Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid

Abstract

We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

Development and characterization of microsatellite loci for the Neotropical orchid Trichocentrum pumilum

“…pumilum apparently is not under threat or in danger of extinction (IUCN 2002). However, the four populations considered in our study, collected from fragmented forest areas in the State of São Paulo, showed low within genetic variability, similar to the findings of Pandey et al (2015) with Cypripedium kentuckiense, a terrestrial orchid native to North America (A = 4.00; H o = 0.436; H e = 0.448), which might be indicative of the occurrence of evolutionary processes, such as population fragmentation, reduction in gene flow and genetic drift, leading to a decrease of genetic diversity. Higher levels of genetic diversity were found by Trapnell et al (2015) evaluating five populations of the epiphytic Dendrobium The apparent outcrossing rate (tˆa) showed values below 0.60 for each T. pumilum population, averaging 0.508, which is an indication that this species presents a mixed mating system, which may explain the higher levels of fixation index and lower levels of genetic diversity.…”

Seed dispersal and realized gene flow of two forest orchids in a fragmented landscape

“…He = 0.77–0.92 in Ophrys sp . ; Soliva & Widmer 2003; He = 0.62–0.81 in Gymnadenia conopsea ; Gustafsson 2000; He = 0.44–0.60 in Epidendrum secundum ; Pinheiro et al 2014; He = 0.35–0.54 in Cypripedium kentuckiense ; Pandey et al 2015).…”

Genetic diversity and population structure of the endangered orchid Pelatantheria scolopendrifolia (Orchidaceae) in Korea

“…A total of 15 polymorphic microsatellite markers were successfully amplified in all individuals from 11 populations, showing observed heterozygosity values from 0.156 to 1.000 (mean Ho = 0.481) and expected heterozygosity from 0.119 to 0.527 (mean He = 0.325). Although the values of heterozygosity were similar to or lower than those of other orchid species, for example, Caladenia huegelii (mean Ho = 0.551 and He = 0.690) [ 58 ] and Cypripedium kentuckiense (mean Ho = 0.436 and He = 0.448) [ 20 ], the presence of private alleles and the average number of alleles per locus of 5.13 suggest that the markers were appropriate for evaluating genetic diversity in this study. We could not verify the transferability of microsatellite markers into closely related species due to there being only one genus one species in Korea.…”