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Wróblewska A, Ostrowiecka B, Brzosko E, Jermakowicz E, Tałałaj I, Mirski P. The patterns of inbreeding depression in food-deceptive Dactylorhiza orchids. FRONTIERS IN PLANT SCIENCE 2024; 15:1244393. [PMID: 38590747 PMCID: PMC10999633 DOI: 10.3389/fpls.2024.1244393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
Introduction Inbreeding depression (ID) in food-deceptive plants have been reported previously, however, it has not been often proven that selfed seeds germinate better than outbred ones or that selfing affects ID. To resolved these issues, food-deceptive related Dactylorhiza majalis, D. incarnata var. incarnata and D. fuchsii orchids were investigated. Methods Hand pollination treatments and control pollination were conducted. Fruit set, number of seeds per fruit, seed length, number of well-developed seeds per fruit, and proportion of in vitro asymbiotic germination seeds, were analyzed in relation to inflorescence levels and used as fitness indicators for these orchids. The ID and pollen limitation were measured. Results The lowest ID (δ = -1.000) was in D. majalis, and present in combination with a high pollen limitation in its populations. D. fuchsii showed higher ID (δ = 0.366), and D. incarnata var. incarnata weak ID (δ = 0.065), although ID varied between its fitness components. The seed number per fruit differed significantly between the treatments and the inflorescence levels in treatments. Discussion This study emphasizes that the breeding system rather than the flower position on the inflorescence shaped the quality and quantity of reproductive output. The ID and its effect on germination of food-deceptive orchid seeds undoubtedly played an important role.
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Affiliation(s)
- Ada Wróblewska
- Faculty of Biology, University of Bialystok, Białystok, Poland
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Zhang D, Zhao XW, Li YY, Ke SJ, Yin WL, Lan S, Liu ZJ. Advances and prospects of orchid research and industrialization. HORTICULTURE RESEARCH 2022; 9:uhac220. [PMID: 36479582 PMCID: PMC9720451 DOI: 10.1093/hr/uhac220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Jie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Lun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Brooks E, Slender AL, Cu S, Breed MF, Stangoulis JCR. A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01468-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractUnderstanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy (Acanthocladium dockeri) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.
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Genetic Diversity of Campomanesia adamantium and Its Correlation with Land Use and Land Cover. DIVERSITY 2021. [DOI: 10.3390/d13040160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
(1) Background: Campomanesia adamantium is an endemic species of the Cerrado and this biome has been under threat by its constant degradation. The genetic diversity of C. adamantium was characterized using species-specific microsatellites in two different time periods and correlations of these parameters of genetic diversity with the land use and land cover data. (2) Methods: We used 10 microsatellite loci to analyze C. adamantium from five populations, collected in 2011 and 2017. Maps of land use and land cover of the collection sites in both years were generated and subsequently correlated with genetic diversity. (3) Results: No significant loss of genetic diversity was observed in the analyzed period and a positive inbreeding coefficient was observed in all populations. AMOVA and STRUCTURE showed that there is no population structure between years and populations. Significant Pearson correlations were observed in 2017 between parameters of genetic diversity and land use and land cover, with a positive correlation between expected heterozygosity and secondary vegetation, and a negative correlation between inbreeding coefficient and exposed soil. (4) Conclusions: There was no decline in genetic diversity from 2011 to 2017. The high rates of the inbreeding coefficient could lead, for the species, in the long run, to an inbreeding depression as the Cerrado fragmentation might cause a population bottleneck.
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Ketema S, Tesfaye B, Keneni G, Amsalu Fenta B, Assefa E, Greliche N, Machuka E, Yao N. DArTSeq SNP-based markers revealed high genetic diversity and structured population in Ethiopian cowpea [Vigna unguiculata (L.) Walp] germplasms. PLoS One 2020; 15:e0239122. [PMID: 33031381 PMCID: PMC7544073 DOI: 10.1371/journal.pone.0239122] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/31/2020] [Indexed: 01/20/2023] Open
Abstract
Cowpea [Vigna unguiculata (L.) Walp] is one of the important climate-resilient legume crops for food and nutrition security in sub-Saharan Africa. Ethiopia is believed to harbor high cowpea genetic diversity, but this has not yet been efficiently characterized and exploited in breeding. The objective of this study was to evaluate the extent and pattern of genetic diversity in 357 cowpea accestions comprising landraces (87%), breeding lines (11%) and released varieties (2%), using single nucleotide polymorphism markers. The overall gene diversity and heterozygosity were 0.28 and 0.12, respectively. The genetic diversity indices indicated substantial diversity in Ethiopian cowpea landraces. Analysis of molecular variance showed that most of the variation was within in the population (46%) and 44% between individuals, with only 10% of the variation being among populations. Model-based ancestry analysis, the phylogenetic tree, discriminant analysis of principal components and principal coordinate analysis classified the 357 genotypes into three well-differentiated genetic populations. Genotypes from the same region grouped into different clusters, while others from different regions fell into the same cluster. This indicates that differences in regions of origin may not be the main driver determining the genetic diversity in cowpea in Ethiopia. Therefore, differences in sources of origin, as currently distributed in Ethiopia, should not necessarily be used as indices of genetic diversity. Choice of parental lines should rather be based on a systematic assessment of genetic diversity in a specific population. The study also suggested 94 accesstions as core collection which retained 100% of the genetic diversity from the entire collection. This core set represents 26% of the entire collection pinpointing a wide distribution of the diversity within the ethiopian landraces. The outcome of this study provided new insights into the genetic diversity and population structure in Ethiopian cowpea genetic resources for designing effective collection and conservation strategies for efficient utilization in breeding.
