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Rodríguez-Buján I, Díaz-Tapia P, Fagúndez J. Genetic and morphological evidence support the specific status of the endemic Ericaandevalensis (Ericales, Ericaceae). PHYTOKEYS 2024; 244:57-76. [PMID: 39006938 PMCID: PMC11245639 DOI: 10.3897/phytokeys.244.120914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/23/2024] [Indexed: 07/16/2024]
Abstract
Assessing the taxonomic status of closely related taxa is crucial in plant systematics and can have important implications for conservation and human plant use. Ericaandevalensis Cabezudo & Rivera is a metallophyte endemic species from highly metal-polluted soils of SW Iberian Peninsula, an area with a mining history going back more than 5,000 years. Ericaandevalensis is closely related to Ericamackayana Bab., a northern Iberian species also present in western Ireland. The status of E.andevalensis as a species or subspecies subordinated to E.mackayana is subject to debate. Here, we assessed the genetic and phenotypic relationship between both species, including the population structure of E.andevalensis. We used high throughput sequencing to determine genome-wide Single Nucleotide Polymorphisms (SNPs), and morphometric analyses from 35 reproductive and vegetative traits. The morphological analysis showed at least eight characters that can discriminate the two species, from which ovary hairiness and the size of leaf glandular hairs were the most informative. Genetic analyses showed that each species formed a monophyletic cluster with full support, separated by an interspecific genetic distance >4-fold higher than intra-specific distance. Population genetic analyses of E.andevalensis shows that populations are highly structured, with the Portuguese one as the most isolated and less variable. These results support the recognition of E.andevalensis as a distinct species with a highly constrained ecological requirements and a narrow geographic distribution, but with a limited gene flow between populations. We discuss the implications of these outcomes in conservation policies and potential uses of E.andevalensis such as decontamination of polluted soils.
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Affiliation(s)
- Iván Rodríguez-Buján
- Universidade da Coruña, BIOCOST research group, Centro Interdisciplinar de Química e Bioloxía (CICA), Rúa As Carballeiras, 15071, A Coruña, Spain
| | - Pilar Díaz-Tapia
- Universidade da Coruña, Facultade de Ciencias, Departamento de Bioloxía, 15071, A Coruña, Spain
| | - Jaime Fagúndez
- Universidade da Coruña, BIOCOST research group, Centro Interdisciplinar de Química e Bioloxía (CICA), Rúa As Carballeiras, 15071, A Coruña, Spain
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Taichi N, Nakahama N, Ohmido N, Ushimaru A. Habitat diversification associated with urban development has a little effect on genetic structure in the annual native plant Commelina communis in an East Asian megacity. Ecol Evol 2024; 14:e10975. [PMID: 38384819 PMCID: PMC10880129 DOI: 10.1002/ece3.10975] [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: 10/04/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024] Open
Abstract
Urban development greatly alters the natural and semi-natural habitats of native plants. Urbanisation results in a range of diverse habitats including remnant agricultural lands, urban parks, and roadside habitats. This habitat diversity often promotes trait divergence within urban areas. However, the mechanisms by which diverse urban habitats influence the population genetic structure of individual plant species remain poorly understood. We investigated the effects of urbanisation on genetic diversity and structure within 24 Commelina communis populations across diverse habitat types (rural agricultural land, urban agricultural land, urban park land, and urban roadsides) within the Kyoto-Osaka-Kobe megacity in Japan. We conducted multiplexed inter-simple sequence repeat genotyping to compare genetic diversity among populations in different habitats. We also examined the correlation between Nei's genetic distance and geographic and environmental distances and performed principal coordinate analysis (PCoA) to evaluate genetic differentiation among urban habitats. There were no significant differences in genetic diversity indices between urban and rural populations and among urban habitat types. Although we detected no isolation-by-distance structure in population pairs of the same habitat type and in those of different habitats, the difference in surrounding landscape facilitated genetic differentiation not only between urban and rural habitats but also between different urban habitats. PCoA revealed no clear genetic differentiation among rural and urban habitat populations. Our findings indicate that the establishment of diverse habitat types through urbanisation has no and little impact on genetic diversity and structure, respectively, in C. communis, likely due to its high selfing rate and ability to adapt to urban conditions.
