1
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Franzoni J, Astuti G, Peruzzi L. Weak Genetic Isolation and Putative Phenotypic Selection in the Wild Carnation Dianthus virgineus (Caryophyllaceae). BIOLOGY 2023; 12:1355. [PMID: 37887065 PMCID: PMC10604185 DOI: 10.3390/biology12101355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]
Abstract
By relating genetic divergence at neutral loci, phenotypic variation, and geographic and environmental distances, it is possible to dissect micro-evolutionary scenarios involving natural selection and neutral evolution. In this work, we tested the patterns of intraspecific genetic and phenotypic variation along an elevational gradient, using Dianthus virgineus as study system. We genotyped genome-wide SNPs through ddRAD sequencing and quantified phenotypic variation through multivariate morphological variation. We assessed patterns of variation by testing the statistical association between genetic, phenotypic, geographic, and elevational distances and explored the role of genetic drift and selection by comparing the Fst and Pst of morphometric traits. We revealed a weak genetic structure related to geographic distance among populations, but we excluded the predominant role of genetic drift acting on phenotypic traits. A high degree of phenotypic differentiation with respect to genetic divergence at neutral loci allowed us to hypothesize the effect of selection, putatively fuelled by changing conditions at different sites, on morphological traits. Thus, natural selection acting despite low genetic divergence at neutral loci can be hypothesized as a putative driver explaining the observed patterns of variation.
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Affiliation(s)
- Jacopo Franzoni
- PLANTSEED Lab, Department of Biology, University of Pisa, 56127 Pisa, Italy;
| | - Giovanni Astuti
- Botanic Garden and Museum, University of Pisa, 56126 Pisa, Italy;
| | - Lorenzo Peruzzi
- PLANTSEED Lab, Department of Biology, University of Pisa, 56127 Pisa, Italy;
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2
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [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: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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3
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Wong ELY, Nevado B, Hiscock SJ, Filatov DA. Rapid evolution of hybrid breakdown following recent divergence with gene flow in Senecio species on Mount Etna, Sicily. Heredity (Edinb) 2023; 130:40-52. [PMID: 36494489 PMCID: PMC9814926 DOI: 10.1038/s41437-022-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
How do nascent species evolve reproductive isolation during speciation with on-going gene flow? How do hybrid lineages become stabilised hybrid species? While commonly used genomic approaches provide an indirect way to identify species incompatibility factors, synthetic hybrids generated from interspecific crosses allow direct pinpointing of phenotypic traits involved in incompatibilities and the traits that are potentially adaptive in hybrid species. Here we report the analysis of phenotypic variation and hybrid breakdown in crosses between closely-related Senecio aethnensis and S. chrysanthemifolius, and their homoploid hybrid species, S. squalidus. The two former species represent a likely case of recent (<200 ky) speciation with gene flow driven by adaptation to contrasting conditions of high- and low-elevations on Mount Etna, Sicily. As these species form viable and fertile hybrids, it remains unclear whether they have started to evolve reproductive incompatibility. Our analysis represents the first study of phenotypic variation and hybrid breakdown involving multiple Senecio hybrid families. It revealed wide range of variation in multiple traits, including the traits previously unrecorded in synthetic hybrids. Leaf shape, highly distinct between S. aethnensis and S. chrysanthemifolius, was extremely variable in F2 hybrids, but more consistent in S. squalidus. Our study demonstrates that interspecific incompatibilities can evolve rapidly despite on-going gene flow between the species. Further work is necessary to understand the genetic bases of these incompatibilities and their role in speciation with gene flow.
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Affiliation(s)
- Edgar L. Y. Wong
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,grid.507705.0Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Bruno Nevado
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,grid.9983.b0000 0001 2181 4263Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Simon J. Hiscock
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,Oxford Botanic Garden and Arboretum, Oxford, UK
| | - Dmitry A. Filatov
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK
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4
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Tavares MM, Ferro M, Leal BSS, Palma‐Silva C. Speciation with gene flow between two Neotropical sympatric species (
Pitcairnia
spp.: Bromeliaceae). Ecol Evol 2022; 12:e8834. [PMID: 35509614 PMCID: PMC9055293 DOI: 10.1002/ece3.8834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Marília Manuppella Tavares
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Milene Ferro
- Departamento de Biologia Geral e Aplicada Universidade Estadual Paulista Rio Claro Brazil
| | - Bárbara Simões Santos Leal
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Clarisse Palma‐Silva
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
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5
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Portinha B, Avril A, Bernasconi C, Helanterä H, Monaghan J, Seifert B, Sousa VC, Kulmuni J, Nouhaud P. Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Mol Ecol 2022; 31:3416-3431. [PMID: 35460311 PMCID: PMC9320829 DOI: 10.1111/mec.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole‐genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent‐based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (c. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2–19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.
