1. bookVolume 54 (2005): Issue 1-6 (December 2005)
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eISSN
2509-8934
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22 Feb 2016
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English
access type Open Access

Chloroplast and Total Genomic Diversity in the Endemic Costa Rican Tree Lonchocarpus costaricensis (J. D. Smith) Pittier (Papilionaceae)

Published Online: 19 Oct 2017
Volume & Issue: Volume 54 (2005) - Issue 1-6 (December 2005)
Page range: 293 - 300
Received: 26 Jul 2005
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
Abstract

In Mesoamerica, tropical dry forest is a highly threatened habitat, and species endemic to this environment are under extreme pressure. The tree species, Lonchocarpus costaricensis is endemic to the dry northwest of Costa Rica and southwest Nicaragua. It is a locally important species but, as land has been cleared for agriculture, populations have experienced considerable reduction and fragmentation. To assess current levels and distribution of genetic diversity in the species, a combination of chloroplast-specific (cpDNA) and whole genome DNA markers (amplified fragment length polymorphism, AFLP) were used to fingerprint 121 individual trees in 6 populations. Two cpDNA haplotypes were identified, distributed among populations such that populations at the extremes of the distribution showed lowest diversity. A large number (487) of AFLP markers were obtained and indicated that diversity levels were highest in the two coastal populations (Cobano, Matapalo, H = 0.23, 0.28 respectively). Population differentiation was low overall, FST = 0.12, although Matapalo was strongly differentiated from all other populations (FST = 0.16-0.22), apart from Cobano (FST = 0.11). Spatial genetic structure was present in both datasets at different scales: cpDNA was structured at a range-wide distribution scale, whilst AFLP data revealed genetic neighbourhoods on a population scale. In general, the habitat degradation of recent times appears not to have yet impacted diversity levels in mature populations. However, although no data on seed or saplings were collected, it seems likely that reproductive mechanisms in the species will have been affected by land clearance. It is recommended that efforts should be made to conserve the extant genetic resource base and further research undertaken to investigate diversity levels in the progeny generation.

Keywords

AYRES, D. R. and F. J. RYAN (1999): Genetic diversity and structure of the narrow endemic Wyethia reticulata and its congener W. bolanderi (Asteraceae) using RAPD and allozyme techniques. American Journal of Botany 86: 344-353.10.2307/2656756Open DOISearch in Google Scholar

BALANDRIN, M. F., J. A. KLOCKE, E. S. WURTELE and W. H. BOLLINGER (1985): Natural plant chemicals: sources of industrial and medicinal materials. Science 228: 1154-1160. 10.1126/science.38901823890182Search in Google Scholar

BAWA, K. and S. DAYANANDAN (1998): Global climate change and tropical forest genetic resources. Climatic change 39: 473-485.10.1023/A:1005360223639Search in Google Scholar

BAWA, K. S. and P. S. ASHTON (1991): Conservation of rare trees in tropical rain forests: a genetic perspective., pp. in Genetics and conservation of rare plants., edited by D. A. FALK and K. E. HOLSINGER, Oxford University Press., New York.Search in Google Scholar

BIRKY, C. W. (1995): Uniparental Inheritance of Mitochondrial and Chloroplast Genes - Mechanisms and Evolution. Proceedings of the National Academy of Sciences of the United States of America 92: 11331-11338.10.1073/pnas.92.25.11331403948524780Open DOISearch in Google Scholar

CAVERS, S., C. NAVARRO, P. HOPKINS, R. A. ENNOS and A. J. LOWE (2005): Regional and population-scale influences on genetic diversity partitioning within Costa Rican populations of the pioneer tree Vochysia ferruginea Mart. Silvae Genetica.10.1515/sg-2005-0037Open DOISearch in Google Scholar

CESPEDES, M., M. V. GUTIERREZ, N. M. HOLBROOK and O. J. ROCHA (2003): Restoration of genetic diversity in the dry forest tree Swietenia macrophylla (Meliaceae) after pasture abandonment in Costa Rica. Molecular Ecology 12: 3201-3212.10.1046/j.1365-294X.2003.01986.xOpen DOISearch in Google Scholar

COATES, A. G. and J. A. OBANDO (1996): The Geologic Evolution of the Central American Isthmus, pp. 21-56 in Evolution and Environment in Tropical America edited by JACKSON, B. C., A. F. BUDD and A. G. COATES. The University of Chicago Press, Chicago.Search in Google Scholar

DEGEN, B., R. J. PETIT and A. KREMER (2001): SGS - Spatial Genetic Software: A computer program for analysis of spatial genetic and phenotypic structures of individuals and populations. Journal of Heredity 92: 447-448.10.1093/jhered/92.5.44711773257Open DOISearch in Google Scholar

