demanding later colonizing species (Q. aliena). Analysis of leaf traits revealed greater divergence in mixed than in pure oak stands. This was mostly due to the later colonizing species being characterized by more resource-conservative traits in the presence of the other species. Controlling for relevant environmental differences did not alter these conclusions. These results suggest that asymmetric trait divergence can take place where species coexist, possibly due to the imbalance in demographic history of species resulting in asymmetric inter-specific selection pressures.
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Affiliation(s)
- Fang K Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Min Qi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Rémy J Petit
- Université de Bordeaux, INRAE, BIOGECO, F-33610, Cestas, France
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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:ijms23179980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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Qiao Q, Ye M, Wu C, Wang J, Liu Q, Tao J, Zhang L, Feng Z. Analysis of leaf morphology variation and genetic diversity via SRAP markers for near-threatened plant Acer truncatum. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Silliman K, Zhao H, Justice M, Thongda W, Bowen B, Peatman E. Complex introgression among three diverged largemouth bass lineages. Evol Appl 2021; 14:2815-2830. [PMID: 34950231 PMCID: PMC8674896 DOI: 10.1111/eva.13314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/30/2022] Open
Abstract
Hybrid zones between diverged lineages offer a unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships among these Mobile Delta bass populations, M. salmoides and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.
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Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Honggang Zhao
- Department of Natural ResourcesCornell UniversityIthacaNew YorkUSA
| | - Megan Justice
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
| | - Bryant Bowen
- Georgia Department of Natural ResourcesSocial CircleGeorgiaUSA
| | - Eric Peatman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Li
X, Wei G, El-Kassaby YA, Fang Y. Hybridization and introgression in sympatric and allopatric populations of four oak species. BMC PLANT BIOLOGY 2021; 21:266. [PMID: 34107871 PMCID: PMC8188795 DOI: 10.1186/s12870-021-03007-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/05/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization. RESULTS Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844-0.944) and moderate differentiation (FST = 0.037-0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize. CONCLUSIONS Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.
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Affiliation(s)
- Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Gaoming Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
- School of Physics and Electronics Henan University, Jinming Avenue, Jinming District, Kaifeng, 475001 PR China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
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Chen XD, Yang J, Guo YF, Zhao YM, Zhou T, Zhang X, Ju MM, Li ZH, Zhao GF. Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Quercus fabri Hance in Subtropical China. FRONTIERS IN PLANT SCIENCE 2021; 11:583284. [PMID: 33613578 PMCID: PMC7889815 DOI: 10.3389/fpls.2020.583284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.
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Affiliation(s)
- Xiao-Dan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yu-Fan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yue-Mei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Miao-Miao Ju
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
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Peñaloza‐Ramírez JM, Rodríguez‐Correa H, González‐Rodríguez A, Rocha‐Ramírez V, Oyama K. High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae). Ecol Evol 2020; 10:4204-4219. [PMID: 32489590 PMCID: PMC7246204 DOI: 10.1002/ece3.6189] [Citation(s) in RCA: 4] [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: 05/06/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/19/2022] Open
Abstract
The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans-Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within-population genetic diversity was high (mean h S = 0.72), and among-population genetic differentiation showed a strong phylogeographic structure (N ST = 0.630 > G ST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.
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Affiliation(s)
- Juan Manuel Peñaloza‐Ramírez
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMéxico
| | - Hernando Rodríguez‐Correa
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMéxico
| | | | | | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMéxico
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Kremer A, Hipp AL. Oaks: an evolutionary success story. THE NEW PHYTOLOGIST 2020; 226:987-1011. [PMID: 31630400 PMCID: PMC7166131 DOI: 10.1111/nph.16274] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 09/13/2019] [Indexed: 05/10/2023]
Abstract
The genus Quercus is among the most widespread and species-rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro- and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.
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Affiliation(s)
- Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, 69 Route
d'Arcachon, 33612 Cestas, France
| | - Andrew L. Hipp
- The Morton Arboretum, Lisle IL 60532-1293, USA
- The Field Museum, Chicago IL 60605, USA
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15
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Wehenkel C, Mariscal-Lucero SDR, González-Elizondo MS, Aguirre-Galindo VA, Fladung M, López-Sánchez CA. Tall Pinus luzmariae trees with genes from P. herrerae. PeerJ 2020; 8:e8648. [PMID: 32149029 PMCID: PMC7049253 DOI: 10.7717/peerj.8648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
CONTEXT Pinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands. AIMS We aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico. METHODS AFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501. RESULTS Hybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population. CONCLUSIONS This is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture.