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Affiliation(s)
- Nakata Taichi
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Naoyuki Nakahama
- Institute of Natural and Environmental SciencesUniversity of HyogoSandaJapan
- Museum of Nature and Human ActivitiesHyogoJapan
| | - Nobuko Ohmido
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Atushi Ushimaru
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
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Choi I, Han E, Wojciechowski MF, Heo T, Park J, Yang J, Gantsetseg A, Cheon K, Tamaki I, Lee J. The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome-wide SNP markers. Ecol Evol 2023; 13:e10252. [PMID: 37404698 PMCID: PMC10316687 DOI: 10.1002/ece3.10252] [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: 02/27/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Similar to the global phenomenon, many plant species endemic to Korean limestone karst forests are at risk of extinction due to human intervention. Zabelia tyaihyonii is a familiar shrub, called "Hardy abelia" and "Fragrant abelia" growing in the karst forests of Korea, where it is one of the most threatened species. We investigated the genetic structure and demographic history of Z. tyaihyonii, which allow us to develop appropriate conservation and management strategies. The genetic structure was evaluated using a total of 187 samples from 14 populations, covering the entire distribution of Z. tyaihyonii in South Korea. We utilized 254 and 1753 SNP loci obtained via MIG-seq (Multiplexed ISSR Genotyping by sequencing) for structure and demographic analyses, respectively. The population demographic modeling was performed with site frequency spectrum. To gain further historical insights, we also employed ENM (Ecological Niche Modeling). We found two distinct clusters (CLI and CLII) of ancient origin (ca. 490 ka). Despite CLII experiencing a more severe bottleneck, both clusters showed similar levels of genetic diversity, indicating mutual historical gene flow. Their historical distribution range seems to have changed very little. We proposed a historical distribution scenario for Z. tyaihyonii, taking into account its intrinsic factors, and emphasized a more complex response to Quaternary climate change beyond simple allopatric speciation models. These findings provide valuable insights for conservation and management strategies for Z. tyaihyonii.
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Affiliation(s)
- In‐Su Choi
- Department of Biological Sciences and BiotechnologyHannam UniversityDaejeonKorea
| | - Eun‐Kyeong Han
- Department of Biology EducationChonnam National UniversityGwangjuKorea
| | | | - Tae‐Im Heo
- Division of Baekdudaegan Biodiversity ConservationBaekdudaegan National ArboretumBonghwaKorea
| | - Jong‐Soo Park
- Division of BotanyHonam National Institute of Biological ResourcesMokpoKorea
| | - Jong‐Cheol Yang
- Division of Baekdudaegan Biodiversity ConservationBaekdudaegan National ArboretumBonghwaKorea
| | | | | | | | - Jung‐Hyun Lee
- Department of Biology EducationChonnam National UniversityGwangjuKorea
- School of Life SciencesArizona State UniversityTempeArizonaUSA
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Nagasawa K, Fukushima K, Setoguchi H, Katsuyama M, Sakaguchi S. Extreme low pH, not Al 3+ , is a key abiotic stressor for the extremophyte Carex angustisquama (Cyperaceae) in highly acidic solfatara fields. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:551-562. [PMID: 36825368 DOI: 10.1111/plb.13514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/20/2023] [Indexed: 05/17/2023]
Abstract
Volcanic acidification creates extreme soil conditions, where rhizotoxicity from extremely low pH (2-3) and high Al3+ strongly inhibit plant growth. C. angustisquama is a dominant extremophyte in highly acidic solfatara fields, where no other vascular plants can survive. Here we investigated the key abiotic stressor determining survival of this extremophyte. Soil analyses and topographic surveys were conducted to examine the effects of low pH and Al3+ , two major abiotic stressors in acidic soils, on the occurrence of C. angustisquama in solfatara fields. Hydroponic culture experiments were also performed to test its growth responses to these stressors. In field surveys, the spatial distribution of soil pH was consistent with vegetation zonation within a solfatara field. In contrast, soil exchangeable Al content was overall low due to strong eluviation. Statistical analysis also supported the significant role of soil pH in determining the distribution of C. angustisquama in a solfatara field. Furthermore, hydroponic culture experiments revealed a higher tolerance of C. angustisquama to low pH than a sister species, especially in the range pH 2-3, corresponding to the pH values of the actual habitats of C. angustisquama. Conversely, no significant interspecific difference was detected in Al3+ tolerance, indicating that both species had high Al3+ tolerance. This study suggests that low pH is a critical abiotic stressor leading to formation of the extremophyte in highly acidic solfatara fields. In contrast, C. angustisquama displayed high tolerance to Al3+ toxicity, probably acquired prior to speciation.