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Affiliation(s)
- Beatriz Portinha
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal
| | - Amaury Avril
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | | | - Heikki Helanterä
- Ecology and Genetics research unit, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | | | | | - Vitor C Sousa
- cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
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6
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Jacobs SJ, Grundler MC, Henriquez CL, Zapata F. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae). Sci Rep 2021; 11:24013. [PMID: 34907249 PMCID: PMC8671583 DOI: 10.1038/s41598-021-03419-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal}
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\begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
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Affiliation(s)
- Sarah J Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,Department of Botany, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
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7
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Portella RO, Cordeiro EMG, Marques APS, Ming LC, Zucchi MI, Lima MP, Martins ER, Hantao LW, Sawaya ACHF, Semir J, Pinheiro JB, Marques MOM. Evidence of altitudinal gradient modifying genomic and chemical diversity in populations of Lychnophora pinaster Mart. PHYTOCHEMISTRY 2021; 192:112898. [PMID: 34492545 DOI: 10.1016/j.phytochem.2021.112898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/27/2021] [Accepted: 08/03/2021] [Indexed: 05/28/2023]
Abstract
Lychnophora pinaster Mart. (Asteraceae) is endemic to the Brazilian Cerrado. It is distributed along the altitudinal gradient of the mountainous ranges of the state of Minas Gerais. This study aimed to evaluate the influence of altitude on the genetic diversity of L. pinaster populations and the effects of altitude and climatic factors on essential oil chemical composition. Essential oils from L. pinaster populations from the north (North 01, North 02, and North 03, 700-859 m) and the Metropolitan region of Belo Horizonte (MhBH 01 and MrBH 02, 1366-1498 m) were analyzed. SNP markers from L. pinaster in these regions and Campos das Vertentes (CV 01, CV 02, and CV 03, 1055-1292 m) were also analyzed. The main compounds in essential oils were 14-hydroxy-α-humulene (North 01 and North 03), cedr-8(15)-en-9-α-ol (North 02), 14-acetoxy-α-humulene (MrBH 01), and 4-oxo-15-nor-eudesman-11-ene (MrBH 02). Hierarchical cluster and heatmap analyses showed that the North and MrBH populations included five different groups, indicating the chemical composition of essential oils is distinct in each population. Furthermore, principal component analysis showed that higher altitudes (1366 m and 1498 m) in the MrBH influence the chemical composition of essential oils, and climatic factors determine the chemical composition in North region. The genetic diversity showed that most alleles are in Hardy-Weinberg equilibrium and imply high genetic variation and genetic polymorphisms between populations. Furthermore, the results of Mantel tests (R = 0.3861517; p = 0.04709529; R = 0.9423121; p = 0.02739726) also showed that higher altitude (>1360 m) shapes the genetic diversity at the MrBH. The genetic structure showed that higher altitudes (>1360 m) contribute to the structure of the MrBH populations, but not to North and CV populations. Therefore, the altitudinal ranges of Minas Gerais mountainous ranges determine the higher genetic and chemical diversity of L. pinaster populations.