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Affiliation(s)
- Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Samantha del Rocío Mariscal-Lucero
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
- Instituto Tecnológico del Valle del Guadiana, Tecnológico Nacional de México, Durango, Mexico
| | | | - Víctor A. Aguirre-Galindo
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Carlos A. López-Sánchez
- Department of Organisms and Systems Biology, University of Oviedo, Polytechnic School of Mieres, Asturias, Spain
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Rubini Pisano A, Moré M, Cisternas MA, Raguso RA, Benitez-Vieyra S. Breakdown of species boundaries in Mandevilla: floral morphological intermediacy, novel fragrances and asymmetric pollen flow. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:206-215. [PMID: 30317685 DOI: 10.1111/plb.12924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/10/2018] [Indexed: 05/26/2023]
Abstract
Phenotypic intermediacy is an indicator of putative hybrid origin and has provided the main clues to discovering hybrid plants in nature. Mandevilla pentlandiana and M. laxa (Apocynaceae) are sister species with clear differences in floral phenotype and associated pollinator guilds: diurnal Hymenoptera and nocturnal hawkmoths, respectively. The presence of individuals with intermediate phenotypes in a wild population raises questions about the roles of visual and olfactory signals (i.e. corolla morphology and floral fragrances) as barriers to interbreeding, and how the breakdown of floral isolation occurs. We examined phenotypic variation in a mixed Mandevilla population, analysing the chemical composition of floral fragrances, characterising floral shape through geometric morphometrics and assessing individual grouping through taxonomically relevant traits and an unsupervised learning algorithm. We quantified the visitation frequencies of floral visitors and tracked their foraging movements using pollen analogues. The presence of morphologically intermediate individuals and pollen analogue movement suggested extensive hybridisation between M. laxa and M. pentlandiana, along with asymmetrical rates of backcrossing between these putative hybrids and M. laxa. Floral volatiles from putative hybrid individuals showed a transgressive phenotype, with additional compounds not emitted by either parental species. Our results suggest the presence of a hybrid swarm between sympatric M. pentlandiana and M. laxa and indicate that initial hybridisation events between these parental species are rare, but once they occur, visits between putative hybrids and M. laxa are common and facilitate continued introgression.
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Affiliation(s)
- A Rubini Pisano
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Instituto Multidisciplinario de Biología Vegetal (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - M Moré
- Instituto Multidisciplinario de Biología Vegetal (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - M A Cisternas
- Instituto Multidisciplinario de Biología Vegetal (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
- Jardín Botánico Nacional, Viña del Mar, Chile
| | - R A Raguso
- Department of Neurobiology and Behavior, Cornell University, Ithaca, USA
| | - S Benitez-Vieyra
- Instituto Multidisciplinario de Biología Vegetal (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
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17
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Castillo-Mendoza E, Salinas-Sánchez D, Valencia-Cuevas L, Zamilpa A, Tovar-Sánchez E. Natural hybridisation among Quercus glabrescens, Q. rugosa and Q. obtusata (Fagaceae): Microsatellites and secondary metabolites markers. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:110-121. [PMID: 30117248 DOI: 10.1111/plb.12899] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/12/2018] [Indexed: 06/08/2023]
Abstract
Natural hybridisation has significant ecological, genetic and evolutionary consequences altering morphological and chemical characters of individuals. Quercus glabrescens, Q. rugosa and Q. obtusata are white oak species well separated by their morphological characters when they occur in allopatry in Mexican temperate forests. However, in sympatry, individuals with atypical morphology have been observed, suggesting hybridisation events. In this study, we determined, with microsatellites and secondary metabolites, if interspecific gene flow occurs when these three oak species coexist in sympatry. In total, 180 individuals belonging to seven populations [three allopatric (one for each parental species) and four sympatric sites] were analysed. Allopatric populations represent well-defined genetic groups and the sympatric populations showed genetic evidence of hybridisation between Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata. The hybridisation percentage varied between sites and combination of involved species. We registered the presence of unique flavonoid compounds for Q. glabrescens (caffeic acid and flavonol 2), Q. rugosa (flavonol 5) and Q. obtusata (flavonol 1). Three compounds (quercetin rhamnoside, flavonol 3 and alkyl coumarate) were expressed in all taxa. Finally, the hybrid genotypes identified in this study (Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata) showed specific chemical profiles, resulting from a combination of those of their parental species. These results show that hybridisation events between these oak species alter chemical expression of secondary metabolites, creating a mosaic of resources and conditions that provide the substrate for different combinations of foliar-associated species such as herbivores, endophytic fungi or epiphyte plants.