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Affiliation(s)
- K Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - K Fukushima
- The Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - H Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - M Katsuyama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - S Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
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Nagasawa K, Fukumoto S, Setoguchi H, Ishihara M, Hiratsuka KI, Masuda K, Sakaguchi S. Genetic purity of a rear-edge population of Carex podogyna Franch. et Sav. (Cyperaceae) maintained under interspecific hybridization. Gene 2022; 97:93-99. [PMID: 35545526 DOI: 10.1266/ggs.21-00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Interspecific hybridization is a critical issue in conservation biology because it may drive small populations to extinction through direct or indirect processes. In this study, to develop a conservation strategy for an endangered rear-edge population of Carex podogyna in Ashiu, Kyoto, Japan, we performed a molecular genetic analysis of the wild population and an ex-situ population established from wild seeds. Microsatellite genotypic data revealed a complete loss of genetic diversity in the wild population, suggesting that it has long been prone to genetic drift due to isolation as a small population. In contrast, microsatellite analysis of 13 ex-situ individuals detected multiple alleles that are not harbored in the wild C. podogyna population. Sequence analysis revealed that these individuals are likely natural hybrids between C. podogyna and a co-occurring species, C. curvicollis, although established hybrids have never been found in the natural habitat. Based on our observation of variegated leaves in hybrid individuals, we propose that hybrids have been excluded by natural selection and/or interspecific competition caused by insufficient productivity of photosynthesis, although other genetic and ecological factors may also be influential. Overall, this study indicates that natural mechanisms selectively removing the hybrids have maintained the genetic purity of this rear-edge population of C. podogyna, and also emphasizes the importance of genetic assessment in ex-situ conservation programs.
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Affiliation(s)
- Koki Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University
| | | | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Masae Ishihara
- Ashiu Forest Research Station, Field Science Education and Research Center, Kyoto University
| | | | - Kazutoshi Masuda
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University
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Kolis KM, Berg CS, Nelson TC, Fishman L. Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers. Evolution 2022; 76:765-781. [PMID: 35266558 DOI: 10.1111/evo.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 01/21/2023]
Abstract
Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.
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Affiliation(s)
- Kory M Kolis
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: O'Connor Center for the Rocky Mountain West, University of Montana, Missoula, MT, 59812
| | - Colette S Berg
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: Embark Veterinary, Inc., Boston, Massachusetts, 02210
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
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Nagasawa K, Setoguchi H, Maki M, Sawa K, Horie K, Sakaguchi S. Species cohesion of an extremophyte (Carex angustisquama, Cyperaceae) in solfatara fields maintained under interspecific natural hybridization. ANNALS OF BOTANY 2021; 128:343-356. [PMID: 34104952 PMCID: PMC8389175 DOI: 10.1093/aob/mcab069] [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: 04/08/2021] [Accepted: 05/30/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Hybridization is the main driver of plant diversification, and gene flow via hybridization has multifaceted effects on plant evolution. Carex angustisquama is an extremophyte that grows on soils heavily acidified by volcanism. Despite its habitat distinct from that of other species, this species is known to form interspecific hybrids, implying interspecific gene flow. It is crucial to verify the extent and direction of interspecific gene flow between C. angustisquama and closely related species to understand the evolutionary process of an extremophyte in solfatara fields. METHODS In this study, expressed sequence tag-simple sequence repeat markers were utilized to infer the extent and direction of interspecific gene flow between C. angustisquama and closely related species. KEY RESULTS Bayesian clustering and simulation analyses revealed that all individuals of the three hybrid species were classified into the first hybrid generation or first backcross to C. angustisquama; therefore, current interspecific gene flow is limited. Moreover, in the Bayesian inference of historical gene flow based on multispecies samples, the model that assumed no interspecific gene flow was the most strongly supported across all species pairs, including phylogenetically close but ecologically distinctive species pairs. CONCLUSIONS Our results revealed that interspecific gene flow between C. angustisquama and its related species has been limited both currently and historically. Moreover, our results of Bayesian inference of historical gene flow indicated that extrinsic, rather than intrinsic, factors probably act as isolating barriers between Carex species, with hybrid breakdown via microhabitat segregation being the probable potential barrier. Overall, our findings provide insights into the evolutionary process of an extremophyte in solfatara fields and offer an important example of the mechanisms of diversification of the speciose genus Carex.
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Affiliation(s)
- Koki Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | | | - Kenji Horie
- Asahikawa City Northern Wild Plants Garden, Asahikawa, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
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