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Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01428-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Velasco-García MV, Ramírez-Herrera C, López-Upton J, Valdez-Hernández JI, López-Sánchez H, López-Mata L. Diversity and Genetic Structure of Dioon holmgrenii (Cycadales: Zamiaceae) in the Mexican Pacific Coast Biogeographic Province: Implications for Conservation. PLANTS 2021; 10:plants10112250. [PMID: 34834614 PMCID: PMC8623071 DOI: 10.3390/plants10112250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022]
Abstract
Dioon holmgrenii De Luca, Sabato et Vázq.Torres is an endangered species; it is endemic and its distribution is restricted to the biogeographic province of the Mexican Pacific Coast. The aim of this work was to determine the diversity and genetic structure of nine populations. The genetic diversity parameters and Wright’s F statistics were determined with six microsatellite loci. The genetic structure was determined by using the Structure software and by a discriminant analysis. The genetic diversity of the populations was high. The proportion of polymorphic loci was 0.89, the observed heterogeneity was higher (Ho = 0.62 to 0.98) than expected (He = 0.48 to 0.78), and the fixation index was negative (IF = −0.091 to −0.601). Heterozygous deficiency (FIT = 0.071) was found at the species level and heterozygotes excess (FIS = −0.287) at the population level. The genetic differentiation between populations was high (FST = 0.287), with the number of migrants less than one. Three groups of populations were differentiated, and the variation within populations, between populations, and between groups was: 65.5, 26.3, and 8.2%, respectively. Multiple factors explain the high genetic diversity, while the genetic structure is due to geographic barriers. Community reserves are urgent in at least one most diverse population of each group.
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Affiliation(s)
- Mario Valerio Velasco-García
- Centro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales-Instituto Nacional de Investigaciones Agrícolas Pecuarias y Forestales (INIFAP), Avenida Progreso 5, Coyoacán, Ciudad de Mexico 04010, Mexico;
| | - Carlos Ramírez-Herrera
- Colegio de Postgraduados, Carretera Mexico-Texcoco km 36.5, Montecillo, Texcoco 56230, Mexico; (J.L.-U.); (J.I.V.-H.); (L.L.-M.)
- Correspondence: ; Tel.: +52-55-7378-6568
| | - Javier López-Upton
- Colegio de Postgraduados, Carretera Mexico-Texcoco km 36.5, Montecillo, Texcoco 56230, Mexico; (J.L.-U.); (J.I.V.-H.); (L.L.-M.)
| | - Juan Ignacio Valdez-Hernández
- Colegio de Postgraduados, Carretera Mexico-Texcoco km 36.5, Montecillo, Texcoco 56230, Mexico; (J.L.-U.); (J.I.V.-H.); (L.L.-M.)
| | - Higinio López-Sánchez
- Colegio de Postgraduados, Boulevard Forjadores de Puebla No. 205, Santiago Momoxpan, San Pedro Cholula. C.P., Puebla 72760, Mexico;
| | - Lauro López-Mata
- Colegio de Postgraduados, Carretera Mexico-Texcoco km 36.5, Montecillo, Texcoco 56230, Mexico; (J.L.-U.); (J.I.V.-H.); (L.L.-M.)
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Does Phytogeography Change with Shifts in Geopolitics? The Curious Case of Cycads in the United States. DIVERSITY 2020. [DOI: 10.3390/d12120445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The United States is currently home to five native cycad species. We provide a discussion on these five cycad species to illuminate how evolutionary and geopolitical processes influence phytogeography and published checklists of threatened plants. The number of threatened species in need of protection within any given country is a product of speciation that is contingent with evolutionary processes. However, this number may change instantaneously along with shifting of geopolitical boundaries brought about by armed conflict between rival states and multilateral negotiations. There are five contemporary cycad species within the United States, and the various historical bilateral and multilateral agreements that have generated this list are reviewed. Three of these five cycad species are threatened and in need of urgent protection. A discussion on the history of United States cycads as a microcosm of worldwide conservation issues is presented, with a focus on how federal conservation endeavors of individual nations may influence the world’s biodiversity crisis.