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Affiliation(s)
- E Castillo-Mendoza
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CdMx, México
- Laboratorio de Marcadores Moleculares, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - D Salinas-Sánchez
- Laboratorio de Fitoquímica, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - L Valencia-Cuevas
- Laboratorio de Marcadores Moleculares, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - A Zamilpa
- Centro de Investigación Biomédica del Sur (CIBIS-IMSS), Xochitepec, Morelos, México
| | - E Tovar-Sánchez
- Laboratorio de Marcadores Moleculares, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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18
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Kim BY, Wei X, Fitz-Gibbon S, Lohmueller KE, Ortego J, Gugger PF, Sork VL. RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercussect.Quercus: Fagaceae). Mol Ecol 2018; 27:4556-4571. [DOI: 10.1111/mec.14869] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 07/25/2018] [Accepted: 08/29/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Bernard Y. Kim
- Department of Ecology and Evolutionary Biology; University of California at Los Angeles; Los Angeles California
| | - Xinzeng Wei
- Department of Ecology and Evolutionary Biology; University of California at Los Angeles; Los Angeles California
- Key Laboratory of Aquatic Botany and Watershed Ecology; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan Hubei China
| | - Sorel Fitz-Gibbon
- Department of Ecology and Evolutionary Biology; University of California at Los Angeles; Los Angeles California
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology; University of California at Los Angeles; Los Angeles California
- Department of Human Genetics; David Geffen School of Medicine; University of California; Los Angeles California
| | - Joaquín Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana, EBD-CSIC; Seville Spain
| | - Paul F. Gugger
- Department of Ecology and Evolutionary Biology; University of California at Los Angeles; Los Angeles California
- Appalachian Laboratory; University of Maryland Center for Environmental Science; Frostburg Maryland
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California at Los Angeles; Los Angeles California
- Institute of the Environment and Sustainability; University of California; Los Angeles California
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Fitzek E, Delcamp A, Guichoux E, Hahn M, Lobdell M, Hipp AL. A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting. Ecol Evol 2018; 8:5837-5851. [PMID: 29938097 PMCID: PMC6010771 DOI: 10.1002/ece3.4122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 11/16/2022] Open
Abstract
DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite-associated DNA sequencing (RAD-seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.
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Affiliation(s)
- Elisabeth Fitzek
- HerbariumThe Morton ArboretumLisleIllinois
- Present address:
Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois
| | - Adline Delcamp
- Site de Pierroton, Platforme Genome TranscriptomeINRACESTASFrance
- UMR1202 Biodiversité Gènes and CommunautésUniversity of BordeauxCESTASFrance
| | - Erwan Guichoux
- Site de Pierroton, Platforme Genome TranscriptomeINRACESTASFrance
- UMR1202 Biodiversité Gènes and CommunautésUniversity of BordeauxCESTASFrance
| | | | | | - Andrew L. Hipp
- HerbariumThe Morton ArboretumLisleIllinois
- Department of BotanyThe Field MuseumChicagoIllinois
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Lyu J, Song J, Liu Y, Wang Y, Li J, Du FK. Species Boundaries Between Three Sympatric Oak Species: Quercus aliena, Q. dentata, and Q. variabilis at the Northern Edge of Their Distribution in China. FRONTIERS IN PLANT SCIENCE 2018; 9:414. [PMID: 29662501 PMCID: PMC5890165 DOI: 10.3389/fpls.2018.00414] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Oaks are important timber trees with wide distributions in China, but few genetic studies have been conducted on a fine scale. In this study, we seek to investigate the genetic diversity and differentiation of three sympatric oak species (Quercus aliena Blume, Quercus dentata Thunb. ex Murray, and Quercus variabilis Blume) in their northern distribution in China using 17 bi-parentally inherited nSSRs markers and five maternally inherited chloroplast DNA (cpDNA) fragments. Both the cpDNA and the nSSRs show a high level of genetic differentiation between different oak sections. The chloroplast haplotypes are clustered into two lineages. Clear species boundaries are detected between Q. variabilis and either Q. aliena or Q. dentata. The sharing of chloroplast haplotype H1 between Q. aliena and Q. dentata suggests very recent speciation and incomplete lineage sorting or introgression of H1 from one species to another. The nSSRs data indicate a complete fixation of variation within sites for all three oak species, and that extensive gene flow occurs within species whereas only limited gene flow is detected between Q. aliena and Q. dentata and nearly no gene flow can be detected between Q. aliena and Q. variabilis and between Q. dentata and Q. variabilis. Prezygotic isolation may have contributed to the species boundaries of these three sympatric oak species.