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Affiliation(s)
- Roberto O Portella
- Universidade de Taubaté, Av. Tiradentes, 500, Bom Conselho, CEP: 12030-180, Taubaté, SP, Brazil; Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Erick M G Cordeiro
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Ana Paula S Marques
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Lin C Ming
- Departamento de Horticultura, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua José Barbosa de Barros, 1780, CEP: 18610-307, Botucatu, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Maria P Lima
- Coordenação de Inovação Tecnológica, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Aleixo, CEP: 69011-970, Manaus, AM, Brazil
| | - Ernane R Martins
- Instituto de Ciências Agrárias, Universidade Federal de Minas Gerais, Av. Universitária, 1000, Universitário, CEP: 39404-547, Montes Claros, MG, Brazil
| | - Leandro W Hantao
- Instituto de Química, Universidade Estadual de Campinas, Rua Monteiro Lobato, 270, CEP: 13083-862, Campinas, SP, Brazil
| | - Alexandra C H F Sawaya
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200, Cidade Universitária, CEP: 13083-871, Campinas, SP, Brazil
| | - João Semir
- Departamento de Botânica, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Barão Geraldo, CEP: 13083-862, Campinas, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CEP: 13418-900, Piracicaba, SP, Brazil
| | - Marcia O M Marques
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico, Avenida Barão de Itapura, 1481, Botafogo, CEP: 13020-902, Campinas, SP, Brazil.
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8
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Wambulwa MC, Milne R, Wu Z, Spicer RA, Provan J, Luo Y, Zhu G, Wang W, Wang H, Gao L, Li D, Liu J. Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives. Ecol Evol 2021; 11:10794-10812. [PMID: 34429882 PMCID: PMC8366862 DOI: 10.1002/ece3.7906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Mountain ecosystems support a significant one-third of all terrestrial biodiversity, but our understanding of the spatiotemporal maintenance of this high biodiversity remains poor, or at best controversial. The Himalaya hosts a complex mountain ecosystem with high topographic and climatic heterogeneity and harbors one of the world's richest floras. The high species endemism, together with increasing anthropogenic threats, has qualified the Himalaya as one of the most significant global biodiversity hotspots. The topographic and climatic complexity of the Himalaya makes it an ideal natural laboratory for studying the mechanisms of floral exchange, diversification, and spatiotemporal distributions. Here, we review literature pertaining to the Himalaya in order to generate a concise synthesis of the origin, distribution, and climate change responses of the Himalayan flora. We found that the Himalaya supports a rich biodiversity and that the Hengduan Mountains supplied the majority of the Himalayan floral elements, which subsequently diversified from the late Miocene onward, to create today's relatively high endemicity in the Himalaya. Further, we uncover links between this Miocene diversification and the joint effect of geological and climatic upheavals in the Himalaya. There is marked variance regarding species dispersal, elevational gradients, and impact of climate change among plant species in the Himalaya, and our review highlights some of the general trends and recent advances on these aspects. Finally, we provide some recommendations for conservation planning and future research. Our work could be useful in guiding future research in this important ecosystem and will also provide new insights into the maintenance mechanisms underpinning other mountain systems.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Department of Life SciencesSchool of Pure and Applied SciencesSouth Eastern Kenya UniversityKituiKenya
| | - Richard Milne
- Institute of Molecular Plant SciencesSchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Zeng‐Yuan Wu
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Robert A. Spicer
- CAS Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesXishuangbannaChina
- School of Environment, Earth and Ecosystem SciencesThe Open UniversityMilton KeynesUK
| | - Jim Provan
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Ya‐Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Guang‐Fu Zhu
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Wan‐Ting Wang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lian‐Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - De‐Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
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9
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Pflugbeil G, Affenzeller M, Tribsch A, Comes HP. Primary hybrid zone formation in Tephroseris helenitis (Asteraceae), following postglacial range expansion along the central Northern Alps. Mol Ecol 2021; 30:1704-1720. [PMID: 33548078 PMCID: PMC8048512 DOI: 10.1111/mec.15832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/26/2022]
Abstract
Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental-selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid-Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate-driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species' postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long-term, west-to-east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.
