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Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations

Citation

Trapnell, Dorset; Hamrick, J. L. (2022), Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations, Dryad, Dataset, https://doi.org/10.5061/dryad.kd51c5b8x

Abstract

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

Methods

Study sites and sampling

Samples were obtained from five E. radicans collection sites growing on lava flows of different ages. At all five sample sites, we made every effort to avoid collection of multiple samples from obviously clonal individuals. The two Arenal Slope (AS) sites are located on the southwestern slope of Volcán Arenal where lava, rocks and ash were deposited during the 1992 eruption (Soto & Sjoböhm, 2005; Fig. 1). The two Tabacón Springs (TS) sites occur on an older lava flow last disturbed by bomb and block bombardment, and ash fall in 1968 (Soto & Sjoböhm, 2005; Fig. 1). The TS sites are separated from the AS sites by approximately 4.7 km. The Arenal 1968 (SE) site is on a lava field deposited during the 1968 eruption (Fig. 1). This site is ~2.3 km from AS and ~2.7 km from TS. 

Arenal Slope Sites (AS) - In April 2004, leaves were collected at the first Arenal Slope site (10.4504° N and 84.7250° W) from 96 individuals (AS-1). In April 2010, leaves were collected at the second Arenal Slope site from 103 individuals (AS-2). The two AS sample sites are separated by ~90 m. From a central point for each of the two AS collections, a transect line was placed successively in a radial pattern and a leaf was collected from every individual, with its distance and angle relative to the central point recorded. 

Tabacón Springs Sites (TS) - At the Tabacón Springs location (10.4924° N and 84.7197° W), samples were collected from 209 individuals in April 2005 (TS-1) and 166 individuals in April 2010 (TS-2). These two sites are separated by ~45 m. Due to the higher density of individuals, the TS collections represented a sub-sample of the total number of E. radicans individuals. For TS-1 a baseline was established and 8m long transect lines were placed perpendicular to the baseline at 0.8m intervals. At 0.8m intervals along each of 21 transect lines, a leaf was collected from the nearest individual and its distance from the 0.8m interval mark on the transect line was recorded. For TS-2, because of differing terrain, 11m long transect lines were placed perpendicular to the baseline at 0.8m intervals. At 1m intervals along each of these 20 transect lines, a leaf was collected from the nearest individual and its distance from the 1m interval mark on the transect line was recorded.  

Arenal 1968 Site (SE) - At this site (10.4705° N and 84.7317° W), because of the more challenging terrain, 116 samples were collected from the nearest E. radicans encountered on either side of a 20m transect line and the distance of each plant from the transect line was recorded.

To compare the genetic composition of lava flow populations with populations in the surrounding landscape, additional regional populations were sampled. A mean of 47 individuals (range 42–50) was collected from each of four E. radicans populations located within 1.5 to 26.8 km (mean = 17.4 km) of the study sites. While we did not survey the surrounding landscape comprehensively, we collected from every population found in the vicinity. 

Genotyping

Leaves were snap frozen in liquid nitrogen within a few hours of collection and sent to the University of Georgia in an ultra-cold dry shipper. Leaves were crushed in chilled mortars with a pestle, liquid nitrogen, and a pinch of sea sand to disrupt cellular compartmentalization. Enzymes were extracted from E. radicans tissue with a polyvinylpyrrolidone-phosphate extraction buffer (Mitton et al., 1979). The resulting slurry containing crude protein extract was absorbed onto 4x6 mm wicks punched from Whatman 3 mm chromatography paper. Wicks were stored in microtest plates at -70°C until used for electrophoresis. Wicks were placed in horizontal starch gels (10%) and electrophoresis was performed. 

Nine enzyme stains in five buffer systems resolved one monomorphic and 14 putative polymorphic loci. Enzymes stained and polymorphic loci (in parentheses) for each buffer system were: (1) system 4, malate dehydrogenase (EC 1.1.1.37; Mdh-1, Mdh-2), 6-phosphogluconate dehydrogenase (EC 1.1.1.44; 6-Pgd-2) and shikimic dehydrogenase (EC 1.1.1.25; Skdh);  (2) system 8-, aspartate aminotransferase (EC 2.6.1.1; Aat-1, Aat-2), and fluorescent esterase (EC 3.1.1-; Fe-2, Fe-3); (3) system 10, triosephosphate isomerase (EC 5.3.1.1; Tpi-1, Tpi-2) and UTP-glucose-1-phosphate (EC 2.7.7.9; Ugpp-1); (4) system 11, isocitrate dehydrogenase (EC 1.1.1.42; Idh), and phosphoglucoisomerase (EC 5.3.1.9; Pgi-2);  (5) system 6, fluorescent esterase (EC 3.1.1-; Fe-4). 

All buffer and stain recipes were adapted from Soltis et al. (1983) except Aat (Cheliak & Pitel, 1984) and Ugpp (Manchenko, 1994). Buffer system 8- is a modification of buffer system 8 described by Soltis et al. (1983). Banding patterns of both species were consistent with Mendelian inheritance patterns expected for each enzyme system (Weeden & Wendel, 1989) and were consistent with disomic inheritance expected for diploid individuals.

Usage Notes

Excel

Funding

Andrew W. Mellon Foundation, Award: Organization for Tropical Studies