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Affiliation(s)
- Selamawit Ketema
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, Melkassa, Ethiopia
- School of Plant and Horticultural Science, Hawassa University, Hawassa, Ethiopia
| | - Bizuayehu Tesfaye
- School of Plant and Horticultural Science, Hawassa University, Hawassa, Ethiopia
| | - Gemechu Keneni
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Berhanu Amsalu Fenta
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, Melkassa, Ethiopia
| | - Ermias Assefa
- Ethiopian Biotechnology Institute, Genomic Research Directorate, Addis Ababa, Ethiopian
| | | | - Eunice Machuka
- Biosciences Eastern and Central Africa - International Livestock Research Institute (BecA - ILRI) Hub, Nairobi, Kenya
| | - Nasser Yao
- Biosciences Eastern and Central Africa - International Livestock Research Institute (BecA - ILRI) Hub, Nairobi, Kenya
- * E-mail:
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Nazareno AG, Neto LM, Buzatti RSDO, van den Berg C, Forzza RC. Four raised to one equals one: A genetic approach to the Pseudolaelia vellozicola complex does not follow a math rule. Ecol Evol 2020; 10:4562-4569. [PMID: 32551043 PMCID: PMC7297771 DOI: 10.1002/ece3.6148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 11/20/2022] Open
Abstract
Pseudolaelia is a genus endemic to the eastern Brazilian Atlantic Forest, consisting of 12 accepted species. Some Pseudolaelia species, such as P. vellozicola, P. aguadocensis, P. oliveirana, and P. regentii, referred to here as the PV complex, present extensive intra- and interpopulation morphological polymorphism, raising uncertainty regarding their circumscriptions. Although previous morphological analyses were used to solve the generic boundaries in the PV complex, persuasive genetic evidence is lacking. In order to test the hypothesis that the group under investigation contains only one taxon, amplification profiles of five intersimple sequence repeat (ISSR) markers were used to evaluate genetic diversity, genetic structure, and the relationships among the PV complex species. A total of 134 reproductive individuals were sampled in eight insular populations. Intrapopulation genetic analysis indicated low levels of genetic diversity. Analysis of genetic structure revealed that each of the eight sample locations can be considered unique biological populations as they are highly differentiated from each other. The Mantel test showed a high and positive correlation between genetic and geographic distance (r = .841, p < .002), indicating isolation by distance. The results are consistent with that expected for plants with insular geographical distribution. When testing for the null hypothesis, the low levels of genetic variation among species (F CT = 0.155) suggest that the populations constitute only one highly polymorphic species with a wide distribution.
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Affiliation(s)
| | | | | | - Cássio van den Berg
- Department of Biological SciencesUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
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Garot E, Joët T, Combes MC, Lashermes P. Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors. Heredity (Edinb) 2019; 122:833-847. [PMID: 30478354 PMCID: PMC6781115 DOI: 10.1038/s41437-018-0168-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/09/2018] [Indexed: 01/23/2023] Open
Abstract
Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.
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Affiliation(s)
- Edith Garot
- IRD, University of Montpellier, DIADE, Montpellier, France
| | - Thierry Joët
- IRD, University of Montpellier, DIADE, Montpellier, France
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Gardiner LM, Rakotoarinivo M, Rajaovelona LR, Clubbe C. Population genetics data help to guide the conservation of palm species with small population sizes and fragmented habitats in Madagascar. PeerJ 2017; 5:e3248. [PMID: 28480141 PMCID: PMC5419215 DOI: 10.7717/peerj.3248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/29/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The need to incorporate genetic data into conservation management decisions is increasingly recognised. However, many published studies represent a 'gold standard' of sampling, techniques, and analyses. Such rigour is often not possible with limited funding and resourcing available for developing plans for the increasing number of threatened species requiring conservation management. Two endemic palm species of the Itremo Massif in central Madagascar, Dypsis ambositrae and D. decipiens, are known to be threatened with extinction and conservation management for these species is a priority for the newly created protected area in the region. METHODS The genetic diversity of these two species was studied using the relatively low-cost and rapid AFLP technique. DNA fragments generated using three primer combinations were analysed for 20 and 50 individuals of the two species, respectively, from across their ranges. RESULTS Genetic diversity was relatively low for both species. The two sites where the highly restricted D. ambositrae grows were found to be genetically distinct (although overall heterozygosity was low). Despite having a much wider distribution and relatively large population, D. decipiens did not show clear geographical nor genetic groupings and had similarly low genetic heterozygosity to D. ambositrae. DISCUSSION AND RECOMMENDATIONS With so few individuals remaining in the wild and two genetically distinct subpopulations, it is recommended that both sites of D. ambositrae are conserved and that seed are collected from both for ex situ conservation and potential future reintroduction. It may be less important to focus resources on conserving or collecting ex situ material from all sites where D. decipiens is found, as the genetic diversity represented by each subpopulation is limited and increasing sampling may not protect significantly higher levels of genetic diversity. This study provides data that inform and support conservation decisions taken for both species within this region, and in the management of the newly designated Itremo Massif Protected Area, which covers most of the sites where these two species remain in the wild.