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Affiliation(s)
- Georg Pflugbeil
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Andreas Tribsch
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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10
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Rana SK, Luo D, Rana HK, Chen S, Sun H. Molecular phylogeny, biogeography and character evolution of the montane genus Incarvillea Juss. (Bignoniaceae). PLANT DIVERSITY 2021; 43:1-14. [PMID: 33778220 PMCID: PMC7987631 DOI: 10.1016/j.pld.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 06/01/2023]
Abstract
The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau (QTP) fosters habitat fragmentation that drives morphological differentiation of mountain plant species. Consequently, determining phylogenetic relationships between plant subgenera using morphological characters is unreliable. Therefore, we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus Incarvillea. We determined the taxonomic position of the genus Incarvillea within its family and inferred the biogeographical origin of taxa through Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) analyses using three molecular data sets (trnL-trnF sequences, nr ITS sequences, and a data set of combined sequences) derived from 81% of the total species of the genus Incarvillea. Within the genus-level phylogenetic framework, we examined the character evolution of 10 key morphological characters, and inferred the ancestral area and biogeographical history of the genus. Our analyses revealed that the genus Incarvillea is monophyletic and originated in Central Asia during mid-Oligocene ca. 29.42 Ma. The earliest diverging lineages were subsequently split into the Western Himalaya and Sino-Himalaya during the early Miocene ca. 21.12 Ma. These lineages resulted in five re-circumscribed subgenera (Amphicome, Olgaea, Niedzwedzkia, Incarvillea, and Pteroscleris). Moreover, character mapping revealed the ancestral character states of the genus Incarvillea (e.g., suffruticose habit, cylindrical capsule shape, subligneous capsule texture, absence of capsule wing, and loculicidal capsule dehiscence) that are retained at the earliest diverging ancestral nodes across the genus. Our phylogenetic tree of the genus Incarvillea differs from previously proposed phylogenies, thereby recommending the placement of the subgenus Niedzwedzkia close to the subgenus Incarvillea and maintaining two main divergent lineages.
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Affiliation(s)
- Santosh Kumar Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dong Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hum Kala Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shaotian Chen
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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11
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Criado Ruiz D, Villa Machío I, Herrero Nieto A, Nieto Feliner G. Hybridization and cryptic speciation in the Iberian endemic plant genus Phalacrocarpum (Asteraceae-Anthemideae). Mol Phylogenet Evol 2020; 156:107024. [PMID: 33271372 DOI: 10.1016/j.ympev.2020.107024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 01/28/2023]
Abstract
Understanding the role and impact of reticulation in phylogenetic inquiry has improved with extended use of high throughput sequencing data. Yet, due to the dynamism of genomes over evolutionary time, disentangling old hybridization events remains a serious challenge. Phalacrocarpum (DC.) Willk. is one of the 27 Iberian endemic plant genera, currently considered monotypic but including three subspecies. Its uncertain phylogenetic relationships within tribe Anthemideae (Asteraceae) point to an Early Miocene divergence from its sister group, and its persistent taxonomic instability has been proposed to be due to hybridization. We aim at understanding the evolutionary history of this genus using SNPs called from a genotyping-by-sequencing (GBS) analysis, Sanger sequences-from three plastid DNA regions (psbJ-petA, petB-petD, trnH-psbA) and the nuclear ribosomal ITS regions (cloned)-as well as leaf morphometric multivariate analysis. SNP data and Sanger sequences strongly support the unforeseen existence of a cryptic species in the eastern populations of P. oppositifolium subsp. anomalum. Broad molecular and morphometric patterns of variation found in conflictive populations from the Sanabria Valley region convincingly identify a recent previously undocumented hybrid zone. By contrast, evidence is less conclusive on relationships between subspecies hoffmannseggii, oppositifolium and a second conflictive group distributed along the Galician-Portuguese border (Orense massifs). Although genetic clustering analysis of SNP data suggests that the former subspecies was the maternal progenitor in hybridization events that gave rise to the other two groups, we found considerable uniqueness of ITS ribotypes and plastid haplotypes in them. This result, in the context of Pleistocene climatically-driven range shifts in NW Iberian Peninsula, can be due to periods of isolation, genetic bottlenecks and drift superimposed on old hybridization events. Our study confirms the idea that unravelling old hybridization events may be compromised by the suite of evolutionary processes accumulated subsequently, particularly in areas with a history of climatic instability.