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22
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Pham KK, Hipp AL, Manos PS, Cronn RC. A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny. Genome 2017; 60:720-732. [DOI: 10.1139/gen-2016-0191] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%–41% of plastome variation, geography 3%–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.
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Affiliation(s)
- Kasey K. Pham
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - Andrew L. Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Paul S. Manos
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Richard C. Cronn
- Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331-4401, USA
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Gramlich S, Hörandl E. Fitness of natural willow hybrids in a pioneer mosaic hybrid zone. Ecol Evol 2016; 6:7645-7655. [PMID: 30128118 PMCID: PMC6093150 DOI: 10.1002/ece3.2470] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 01/20/2023] Open
Abstract
Hybrid fitness is an important parameter to predict the evolutionary consequences of a hybridization event and to characterize hybrid zones. We studied fitness parameters of F1 and later-generation hybrids between the lowland species Salix purpurea and the alpine S. helvetica that have recently emerged during colonization of an alpine glacier forefield. Fruit production (number of capsules per catkin and fruit set) did not differ between hybrids and parents, but the number of seeds per capsule of F1 hybrids was slightly lower than that of later-generation hybrids and of the parents. Germination rates and seedling growth were tested on three substrates (pH 4.5, 7.0, and 8.0). Germination rates of seeds collected from F1 hybrids were lower on acid and neutral substrates, but equal at pH 8.0 compared to all other groups, while the seeds from later-generation hybrids performed as well as the parents on all three substrates. In seedling growth, the colonizer S. purpurea performed better than all other taxa on all three substrates, while hybrids resembled the subalpine species S. helvetica. Results suggest that endogenous selection acts against F1 hybrids, but favors fitter genotypes in later-generation hybrids. Exogenous selection via soil pH appears to be weak during seedling establishment. The pioneer vegetation on the glacier forefield may offer sufficient niche space for hybrid seedlings. Owing to the relatively high fitness of the hybrids and the scattered distribution of hybrids and parental individuals on the glacier forefield, this hybrid zone can be assigned to a mosaic model, probably facilitating gene flow and introgression between the parental species. As establishment of the hybrid zone appears to be linked to a colonization process, we propose to call it a pioneer mosaic hybrid zone.
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Affiliation(s)
- Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)Georg August University GöttingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)Georg August University GöttingenGöttingenGermany
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Simeone MC, Grimm GW, Papini A, Vessella F, Cardoni S, Tordoni E, Piredda R, Franc A, Denk T. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 2016; 4:e1897. [PMID: 27123376 PMCID: PMC4846808 DOI: 10.7717/peerj.1897] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/15/2016] [Indexed: 01/27/2023] Open
Abstract
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
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Affiliation(s)
- Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Guido W Grimm
- Department of Palaeontology, University of Wien , Wien , Austria
| | - Alessio Papini
- Dipartimento di Biologia, Università degli studi di Firenze , Firenze , Italy
| | - Federico Vessella
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Enrico Tordoni
- Department of Life Science, Università degli studi di Trieste , Trieste , Italy
| | | | - Alain Franc
- INRA, UMR BIOGECO-1202, Cestas, France; UMR BIOGECO-1202, Université Bordeaux, Talence, France
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History , Stockholm , Sweden
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Ávila-Flores IJ, Hernández-Díaz JC, González-Elizondo MS, Prieto-Ruíz JÁ, Wehenkel C. Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico. PLoS One 2016; 11:e0152651. [PMID: 27064490 PMCID: PMC4827862 DOI: 10.1371/journal.pone.0152651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material.