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Aristizábal A, Tuberquia DJ, Sanín MJ. Conservation Genetics of Two Highly Endangered and Poorly Known Species of Zamia (Zamiaceae: Cycadales) in Colombia. J Hered 2019; 109:438-445. [PMID: 29206927 DOI: 10.1093/jhered/esx110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/27/2017] [Indexed: 11/12/2022] Open
Abstract
Genetic diversity is key in providing the variation needed to face stochastic change. Increased habitat loss alters population size and dynamics posing serious threats to the conservation of wild species. Colombia has undergone massive deforestation over the last century, but harbors extraordinary high species diversity of genus Zamia (Cycadales); however, most of the species are under threat. In this study, we targeted the largest accessible remaining populations of 2 closely related species growing as endemics in the Magdalena Valley region of Colombia. We successfully transferred the SSR loci used in previous Zamia studies to these species. In total, we amplified 13 microsatellite loci in 3 wild populations, aiming at: 1) assessing genetic diversity and 2) understanding if the structure found between the 3 populations reflected species and population boundaries due to ecological and historical genetic isolation. We found that the actual population size does not reflect population genetic diversity with a small population (Perales) harboring the highest genetic diversity. In addition, all populations are highly structured regardless of species containment, all showing signs of genetic isolation. Given the high degree of ecological threat, and the inherent biological traits of Cycads, we provide information regarding the prioritization of populations for ex situ management.
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Affiliation(s)
- Arturo Aristizábal
- Facultad de Ciencias y Biotecnología, Universidad CES, Calle 10 A # 22-04, Medellín, Colombia
| | - Dino J Tuberquia
- Facultad de Ciencias y Biotecnología, Universidad CES, Calle 10 A # 22-04, Medellín, Colombia
| | - María José Sanín
- Facultad de Ciencias y Biotecnología, Universidad CES, Calle 10 A # 22-04, Medellín, Colombia
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Clugston JAR, Kenicer GJ, Milne R, Overcast I, Wilson TC, Nagalingum NS. RADseq as a valuable tool for plants with large genomes—A case study in cycads. Mol Ecol Resour 2019; 19:1610-1622. [DOI: 10.1111/1755-0998.13085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022]
Affiliation(s)
- James A. R. Clugston
- School of Biological Sciences The University of Edinburgh Edinburgh UK
- Royal Botanic Garden Edinburgh Edinburgh UK
| | | | - Richard Milne
- School of Biological Sciences The University of Edinburgh Edinburgh UK
| | - Isaac Overcast
- The Graduate Center of the City University of New York New York NY USA
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Lazcano-Lara JC, Ackerman JD. Best in the company of nearby males: female success in the threatened cycad, Zamia portoricensis. PeerJ 2018; 6:e5252. [PMID: 30065868 PMCID: PMC6063211 DOI: 10.7717/peerj.5252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/27/2018] [Indexed: 11/25/2022] Open
Abstract
Variation in plant reproductive success is affected by ecological conditions including the proximity of potential mates. We address the hypothesis that spatial distribution of sexes affects female reproductive success (RS) in the dioecious cycad, Zamia portoricensis. Are the frequencies of males, operational sex ratios, and distances to the nearest mate associated with RS in females? We studied the spatial distribution of sexes in two populations in Puerto Rico and compared RS of target females with the number of males and operational sex ratios. Population structure suggests regular successful recruitment. Adults, males, and females were randomly distributed with respect to one another. Reproductive success of females was highly variable, but was higher in neighborhoods with more males than females and generally decreased with increasing distance to the nearest male, becoming statistically significant beyond 190 cm. This possible mate-finding Allee effect indicates that pollinator movement among plants may be limited for this mutually dependent plant-pollinator interaction. Yet being close to male plants is a matter of chance, perhaps a factor generating the high intra-population genetic diversity in Z. portoricensis.