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Affiliation(s)
- David Criado Ruiz
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014 Madrid, Spain.
| | - Irene Villa Machío
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
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12
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Walter GM, Abbott RJ, Brennan AC, Bridle JR, Chapman M, Clark J, Filatov D, Nevado B, Ortiz-Barrientos D, Hiscock SJ. Senecio as a model system for integrating studies of genotype, phenotype and fitness. THE NEW PHYTOLOGIST 2020; 226:326-344. [PMID: 31951018 DOI: 10.1111/nph.16434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Adrian C Brennan
- School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, UK
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Mark Chapman
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James Clark
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | | | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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13
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Song K, Halvarsson P, Fang Y, Barnaby J, Germogenov N, Sun Y, Höglund J. Genetic differentiation in Sichuan jay (Perisoreus internigrans) and its sibling species Siberian jay (P. infaustus). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01252-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractThe Pleistocene ice age and recent forest fragmentation have both played a significant role in shaping the population genetic variation of boreal coniferous species in the Qinghai-Tibet Plateau (QTP) and Eurasian coniferous forests. The Sichuan jay is one of the least know endemic bird species in QTP coniferous forests in western China while its sibling species, the Siberian Jay, is widespread within the coniferous forests in northern Eurasia. Here we used 11 microsatellite markers to assay genetic diversity across 58 Sichuan jay samples from China and 205 Siberian jay samples from Sweden and Russia. Results showed three distinct genetic clusters from the Sichuan jay sampling. Furthermore, the pair-wise FST values indicated high genetic differentiation not only among the two species but also between Swedish and Russian Siberian jay populations. What is more, a pattern of isolation by distance was found among the analyzed populations. Our study suggests that targeted habitat restoration in fragmented forests and more genetic work is urgently needed for conservation of the Sichuan jay.
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14
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Sun Y, Wen X. Demographic Inference of Divergence and Gene Exchange Between Castanopsis fabri and Castanopsis lamontii. FRONTIERS IN PLANT SCIENCE 2020; 11:198. [PMID: 32194597 PMCID: PMC7066298 DOI: 10.3389/fpls.2020.00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
The cytoplasmic genome of one species may be replaced by that of another species without leaving any trace of past hybridization in its nuclear genome, which can thus confuse the inference of genealogical relationship and evolutionary history of many congeneric species. In this study, we used sequence variations of chloroplast DNA and restriction site-associated DNA to investigate gene exchange between Castanopsis fabri and Castanopsis lamontii, and to infer the divergence history of the two species by comparing different divergence models based on the joint allele frequency spectrum. We evaluated climatic niche similarity of the two species using climatic variables across their entire distribution range in subtropical China. Clear genetic differentiation was revealed between C. fabri and C. lamontii, and gene exchange between the two species was discovered as a consequence of secondary contact. The gene exchange rates were variable across the genome. Gene exchange could allow C. fabri to widen its habitat through pollen swamping and broaden its climatic niche, and the chloroplast genome of C. lamontii is captured by C. fabri during this process. These results further our understanding of the timing and contribution of gene exchange to species divergence in forests.
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Affiliation(s)
- Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agriculture University, Guangzhou, China
| | - Xiangying Wen
- China Office of the Botanic Gardens Conservation International, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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15
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Wong ELY, Nevado B, Osborne OG, Papadopulos AST, Bridle JR, Hiscock SJ, Filatov DA. Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna. Mol Ecol 2019; 29:394-412. [PMID: 31793091 DOI: 10.1111/mec.15319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.