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Affiliation(s)
- Israel Jaime Ávila-Flores
- Doctorado Institucional en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - Maria Socorro González-Elizondo
- CIIDIR Unidad Durango, Instituto Politécnico Nacional, Sigma 119 Fracc, 20 de Noviembre II, Durango, Durango, México, C.P., 34220
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Blv. Durango y Ave, Papaloapan s/n. Col. Valle del Sur, Durango, Durango, México, C.P., 34120
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
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Simeone MC, Grimm GW, Papini A, Vessella F, Cardoni S, Tordoni E, Piredda R, Franc A, Denk T. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 2016. [PMID: 27123376 DOI: 10.7287/peerj.preprints.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
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Affiliation(s)
- Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Guido W Grimm
- Department of Palaeontology, University of Wien , Wien , Austria
| | - Alessio Papini
- Dipartimento di Biologia, Università degli studi di Firenze , Firenze , Italy
| | - Federico Vessella
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Enrico Tordoni
- Department of Life Science, Università degli studi di Trieste , Trieste , Italy
| | | | - Alain Franc
- INRA, UMR BIOGECO-1202, Cestas, France; UMR BIOGECO-1202, Université Bordeaux, Talence, France
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History , Stockholm , Sweden
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Floate KD, Godbout J, Lau MK, Isabel N, Whitham TG. Plant-herbivore interactions in a trispecific hybrid swarm of Populus: assessing support for hypotheses of hybrid bridges, evolutionary novelty and genetic similarity. THE NEW PHYTOLOGIST 2016; 209:832-844. [PMID: 26346922 DOI: 10.1111/nph.13622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/28/2015] [Indexed: 06/05/2023]
Abstract
UNLABELLED Natural systems of hybridizing plants are powerful tools with which to assess evolutionary processes between parental species and their associated arthropods. Here we report on these processes in a trispecific hybrid swarm of Populus trees. Using field observations, common garden experiments and genetic markers, we tested the hypothesis that genetic similarities among hosts underlie the distributions of 10 species of gall-forming arthropods and their ability to adapt to new host genotypes. KEY FINDINGS the degree of genetic relatedness among parental species determines whether hybridization is primarily bidirectional or unidirectional; host genotype and genetic similarity strongly affect the distributions of gall-forming species, individually and as a community. These effects were detected observationally in the wild and experimentally in common gardens; correlations between the diversity of host genotypes and their associated arthropods identify hybrid zones as centres of biodiversity and potential species interactions with important ecological and evolutionary consequences. These findings support both hybrid bridge and evolutionary novelty hypotheses. However, the lack of parallel genetic studies on gall-forming arthropods limits our ability to define the host of origin with their subsequent shift to other host species or their evolution on hybrids as their final destination.
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Affiliation(s)
- Kevin D Floate
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, T1J 4B1, Canada
| | - Julie Godbout
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec (Sainte-Foy), QC, G1V 4C7, Canada
| | - Matthew K Lau
- Merriam-Powell Center for Environmental Research and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec (Sainte-Foy), QC, G1V 4C7, Canada
| | - Thomas G Whitham
- Merriam-Powell Center for Environmental Research and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
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Valencia-Cuevas L, Tovar-Sánchez E. Oak canopy arthropod communities: which factors shape its structure? REVISTA CHILENA DE HISTORIA NATURAL 2015. [DOI: 10.1186/s40693-015-0045-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Huang CL, Ho CW, Chiang YC, Shigemoto Y, Hsu TW, Hwang CC, Ge XJ, Chen C, Wu TH, Chou CH, Huang HJ, Gojobori T, Osada N, Chiang TY. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:834-847. [PMID: 25237766 DOI: 10.1111/tpj.12676] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 06/03/2023]
Abstract
Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.
