Abstract:

This dataset was generated from a field survey conducted in the Chandeleur Islands, Louisiana that explored the relationship between biodiversity (taxonomic and genetic) and oil disturbance in coastal wetlands. The Chandeleur Islands provide a natural setting to investigate these questions as coastal areas in close proximity varied in their exposure to oil from the Deepwater Horizon (DWH) spill. We surveyed genetic diversity of the marsh plant Spartina alterniflora in 0.5m * 0.5m quadrats within natural assemblages of marsh plants only and marsh plants and mangroves (S. alterniflora and Avicennia germinans) across this oiling exposure gradient. We repeated the survey at the beginning and end of the growing season for two years to examine temporal variation in biodiversity. The other related data is available under GRIIDC Unique Dataset Identifier (UDI) R4.x262.212:0005 (doi:10.7266/N7QJ7FBZ).

Suggested Citation:

Randall Hughes, Torrance Hanley, Robyn Zerebecki. 2019. Impact of Deepwater Horizon oil spill on Spartina alterniflora genetic diversity in the Chandeleur Islands, Louisiana from 2015-06-29 to 2016-09-17. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-4q4x-ve61

Purpose:

The purpose of this dataset is to examine the relationship between plant diversity and oil exposure over time.

Data Parameters and Units:

Location: initial group sites (A-D), Latitude: latitude taken at the site (decimal degrees), Longitude: longitude taken at the site (decimal degrees), Oiled: if location previously thought to be oiled or not from the DWH oil spill, Habitat: vegetation assemblage where data was collected, Replicate: quadrat number (i.e., low in low marsh, high in higher marsh), Quadrat_Location: grid location of individual plots within the site, Plot_ID: unique plot identifier, Date: MM/DD/YYYY date that data was collected, Sample_Size: number of Spartina alterniflora leaf tissue samples collected from individual stems, All_Num: number of alleles, Eff_All_Num: effective number of alleles, Ho: observed heterozygosity, Hs: heterozygosity within populations, Ht: total heterozygosity, Gis: inbreeding coefficient, Geno_Num: number of genotypes, Eff_Geno_Num: effective number of genotypes, div: Nei’s genetic diversity corrected for sample size, diu: Nei’s uncorrected genetic diversity, eve: evenness, Eff_Geno_Num / Geno_Num, shc: Shannon index corrected for sample size, shu: Shannon index

Methods:

Each individual was genotyped using 10 microsatellite loci developed for S. alterniflora (SPAR2, SPAR3, SPAR5, SPAR7, SPAR8, SPAR9, SPAR10: Blum et al. 2004; SPAR14, SPAR16, SPAR34: Sloop et al. 2005). Briefly, the Omega Bio-Tek E-Z 96® Plant DNA Kit was used to extract DNA from S. alterniflora leaf tissue that had been stored at -80oC and ground using a Retsch mixer mill MM400 prior to processing. Each PCR reaction consisted of 1 ml DNA template, 5 ml 2X type-it multiplex master mix (Qiagen), 2 ml water, and 0.25 ml of each 10 mM primer: Master Mix 1 included primers for SPAR5, SPAR9, and SPAR10; Master Mix 2 included primers for SPAR2, SPAR3, SPAR14, and SPAR34; and Master Mix 3 included primers for SPAR7, SPAR8, and SPAR16. Using a T100 thermal cycler (Bio-Rad), PCR cycling conditions included initial activation/denaturation at 95oC for 5 min, followed by 28 cycles of 95oC for 30 sec, 60oC for 90 sec, and 72oC for 30 sec, and final extension at 60oC for 30 min. PCR products were separated on a 3730xl Genetic Analyzer (Applied Biosystems) and fragment analysis was performed using GeneMarker version 2.6 (SoftGenetics). Columns ‘All_Num’ to ‘shu’ calculated using GenoDive v2.0b27 (Meirmans and Van Tienderen 2004). Please see GenoDive manual for more detailed information on metrics and calculations.

Provenance and Historical References:

Blum, M. J., Sloop, C. M., Ayres, D. R., & Strong, D. R. (2004). Characterization of microsatellite loci in Spartina species (Poaceae). Molecular Ecology Notes, 4(1), 39-42. doi:10.1046/j.1471-8286.2003.00556.x Meirmans, P. G., & Van Tienderen, P. H. (2004). GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4(4), 792-794. doi:10.1111/j.1471-8286.2004.00770.x Sloop, C. M., McGray, H. G., Blum, M. J., & Strong, D. R. (2005). Characterization of 24 additional microsatellite loci in Spartina species (Poaceae). Conservation Genetics, 6(6), 1049–1052. doi:10.1007/s10592-005-9084-7

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