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Affiliation(s)
- Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
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16
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Papadopulos AST, Igea J, Smith TP, Hutton I, Baker WJ, Butlin RK, Savolainen V. Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of
Howea
in the face of high gene flow. Evolution 2019; 73:1996-2002. [DOI: 10.1111/evo.13813] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/04/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Alexander S. T. Papadopulos
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Molecular Ecology and Fisheries Genetics LaboratoryEnvironment Centre WalesSchool of Natural SciencesBangor University Bangor LL57 2UW United Kingdom
| | - Javier Igea
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Department of Plant SciencesUniversity of Cambridge Cambridge CB2 3EA United Kingdom
| | - Thomas P. Smith
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
| | - Ian Hutton
- Lord Howe Island Museum Lord Howe Island New South Wales Australia
| | | | - Roger K. Butlin
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield S10 2TN United Kingdom
- Department of Marine SciencesUniversity of Gothenburg Gothenburg SE‐405 30 Sweden
| | - Vincent Savolainen
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Royal Botanic Gardens, Kew Richmond TW9 3AB United Kingdom
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17
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Yan LJ, Burgess KS, Zheng W, Tao ZB, Li DZ, Gao LM. Incomplete reproductive isolation between Rhododendron taxa enables hybrid formation and persistence. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:433-448. [PMID: 30192058 DOI: 10.1111/jipb.12718] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
The evolutionary consequences of hybridization ultimately depend on the magnitude of reproductive isolation between hybrids and their parents. We evaluated the relative contributions of pre- and post-zygotic barriers to reproduction for hybrid formation, hybrid persistence and potential for reproductive isolation of hybrids formed between two Rhododendron species, R. spiciferum and R. spinuliferum. Our study established that incomplete reproductive isolation promotes hybrid formation and persistence and delays hybrid speciation. All pre-zygotic barriers to reproduction leading to hybrid formation are incomplete: parental species have overlapping flowering; they share the same pollinators; reciprocal assessments of pollen tube germination and growth do not differ among parents. The absence of post-zygotic barriers between parental taxa indicates that the persistence of hybrids is likely. Reproductive isolation was incomplete between hybrids and parents in all cases studied, although asymmetric differences in reproductive fitness were prevalent and possibly explain the genetic structure of natural hybrid swarms where hybridization is known to be bidirectional but asymmetric. Introgression, rather than speciation, is a probable evolutionary outcome of hybridization between the two Rhododendron taxa. Our study provides insights into understanding the evolutionary implications of natural hybridization in woody plants.
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Affiliation(s)
- Li-Jun Yan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650201, China
- College of Vocational and Technical Education, Yunnan Normal University, Kunming 650092, China
| | - Kevin S Burgess
- Department of Biology, College of Letters & Sciences, Columbus State University, University System of Georgia, 31907-5645 Columbus, GA, USA
| | - Wei Zheng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650201, China
| | - Zhi-Bin Tao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650201, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650201, China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650201, China
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18
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Abbott RJ. A mixing-isolation-mixing model of speciation can potentially explain hotspots of species diversity. Natl Sci Rev 2019; 6:290-291. [PMID: 34691866 PMCID: PMC8291541 DOI: 10.1093/nsr/nwy112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Brennan AC, Hiscock SJ, Abbott RJ. Completing the hybridization triangle: the inheritance of genetic incompatibilities during homoploid hybrid speciation in ragworts ( Senecio). AOB PLANTS 2019; 11:ply078. [PMID: 30740200 PMCID: PMC6360072 DOI: 10.1093/aobpla/ply078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/04/2019] [Indexed: 05/24/2023]
Abstract
A new homoploid hybrid lineage needs to establish a degree of reproductive isolation from its parent species if it is to persist as an independent entity, but the role hybridization plays in this process is known in only a handful of cases. The homoploid hybrid ragwort species, Senecio squalidus (Oxford ragwort), originated following the introduction of hybrid plants to the UK approximately 320 years ago. The source of the hybrid plants was from a naturally occurring hybrid zone between S. aethnensis and S. chrysanthemifolius on Mount Etna, Sicily. Previous studies of the parent species found evidence for multiple incompatibility loci causing transmission ratio distortion of genetic markers in their hybrid progeny. This study closes the hybridization triangle by reporting a genetic mapping analysis of the remaining two paired cross combinations between S. squalidus and its parents. Genetic maps produced from F2 mapping families were generally collinear but with half of the linkage groups showing evidence of genomic reorganization between genetic maps. The new maps produced from crosses between S. squalidus and each parent showed multiple incompatibility loci distributed across the genome, some of which co-locate with previously reported incompatibility loci between the parents. These findings suggest that this young homoploid hybrid species has inherited a unique combination of genomic rearrangements and incompatibilities from its parents that contribute to its reproductive isolation.
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Affiliation(s)
- Adrian C Brennan
- Department of Biosciences, University of Durham, South Road, Durham, UK
- School of Biology, University of St Andrews, St Andrews, Fife, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, UK
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20
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Beichman AC, Huerta-Sanchez E, Lohmueller KE. Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062431] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.