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Affiliation(s)
- Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
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Chybicki IJ, Burczyk J. Seeing the forest through the trees: comprehensive inference on individual mating patterns in a mixed stand of Quercus robur and Q. petraea. ANNALS OF BOTANY 2013; 112:561-74. [PMID: 23788747 PMCID: PMC3718219 DOI: 10.1093/aob/mct131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Sexual reproduction is one of the most important moments in a life cycle, determining the genetic composition of individual offspring. Controlled pollination experiments often show high variation in the mating system at the individual level, suggesting a persistence of individual variation in natural populations. Individual variation in mating patterns may have significant adaptive implications for a population and for the entire species. Nevertheless, field data rarely address individual differences in mating patterns, focusing rather on averages. This study aimed to quantify individual variation in the different components of mating patterns. METHODS Microsatellite data were used from 421 adult trees and 1911 seeds, structured in 72 half-sib families collected in a single mixed stand of Quercus robur and Q. petraea in northern Poland. Using a Bayesian approach, mating patterns were investigated, taking into account pollen dispersal, male fecundity, possible hybridization and heterogeneity in immigrant pollen pools. KEY RESULTS Pollen dispersal followed a heavy-tailed distribution (283 m on average). In spite of high pollen mobility, immigrant pollen pools showed strong genetic structuring among mothers. At the individual level, immigrant pollen pools showed highly variable divergence rates, revealing that sources of immigrant pollen can vary greatly among particular trees. Within the stand, the distribution of male fecundity appeared highly skewed, with a small number of dominant males, resulting in a ratio of census to effective density of pollen donors of 5·3. Male fecundity was not correlated with tree diameter but showed strong cline-like spatial variation. This pattern can be attributed to environmental variation. Quercus petraea revealed a greater preference (74 %) towards intraspecific mating than Q. robur (36 %), although mating preferences varied among trees. CONCLUSIONS Mating patterns can reveal great variation among individuals, even within a single even-age stand. The results show that trees can mate assortatively, with little respect for spatial proximity. Such selective mating may be a result of variable combining compatibility among trees due to genetic and/or environmental factors.
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Affiliation(s)
- Igor J Chybicki
- Department of Genetics, Institute of Experimental Biology, Kazimierz Wielki University, 85064 Bydgoszcz, Poland.
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Salamone I, Govindarajulu R, Falk S, Parks M, Liston A, Ashman TL. Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries. AMERICAN JOURNAL OF BOTANY 2013; 100:939-950. [PMID: 23579477 DOI: 10.3732/ajb.1200624] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Hybrid zones provide "natural laboratories" for understanding the processes of selection, reinforcement, and speciation. We sought to gain insight into the degree of introgression and the extent of ecological-phenotypic intermediacy in the natural hybrid strawberry, Fragaria × ananassa subsp. cuneifolia. • METHODS We used whole-plastome sequencing to identify parental species-specific (Fragaria chiloensis and F. virginiana) chloroplast single-nucleotide polymorphisms and combined the use of these with nuclear microsatellite markers to genetically characterize the hybrid zone. We assessed the potential role of selection in the observed geographic patterns by bioclimatically characterizing the niche of the hybrid populations and phenotypically characterizing hybrid individuals of known genomic constitution. • KEY RESULTS Significant admixture and little overall maternal bias in chloroplast or nuclear genomes suggest a high degree of interfertility among the parental and hybrid species and point to a long history of backcrossing and genetic mixing in the hybrid zone. Even though hybrids were phenotypically intermediate to the parental species, there was a discernible fingerprint of the parental genotype within hybrid individuals. Thus, although the pattern of introgression observed suggests geographic limitations to gene flow, it may be reinforced by selection for specific parental traits in the bioclimatically intermediate habitat occupied by the hybrid. • CONCLUSIONS This work uncovered the genetic complexity underlying the hybrid zone of the wild relatives of the cultivated strawberry. It lays the foundation for experimental dissection of the causes of genomic introgression and nuclear-cytoplasmic disassociation, and for understanding other parts of Fragaria evolutionary history.
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Affiliation(s)
- Isabella Salamone
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Moran EV, Willis J, Clark JS. Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:92-100. [PMID: 22174334 DOI: 10.3732/ajb.1100023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
PREMISE OF THE STUDY Hybridization is pervasive in many plant taxa, with consequences for species taxonomy, local adaptation, and management. Oaks (Quercus spp.) are thought to hybridize readily yet retain distinct traits, drawing into question the biological species concept for such taxa, but the true extent of gene flow is controversial. Genetic data are beginning to shed new light on this issue, but red oaks (section Lobatae), an important component of North American forests, have largely been neglected. Moreover, gene flow estimates may be sensitive to the choice of life stage, marker type, or genetic structure statistic. METHODS We coupled genetic structure data with parentage analyses for two mixed-species stands in North Carolina. Genetic structure analyses of adults (including F(ST), R(ST), G'(ST), and structure) reflect long-term patterns of gene flow, while the percentage of seedlings with parents of two different species reflect current levels of gene flow. KEY RESULTS Genetic structure analyses revealed low differentiation in microsatellite allele frequencies between co-occurring species, suggesting past gene flow. However, methods differed in their sensitivity to differentiation, indicating a need for caution when drawing conclusions from a single method. Parentage analyses identified >20% of seedlings as potential hybrids. The species examined exhibit distinct morphologies, suggesting selection against intermediate phenotypes. CONCLUSIONS Our results suggest that hybridization between co-occurring red oaks occurs, but that selection may limit introgression, especially at functional loci. However, by providing a source of genetic variation, hybridization could influence the response of oaks and other hybridizing taxa to environmental change.