DEMESURE, B., N. SODZI and R. J. PETIT (1995): A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4: 129-131.10.1111/j.1365-294X.1995.tb00201.x7711952Open DOISearch in Google Scholar

DICK, C. W. (2001): Genetic rescue of remnant tropical trees by an alien pollinator. Proceedings of the Royal Society of London B 268: 2391-2396.10.1098/rspb.2001.1781108889111703880Search in Google Scholar

DUMOLIN-LAPEGUE, S., M.-H. PEMONGE and R. J. PETIT (1997): An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology 6: 393-397.10.1046/j.1365-294X.1997.00193.xOpen DOISearch in Google Scholar

EL MOUSADIK, A. and R. J. PETIT (1996): Chloroplast phylogeography of the argan tree of Morocco. Molecular Ecology 5: 547-555.10.1111/j.1365-294X.1996.tb00346.x8794562Open DOISearch in Google Scholar

ENNOS, R. A. (1994): Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72: 250-259.10.1038/hdy.1994.35Search in Google Scholar

FELSENSTEIN, J. (1993): PHYLIP: Phylogeny Inference Package. University of Washington, Seattle, Washington.Search in Google Scholar

GAUER, L. and S. CAVALLI-MOLINA (2000): Genetic variation in natural populations of mate (Ilex paraguarensis A. St.-Hil., Aquifoliaceae) using RAPD markers. Heredity 84: 647-656.10.1046/j.1365-2540.2000.00687.x10886380Open DOISearch in Google Scholar

GILLIES, A. C. M., J. P. CORNELIUS, A. C. NEWTON, C. NAVARRO, M. HERNANDEZ and J. WILSON (1997): Genetic variation in Costa Rican populations of the tropical timber species Cedrela odorata L., assessed using RAPDs. Molecular Ecology 6: 1133-1145.10.1046/j.1365-294X.1997.00287.xOpen DOISearch in Google Scholar

GILLIES, A. C. M., C. NAVARRO, A. J. LOWE, A. C. NEWTON, M. HERNANDEZ, J. WILSON and J. P. CORNELIUS (1999): Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs. Heredity 83: 722-732.10.1046/j.1365-2540.1999.00626.x10651917Open DOISearch in Google Scholar

GITZENDANNER, M. A. and P. S. SOLTIS (2000): Patterns of genetic variation in rare and widespread plant congeners. American Journal of Botany 87(6): 783-792.10.2307/2656886Search in Google Scholar

HALL, P., S. WALKER and K. BAWA (1996): Effect of forest fragmentation on genetic diversity and mating system in a tropical tree, Pithecellobium elegans. Conservation Biology 10: 757-768.10.1046/j.1523-1739.1996.10030757.xSearch in Google Scholar

HAMILTON, M. B. (1999): Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8: 521-522.Search in Google Scholar

HAMRICK, J. L. (1983): The distribution of genetic variation within and among natural plant populations, pp. 335-348 in Genetics and Conservation, edited by C. M.Search in Google Scholar

SCHONEWALD-COX, S. M. CHAMBERS, B. MACBRYDE and W. L. THOMAS, Benjamin/Cummings, Menlo Park, CA. HAMRICK, J. L. (2004): Response of forest trees to global environmental changes. Forest Ecology and Management 197: 323-335.10.1016/j.foreco.2004.05.023Search in Google Scholar

HAMRICK, J. L. and M. J. W. GODT (1989): Allozyme diversity in plant species., pp. 43-63 in Plant population genetics, breeding and genetic resources., edited bySearch in Google Scholar

A. H. D. BROWN, M. T. CLEGG, A. L. KAHLER and B. S. WEIR, Sinauer Associates Inc., Sunderland, MA. HAMRICK, J. L. and M. J. W. GODT (1996): Conservation genetics of endemic plant species., pp. in Conservation Genetics: case studies from nature., edited by J. C.Search in Google Scholar

AVISE and J. L. HAMRICK, Chapman & Hall, New York. HOLDRIDGE, L. R., L. POVEDA and Q. JIMENEZ (1997): Arboles de Costa Rica, Vol. 1, 2nd Edition. Centro Cientifico Tropical, San Jose, Costa Rica.Search in Google Scholar

IUCN (2001): IUCN Red List Categories and Criteria: Version 3.1. IUCN Species Survival Commission. IUCN, Gland, Switzerland and Cambridge, UK. ii + 30 pp. IPCC (Intergovernmental Panel on Climate Change) (2001): Impacts, adaptation and vulnerability to climate change: 2001, third assessment report of the IPCC, Cambridge, UK, University Press. Search in Google Scholar

JANZEN, D. H. (1982): Weight of dry seeds in 1-3-seeded fruits of Lonchocarpus costaricensis (Leguminosae), a Costa Rican wind-dispersed tree. Brenesia 19/20: 363-368.Search in Google Scholar