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Affiliation(s)
- Annabel C. Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
| | - Emilia Huerta-Sanchez
- Department of Molecular and Cell Biology, University of California, Merced, California 95343, USA
- Current affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
- Interdepartmental Program in Bioinformatics and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
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21
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Nevado B, Contreras-Ortiz N, Hughes C, Filatov DA. Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes. THE NEW PHYTOLOGIST 2018; 219:779-793. [PMID: 29862512 DOI: 10.1111/nph.15243] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
Abstract
Mountain ranges are amongst the most species-rich habitats, with many large and rapid evolutionary radiations. The tempo and mode of diversification in these systems are key unanswered questions in evolutionary biology. Here we study the Andean Lupinus radiation to understand the processes driving very rapid diversification in montane systems. We use genomic and transcriptomic data of multiple species and populations, and apply phylogenomic and demographic analyses to test whether diversification proceeded without interspecific gene flow - as expected if Andean orogeny and geographic isolation were the main drivers of diversification - or if diversification was accompanied by gene flow, in which case other processes were probably involved. We uncover several episodes of gene flow between species, including very recent events likely to have been prompted by changes in habitat connectivity during Pleistocene glacial cycles. Furthermore, we find that gene flow between species was heterogeneously distributed across the genome. We argue that exceptionally fast diversification of Andean Lupinus was partly a result of Late Pleistocene glacial cycles, with associated cycles of expansion and contraction driving geographic isolation or secondary contact of species. Furthermore, heterogeneous gene flow across the genome suggests a role for selection and ecological speciation in rapid diversification in this system.
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Affiliation(s)
- Bruno Nevado
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Natalia Contreras-Ortiz
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Apartado Aéreo, 4976, Bogotá, Colombia
- Jardín Botánico de Bogotá 'José Celestino Mutis', Avenida Calle 63 No. 68-95, Bogotá DC, Colombia
| | - Colin Hughes
- Department of Systematic & Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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22
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Ortego J, Gugger PF, Sork VL. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). THE NEW PHYTOLOGIST 2018; 218:804-818. [PMID: 29274282 DOI: 10.1111/nph.14951] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 05/15/2023]
Abstract
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, Seville, E-41092, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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23
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Thorogood CJ, Bauer U, Hiscock SJ. Convergent and divergent evolution in carnivorous pitcher plant traps. THE NEW PHYTOLOGIST 2018; 217:1035-1041. [PMID: 29131340 DOI: 10.1111/nph.14879] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/05/2017] [Indexed: 05/26/2023]
Abstract
Contents Summary 1035 I. Introduction 1035 II. Evolution of the pitcher 1036 III. Convergent evolution 1036 IV. Divergent evolution 1038 V. Adaptive radiation and speciation 1040 VI. Conclusions and perspectives 1040 Acknowledgements 1040 References 1040 SUMMARY: The pitcher trap is a striking example of convergent evolution across unrelated carnivorous plant lineages. Convergent traits that have evolved across pitcher plant lineages are essential for trap function, suggesting that key selective pressures are in action. Recent studies have also revealed patterns of divergent evolution in functional pitcher morphology within genera. Adaptations to differences in local prey assemblages may drive such divergence and, ultimately, speciation. Here, we review recent research on convergent and divergent evolution in pitcher plant traps, with a focus on the genus Nepenthes, which we propose as a new model for research into adaptive radiation and speciation.
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Affiliation(s)
- Chris J Thorogood
- Botanic Garden, University of Oxford, Rose Lane, Oxford, OX1 4AZ, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ulrike Bauer
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Simon J Hiscock
- Botanic Garden, University of Oxford, Rose Lane, Oxford, OX1 4AZ, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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24
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Abbott RJ, Barton NH, Good JM. Genomics of hybridization and its evolutionary consequences. Mol Ecol 2018; 25:2325-32. [PMID: 27145128 DOI: 10.1111/mec.13685] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Richard J Abbott
- School of Biology, University of St Andrews, Mitchell Building, St Andrews, Fife, KY16 9TH, UK
| | - Nicholas H Barton
- Institute of Science and Technology (IST Austria), Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
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25
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Elfekih S, Etter P, Tay WT, Fumagalli M, Gordon K, Johnson E, De Barro P. Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories. PLoS One 2018; 13:e0190555. [PMID: 29364919 PMCID: PMC5783331 DOI: 10.1371/journal.pone.0190555] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 12/16/2017] [Indexed: 12/21/2022] Open
Abstract
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO). Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.