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Affiliation(s)
| | - James D. Ackerman
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
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Molecular and Morphological Phylogenetic Analyses of New World Cycad Beetles: What They Reveal about Cycad Evolution in the New World. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Salas-Leiva DE, Meerow AW, Calonje M, Francisco-Ortega J, Griffith MP, Nakamura K, Sánchez V, Knowles L, Knowles D. Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot. AMERICAN JOURNAL OF BOTANY 2017; 104:757-771. [PMID: 28515078 DOI: 10.3732/ajb.1700054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The Bahamas archipelago is formed by young, tectonically stable carbonate banks that harbor direct geological evidence of global ice-volume changes. We sought to detect signatures of major changes on gene flow patterns and reconstruct the phylogeographic history of the monophyletic Zamia pumila complex across the Bahamas. METHODS Nuclear molecular markers with both high and low mutation rates were used to capture two different time scale signatures and test several gene flow and demographic hypotheses. KEY RESULTS Single-copy nuclear genes unveiled apparent ancestral admixture on Andros, suggesting a significant role of this island as main hub of diversity of the archipelago. We detected demographic and spatial expansion of the Zamia pumila complex on both paleo-provinces around the Piacenzian (Pliocene)/Gelasian (Pleistocene). Populations evidenced signatures of different migration models that have occurred at two different times. Populations on Long Island (Z. lucayana) may either represent a secondary colonization of the Bahamas by Zamia or a rapid and early-divergence event of at least one population on the Bahamas. CONCLUSIONS Despite changes in migration patterns with global climate, expected heterozygosity with both marker systems remains within the range reported for cycads, but with significant levels of increased inbreeding detected by the microsatellites. This finding is likely associated with reduced gene flow between and within paleo-provinces, accompanied by genetic drift, as rising seas enforced isolation. Our study highlights the importance of the maintenance of the predominant direction of genetic exchange and the role of overseas dispersion among the islands during climate oscillations.
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Affiliation(s)
- Dayana E Salas-Leiva
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Alan W Meerow
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Michael Calonje
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Javier Francisco-Ortega
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- Kushlan Tropical Science Institute, 11935 Old Cutler Road, Fairchild Tropical Botanic Garden, Coral Gables, Florida 33156 USA
| | - M Patrick Griffith
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Vanessa Sánchez
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Lindy Knowles
- Bahamas National Trust, P. O. Box N-4105, Bay Street Business Centre, Bay Street, Nassau
| | - David Knowles
- The Bahamas, Bahamas National Trust, Abaco National Park, P.O. Box AB-20953, Marsh Harbour, Abaco, The Bahamas
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Jestrow B, Peguero B, Jiménez F, Cinea W, Hass M, Reeve A, Meerow AW, Griffith MP, Maunder M, Francisco-Ortega J. Genetic diversity and differentiation of the Critically Endangered Hispaniolan palm Coccothrinax jimenezii M.M. Mejía & R.G. García based on novel SSR markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Salas-Leiva DE, Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Stevenson DW, Nakamura K. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads. Mol Ecol Resour 2014; 14:831-45. [PMID: 24444413 DOI: 10.1111/1755-0998.12228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 01/28/2023]
Abstract
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
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Affiliation(s)
- Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA
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Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
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Cycad biodiversity in the Bahamas Archipelago and conservation genetics of the threatened Zamia lucayana (Zamiaceae). ORYX 2013. [DOI: 10.1017/s0030605312000129] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractA conservation assessment for the three cycad species native to the Bahamas Islands is presented. Results are based on field surveys on all islands where these species occur. Zamia angustifolia is native to Eleuthera, Zamia integrifolia is native to Abaco, Andros, Eleuthera, Grand Bahama and New Providence, and Zamia lucayana is endemic to Long Island. Z. angustifolia is of the highest conservation concern because of the small number of adult plants, its restricted distribution and the extensive development occurring within its habitat. Z. integrifolia also has a restricted distribution on Eleuthera and Grand Bahama and, although threatened by urban development in New Providence, it is relatively common on Abaco and Andros. Z. lucayana comprises three populations within a narrow strip of land of c. 1 km2; we propose a reassignment of its current conservation status from Endangered to Critically Endangered. We assessed the genetic structure of Z. lucayana based on 15 polymorphic microsatellite DNA loci; this indicated that the three known populations should be considered a single management unit. However, the high number of private alleles suggests that genetic drift, indicative of recent fragmentation, is progressing. We propose in situ conservation strategies, and we also collected germplasm from a total of 24 populations of these three cycad species, for ex situ conservation.
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