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Affiliation(s)
- Lauren M Gardiner
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Mijoro Rakotoarinivo
- Département de Biologie et Ecologie Végétales, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Landy R Rajaovelona
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom.,Kew Madagascar Conservation Centre, Ivandry, Antananarivo, Madagascar
| | - Colin Clubbe
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
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Chen LN, Cui YZ, Wong KM, Li DZ, Yang HQ. Breeding system and pollination of two closely related bamboo species. AOB PLANTS 2017; 9:plx021. [PMID: 28685014 PMCID: PMC5493747 DOI: 10.1093/aobpla/plx021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 05/21/2017] [Accepted: 05/27/2017] [Indexed: 05/28/2023]
Abstract
An understanding of the breeding systems and pollination of agriculturally important plants is critical to germplasm improvement. Breeding system characteristics greatly influence the amount and spatial distribution of genetic variation within and amongst populations and influence the rarity and extinction vulnerability of plant species. Many woody bamboos have a long vegetative period (20-150 years) followed by gregarious monocarpy. Relatively, little is known about their pollination and breeding systems. We studied these characteristics in wild Dendrocalamus membranaceus populations and cultivated Dendrocalamus sinicus populations distributed in the Yunnan Province of China. Floral morphology, flower visitors and breeding system were studied from 2013 to 2015. Both bamboos were protogynous, but flowering periods of florets overlapped providing opportunities for self-pollination amongst florets, especially in D. membranaceus. There was no agamospermy in either species. Seed set of D. sinicus was low (0.42 ± 0.42 %) under natural pollination but higher (8.89 ± 2.55 %) after artificial xenogamy. Seed set of D. membranaceus was higher (7.49 ± 0.82 %) in mass flowering populations and 2.14 ± 0.25 % in sporadically flowering populations. The Asian honeybee Apis cerana could provide cross-pollination of D. membranaceus and D. sinicus, and flower visitation peaked at 1000-1200 h. Pollination limitation due to lack of pollinators or pollen was detected in the cultivated populations of D. sinicus and sporadically flowering populations of D. membranaceus. Pollination limitation was not obvious within mass flowering populations. Hand pollination could significantly increase seed set of these two bamboo species. Dendrocalamus membranaceus and D. sinicus were self-compatible and have a mixed-mating system with outcrossing being pre-dominant. Their seed production was limited by the quantity of pollen and pollinator activity. Honeybees were observed as effective pollinators.
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Affiliation(s)
- Ling-Na Chen
- Research Institute of Insect Resources, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming 650233, China
| | - Yong-Zhong Cui
- Research Institute of Insect Resources, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming 650233, China
| | - Khoon-Meng Wong
- Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Panlong District, Kunming 650201, China
| | - Han-Qi Yang
- Research Institute of Insect Resources, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming 650233, China
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Abstract
BACKGROUND Due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees, Orchidaceae present particular challenges for conservation. Furthermore, orchids, as potentially the largest family of angiosperms with >26000 species, species complexes and frequent hybrid formation, are complex to catalogue. Following a highlight in 2015, a further seven papers focusing on orchids, their interactions with beneficial organisms, pollinators and mycorrhiza, and other factors relating to their conservation, including threats from human utilization and changing land use, are presented here. CONCLUSIONS The production of an online flora of all known plants and an assessment of the conservation status of all known plant species as far as possible, to guide conservation action are the first two targets of the Global Strategy for Plant Conservation Without knowing how many species there are and how they should be circumscribed, neither of these targets is achievable. Orchids are a fascinating subject for fundamental research with rapid species evolution, specific organ structure and development, but they also suffer from high levels of threat. Effective orchid conservation must take account of the beneficial interactions with fungi and pollinators and the potentially detrimental effects of over-collection and changes in land use.
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Affiliation(s)
- Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
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