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Affiliation(s)
- Emily V Moran
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, 37996, USA.
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Aguirre-Planter É, Jaramillo-Correa JP, Gómez-Acevedo S, Khasa DP, Bousquet J, Eguiarte LE. Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Mol Phylogenet Evol 2012; 62:263-74. [DOI: 10.1016/j.ympev.2011.09.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/27/2022]
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ZENG YANFEI, LIAO WANJIN, PETIT RÉMYJ, ZHANG DAYONG. Geographic variation in the structure of oak hybrid zones provides insights into the dynamics of speciation. Mol Ecol 2011; 20:4995-5011. [DOI: 10.1111/j.1365-294x.2011.05354.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Viscosi V, Cardini A. Leaf morphology, taxonomy and geometric morphometrics: a simplified protocol for beginners. PLoS One 2011; 6:e25630. [PMID: 21991324 PMCID: PMC3184990 DOI: 10.1371/journal.pone.0025630] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022] Open
Abstract
Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature.
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Affiliation(s)
- Vincenzo Viscosi
- Museo Erbario del Molise, Dipartimento di Scienze e Tecnologie per l'Ambiente e il Territorio, Università del Molise, Contrada Fonte Lappone, Pesche, Italy.
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Guichoux E, Lagache L, Wagner S, Léger P, Petit RJ. Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.). Mol Ecol Resour 2011; 11:578-85. [PMID: 21481218 DOI: 10.1111/j.1755-0998.2011.02983.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multiplex PCR is a fast and cost-effective technique allowing increased genotyping throughput of microsatellites. We developed two multiplexes for Quercus petraea and Q. robur, a 12-plex of EST-SSRs (eSSRs) and an 8-plex of genomic SSRs (gSSRs). We studied the origin of allele calling errors at the human reader and software levels. We showed that the robustness of allele identification can be improved by binning on raw peak sizes prior to genetic data analysis. We checked through simulation the power of these markers for species delimitation and hybrid detection. The resolution achieved with all 20 markers was greatly improved compared to that of previous studies based on a subset of the markers. Preliminary PCR tests suggest that these multiplexes might be useful to study other oak species as well. The strategy used for multiplex microsatellite development (from PCR conditions to the definition of allele calling rules) should be broadly applicable.
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Affiliation(s)
- E Guichoux
- INRA, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
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Zeng YF, Liao WJ, Petit RJ, Zhang DY. Exploring species limits in two closely related Chinese oaks. PLoS One 2010; 5:e15529. [PMID: 21152084 PMCID: PMC2994836 DOI: 10.1371/journal.pone.0015529] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/11/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The species status of two closely related Chinese oaks, Quercus liaotungensis and Q. mongolica, has been called into question. The objective of this study was to investigate the species status and to estimate the degree of introgression between the two taxa using different approaches. METHODOLOGY/PRINCIPAL FINDINGS Using SSR (simple sequence repeat) and AFLP (amplified fragment length polymorphism) markers, we found that interspecific genetic differentiation is significant and higher than the differentiation among populations within taxa. Bayesian clusters, principal coordinate analysis and population genetic distance trees all classified the oaks into two main groups consistent with the morphological differentiation of the two taxa rather than with geographic locations using both types of markers. Nevertheless, a few individuals in Northeast China and many individuals in North China have hybrid ancestry according to Bayesian assignment. One SSR locus and five AFLPs are significant outliers against neutral expectations in the interspecific FST simulation analysis, suggesting a role for divergent selection in differentiating species. MAIN CONCLUSIONS/SIGNIFICANCE All results based on SSRS and AFLPS reached the same conclusion: Q. liaotungensis and Q. mongolica maintain distinct gene pools in most areas of sympatry. They should therefore be considered as discrete taxonomic units. Yet, the degree of introgression varies between the two species in different contact zones, which might be caused by different population history or by local environmental factors.
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Affiliation(s)
- Yan-Fei Zeng
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wan-Jin Liao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Rémy J. Petit
- INRA, UMR Biodiversity, Genes and Ecosystems, Cestas, France
- University of Bordeaux, UMR Biodiversity, Genes and Ecosystems, Cestas, France
| | - Da-Yong Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- * E-mail:
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