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Affiliation(s)
- S. Elfekih
- CSIRO, Black Mountain Laboratories, ACT, Australia
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - P. Etter
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
| | - W. T. Tay
- CSIRO, Black Mountain Laboratories, ACT, Australia
| | - M. Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, United Kingdom
| | - K. Gordon
- CSIRO, Black Mountain Laboratories, ACT, Australia
| | - E. Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
| | - P. De Barro
- CSIRO Ecosciences Precinct, Brisbane, QLD, Australia
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26
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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27
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Richards EJ, Martin CH. Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes. PLoS Genet 2017; 13:e1006919. [PMID: 28796803 PMCID: PMC5552031 DOI: 10.1371/journal.pgen.1006919] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity.
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Affiliation(s)
- Emilie J. Richards
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christopher H. Martin
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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28
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Aeschbacher S, Selby JP, Willis JH, Coop G. Population-genomic inference of the strength and timing of selection against gene flow. Proc Natl Acad Sci U S A 2017; 114:7061-7066. [PMID: 28634295 PMCID: PMC5502586 DOI: 10.1073/pnas.1616755114] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.
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Affiliation(s)
- Simon Aeschbacher
- Department of Evolution and Ecology, University of California, Davis, CA 95616;
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - John H Willis
- Department of Biology, Duke University, Durham, NC 27708
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis, CA 95616
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29
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Yang M, He Z, Shi S, Wu CI. Can genomic data alone tell us whether speciation happened with gene flow? Mol Ecol 2017; 26:2845-2849. [PMID: 28345182 DOI: 10.1111/mec.14117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/08/2017] [Accepted: 03/20/2017] [Indexed: 01/02/2023]
Abstract
The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.
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Affiliation(s)
- Ming Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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30
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Ren G, Mateo RG, Liu J, Suchan T, Alvarez N, Guisan A, Conti E, Salamin N. Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing. THE NEW PHYTOLOGIST 2017; 213:1500-1512. [PMID: 27696413 DOI: 10.1111/nph.14221] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/23/2016] [Indexed: 05/28/2023]
Abstract
The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes.
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Affiliation(s)
- Guangpeng Ren
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Rubén G Mateo
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Tomasz Suchan
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany and Botanic Garden, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
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31
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Brennan AC, Hiscock SJ, Abbott RJ. Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient. AOB PLANTS 2016; 8:plw022. [PMID: 27083198 PMCID: PMC4887755 DOI: 10.1093/aobpla/plw022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 03/19/2016] [Indexed: 05/03/2023]
Abstract
Knowledge of the genetic basis of phenotypic divergence between species and how such divergence is caused and maintained is crucial to an understanding of speciation and the generation of biodiversity. The hybrid zone between Senecio aethnensis and S. chrysanthemifolius on Mount Etna, Sicily, provides a well-studied example of species divergence in response to conditions at different elevations, despite hybridization and gene flow. Here, we investigate the genetic architecture of divergence between these two species using a combination of quantitative trait locus (QTL) mapping and genetic differentiation measures based on genetic marker analysis. A QTL architecture characterized by physical QTL clustering, epistatic interactions between QTLs, and pleiotropy was identified, and is consistent with the presence of divergent QTL complexes resistant to gene flow. A role for divergent selection between species was indicated by significant negative associations between levels of interspecific genetic differentiation at mapped marker gene loci and map distance from QTLs and hybrid incompatibility loci. Within-species selection contributing to interspecific differentiation was evidenced by negative associations between interspecific genetic differentiation and genetic diversity within species. These results show that the two Senecio species, while subject to gene flow, maintain divergent genomic regions consistent with local selection within species and selection against hybrids between species which, in turn, contribute to the maintenance of their distinct phenotypic differences.
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Affiliation(s)
- Adrian C Brennan
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife KY16 9TH, UK Estación Biológica de Doñana (EBD-CSIC), Avenida Américo Vespucio s/n, 41092 Sevilla, Spain Present address: School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
| | - Simon J Hiscock
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, Harold Mitchell Building, St Andrews, Fife KY16 9TH, UK
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