DOI: 10.5061/dryad.202d4
title: Data from: Evolutionary history of Lost World frogs (Ph.D. thesis)

description: The Lost World of South America is a unique landscape of flattop mountains
 that are home to hundreds of endemic species. These flattop mountains, or
 tepuis, were formed after millions of years of erosion of the
 high-altitude Guiana Shield plateau. The tepui summits, isolated by their
 surrounding cliffs that can be up to 1000 m tall, are thought of as
 “islands in the sky,” harboring relict flora and fauna that underwent
 vicariant speciation due to plateau fragmentation. High endemicity atop
 tepui summits supports the idea of an ancient “Lost World” biota. However,
 recent work suggests dispersal between lowlands and summits occurred long
 after tepui formation, but neither view (i.e., ancient vicariance vs.
 recent dispersal) has strong empirical support owing to a lack of studies.
 I tested diversification hypotheses of the Guiana Shield highlands by
 estimating divergence times of Tepuihyla, a Guiana Shield endemic genus.
 Diversification among the different species did not support the Lost World
 Hypothesis of summit diversification, but rather recent dispersal
 approximately 50 million years after tepuis formed. This study was the
 first to explicitly test these hypotheses with a tepui endemic vertebrate,
 and as such a significant contribution to our understanding of the
 evolutionary history of this region. After increasing sampling, I focused
 on three of the most recently diverged lineages of Tepuihyla, in order to
 examine population genetics, phylogeography, and species delimitation atop
 these summits. I found high levels of lineage sorting in spite of low
 divergences in both nuclear and mitochondrial genes. I also found an
 unexpected pattern of nuclear versus mitochondrial diversity, suggesting
 the possibility of a recent mitochondrial selective sweep. Species
 delimitation analyses support the existence of a cryptic, undescribed
 summit species. Finally, I obtained a Single Nucleotide Polymorphism
 matrix with next-generation sequencing in order to observe more fine-scale
 population structure atop the Chimantá massif, a formation composed of ten
 tepui summits and intermediate altitudes separating them. I found high
 levels of population structure and assignment atop different tepui summits
 on the massif, indicating that even at extremely low levels of divergence
 the landscape complexity may be fomenting population isolation even at the
 smaller scale of within-massif divergences.
description: Scripts used for STACKS
 pipelineThese are the three
 final scripts used for generating the 5159 SNP matrix that was used as a
 basis for all other data matrices.scripts_STACKSLarge SNP matrix without outlierThis is the matrix used for analyses where all SNPs and taxa were used, excluding the outlier from the Auyan population that was found with the PCA analysis.Snps_5159_no_outl.struOriginal 5159 SNP matrixOriginal 5159 SNP matrix obtained in STACKSSnps_5159.struReduced 1000 SNP matrixReduced matrix, keeping all taxa but reducing SNPs to 1000Snps_1000_no_outl.struReduced 1219 SNP matrixMatrix obtained after eliminating taxa with &gt;30% missing data and SNPs with &gt;6% missing data, resulting in a total of 1219 SNPs.Snps_1219_no_outl.stru