JANZEN, D. H. (1988): Tropical dry forests, the most endangered major tropical ecosystem, pp. 130-137 in Biodiversity, edited by E. O. WILSON, National Academy Press, Washington, DC.Search in Google Scholar

JANZEN, D. H. (1991): How to save tropical biodiversity. American Entomologist 37: 159-171.10.1093/ae/37.3.159Search in Google Scholar

JANZEN, D. H., L. E. FELLOWS and P. G. WATERMAN (1990): What protects Lonchocarpus (Leguminosae) seeds in a Costa Rican dry forest ? Biotropica 22: 272-285.10.2307/2388538Open DOISearch in Google Scholar

KWON, J. A. and C. W. MORDEN (2002): Population genetic structure of two rare tree species (Colubrina oppositifolia and Alphitonia ponderosa, Rhamnaceae) from Hawaiian dry and mesic forests using random amplified polymorphic DNA markers. Molecular Ecology 11: 991-1001.10.1046/j.1365-294X.2002.01497.x12030978Open DOISearch in Google Scholar

LANDE, R. (1988): Genetics and demography in biological conservation. Science 24: 1455-1460.10.1126/science.34204033420403Search in Google Scholar

LOWE, A. J., S. A. HARRIS, P. ASHTON (2004): Ecological Genetics: Design, Analysis and Application. Blackwells, Oxford. 326 pp.Search in Google Scholar

MCLAUGHLIN, J. F., J. J. HELLMANN, C. L. BOGGS and P. R. EHRLICH (2002): Climate change hastens population extinctions. Proceedings of the National Academy of Sciences of the United States of America 99: 6070-6074.10.1073/pnas.05213119912290311972020Search in Google Scholar

MYERS, N., R. A. MITTERMEIER, C. G. MITTERMEIER, G. A. B. DA FONSECA and J. KENT (2000): Biodiversity hotspots for conservation priorities. Nature 403: 853-858.10.1038/3500250110706275Search in Google Scholar

NYBOM, H. and I. V. BARTISH (2000): Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers. Perspectives in Plant Ecology, Evolution and Systematics 3: 93-114.10.1078/1433-8319-00006Open DOISearch in Google Scholar

PAGE, R. D. M. (1996): TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.Search in Google Scholar

PONS, O. and R. J. PETIT (1995): Estimation, variance and optimal sampling of gene diversity I. Haploid locus. Theoretical and Applied Genetics 90: 462-470.10.1007/BF0022199124173939Search in Google Scholar

RUSSELL, J. R., J. C. WEBER, A. BOOTH, W. POWELL, C. SOTELO-MONTES and I. K. DAWSON (1999): Genetic variation of Calycophyllum spruceanum in the Peruvian Amazon Basin, revealed by amplified fragment length polymorphism (AFLP) analysis. Molecular Ecology 8: 199-204.10.1046/j.1365-294X.1999.00551.xSearch in Google Scholar

SANCHEZ-AZOFEIFA, G. A., R. C. HARRISS and D. L. SKOLE (2001): Deforestation in Costa Rica: a quantitative analysis using remote sensing imagery. Biotropica 33: 378-384.10.1111/j.1744-7429.2001.tb00192.xOpen DOISearch in Google Scholar

SCHEMSKE, D. W., B. C. HUSBAND, M. H. RUCKELSHAUS, C. GOODWILLIE, I. M. PARKER and J. G. BISHOP (1994): Evaluating approaches to the conservation of rare and endangered plants. Ecology 75: 584-606.10.2307/1941718Open DOISearch in Google Scholar

TABERLET, P., L. GIELLY, G. PAUTOU and J. BOUVET (1991): Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.10.1007/BF000371521932684Open DOISearch in Google Scholar

VEKEMANS, X., T. BEAUWENS, M. LEMAIRE and I. ROLDANRUIZ (2002): Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology 11: 139-151.10.1046/j.0962-1083.2001.01415.x11903911Open DOISearch in Google Scholar

VOS, P., R. HOGERS, M. BLEEKER, M. REIJANS, T. VAN DE LEE, M. HORNES, A. FRIJTERS, J. POT, J. PELEMAN, M. KUIPER and M. ZABEAU (1995): AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407-4414.10.1093/nar/23.21.44073073977501463Open DOISearch in Google Scholar

WHITE, G. M., D. H. BOSHIER and W. POWELL (1999): Genetic variation within a fragmented population of Swietenia humilis Zucc. Molecular Ecology 8: 1899-1909.10.1046/j.1365-294x.1999.00790.x10620233Search in Google Scholar

ZHIVOTOVSKY, L. A. (1999): Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology 8: 907-913.10.1046/j.1365-294x.1999.00620.x10434412Search in Google Scholar

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