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Population genetic and geographic data of six Neotropical plant species

Citation

Gamba, Diana; Muchhala, Nathan (2022), Population genetic and geographic data of six Neotropical plant species, Dryad, Dataset, https://doi.org/10.5061/dryad.rr4xgxdbf

Abstract

We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the FST statistic) and stronger FSGS (as quantified with the SP statistic) than hummingbird-pollinated species.

Methods

  • GPS coordinates of 30–42 individuals per species from 2–3 sites in northwestern Ecuador were taken with a Garmin GPSMAP device.
  • Genetic data is stored in fastq format and corresponds to quality filtered 2B-RAD sequencing reads (raw reads were generated at the BYU DNA Sequencing Center).
  • These filtered reads were processed as described in the manuscript methods for estimating population genetic parameters in the 'de novo' Stacks v2.3e pipeline.
  • The genepop file was used in GenoDive v3.0 to estimate population genetic structure parameters and the vcf file was used in the R program SNPRelate to produce the gds files and perform a PCA.
  • The input files for SPAGeDi v. 1.3a are stored for each species in the corresponnding txt file, used for FSGS analyses.
  • Db=Drymonia brochidodroma, Dt=Drymonia tenuis, Mt=Meriania tomentosa, Om=Miconia rubescens (for the synonym Ossaea micrantha), Nl=Notopleura longipedunculoides, Pd=Palicourea demissa.