Implications of Clonal Structure for Effective Population Size and Genetic Drift in a Rare Terrestrial Orchid, Cremastra appendiculata MI YOON CHUNG, ∗ JOHN D. NASON,† AND MYONG GI CHUNG ∗ ‡ ∗ Department of Biology, Gyeongsang National University, Jinju 660–701, Republic of Korea †Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, U.S.A. Abstract: Effective population size ( N e ) influences the degree to which random genetic drift changes allele frequencies, increases inbreeding, and decreases genetic diversity, and thus is a parameter of direct relevance to the conservation of rare species. Few empirical data are available, however, concerning the effects of clonal structure on N e in plant species reproducing both sexually and asexually. Using genetic markers and spatial autocorrelation analysis, we quantified the statistical significance and spatial scale of clonal spread of six populations of the rare terrestrial orchid Cremastra appendiculata (D. Don) Makino in a large (180 ha), undisturbed landscape on Oenaro Island, located off of the southeastern coast of South Korea. We used this information to calculate three demographic estimators of N e : the number of ramets within a population, the number of genets, and an estimator that incorporates information on both the number of genets and variation in the number of ramets per genet. Taking clonal structure into account results in up to a fivefold decrease in estimates of N e relative to the ecologically apparent number of individuals within populations. Levels of standing genetic variation are in fact greater than expected given our estimates of N e , leading us to consider historical factors resulting in N e being greater in the past than in present-day populations. Like C. appendiculata, many terrestrial orchids occur in relatively small, spatially isolated populations and are of special concern for conservation. Our results indicate that efforts aimed at the long-term preservation of these species should be based on a sound understanding of the potential for clonal structure and its implications for the sensitivity of populations to losses of genetic diversity and fitness via random genetic drift. Key Words: allozymes, clones, Cremastra appendiculata, effective population size, fitness, Orchidaceae, spatial genetic structure Implicaciones de la Estructura Clonal para el Tama˜ no Poblacional Efectivo y la Deriva G´ enica en una Orqu´ ıdea Terrestre Rara, Cremastra appendiculata Resumen: El tama˜ no poblacional efectivo ( N e ) influye en la proporci´ on en la que las frecuencias al´ elicas son cambiadas por deriva g´ enica aleatoria y disminuye la diversidad gen´ etica, y por lo tanto es un par´ ametro de relevancia directa para la conservaci´ on de especies raras. Sin embargo, existen pocos datos emp´ ıricos sobre los efectos de la estructura clonal sobre N e en especies de plantas de reproducci´ on sexual como asexual. Con el uso de marcadores gen´ eticos y an´ alisis de autocorrelaci´ on espacial cuantificamos la significaci´ on estad´ ıstica de la expansi´ on clonal de seis poblaciones de la orqu´ ıdea terrestre rara Cremastra appendiculata (D. Don) Makino en un paisaje extenso (180 ha) no perturbado en la Isla Oenaro, localizada cerca de la costa sur de Corea del Sur. Utilizamos esta informaci´ on para calcular tres estimadores demogr´ aficos de N e : el n´ umero de r´ amulas en una poblaci´ on, el n´ umero de “genets” y un estimador que incorpora informaci´ on tanto del n´ umero de “genets” y la variaci´ on en el n´ umero de r´ amulas por “genet.” Tomando a la estructura clonal en consideraci´ on resulta en un decremento de hasta cinco veces en las estimaciones de N e en relaci´ on con el ‡Address correspondence to M. G. Chung, email mgchung@nongae.gsnu.ac.kr Paper submitted by July 7, 2003; revised manuscript accepted February 24, 2004. 1515 Conservation Biology, Pages 1515–1524 Volume 18, No. 6, December 2004