DOI: 10.5061/dryad.4j0zpc8f4
title: WorldClim, elevation and distribution data for all palms from: The ecology of palm genomes: Repeat-associated genome size expansion is constrained by aridity

description: Genome size varies 2,400-fold across plants, influencing their evolution
 through changes in cell size and cell division rates which impact plants’
 environmental stress tolerance. Repetitive element expansion explains much
 genome size diversity, and the processes structuring repeat ‘communities’
 are analogous to those structuring ecological communities. However, which
 environmental stressors influence repeat community dynamics has not yet
 been examined from an ecological perspective. We measured genome size and
 leveraged climatic data for 91% of genera within the ecologically diverse
 palm family (Arecaceae). We then generated genomic repeat profiles for 141
 palm species, and analysed repeats using phylogenetically-informed linear
 models to explore relationships between repeat dynamics and environmental
 factors. We show that palm genome size and repeat ‘community’ composition
 are best explained by aridity. Specifically, Ty3-gypsy and TIR elements
 were more abundant in palm species from wetter environments, which
 generally had larger genomes, suggesting amplification. In contrast,
 Ty1-copia and LINE elements were more abundant in drier environments. Our
 results suggest that water stress inhibits repeat expansion through
 selection on upper genome size limits. However, elements which may
 associate with stress-response genes (e.g., Ty1-copia) have amplified in
 arid-adapted palm species. Overall, we provide novel evidence of climate
 influencing the assembly of repeat ‘communities’. 
description: Geographic occurrence data were collated from an existing palm
 distribution dataset which contained occurrence data from GBIF
 (www.gbif.com; dataset https://doi.org/10.15468/dd.at82kf) and from
 herbarium specimens (collected from K and L). To collect data from GBIF,
 all palm names published at that time (March 2018, from WCVP (2020)) were
 searched against the GBIF taxonomic backbone, and occurrences were
 retrieved for the 7,469 names that matched. Occurrences were
 then reconciled to a list of accepted palm names at the time (WCVP, 2020),
 and cleaned based on the GBIF coordinate issue flags and using the R (R
 Development Core Team, 2013) package CoordinateCleaner v1.0-7 (Zizka et
 al., 2019). We first corrected issues such as incorrect coordinate signs,
 and removed coordinates falling into maritime areas, city, province or
 country centroids, biodiversity institutions and coordinates with zero
 values or with an uncertainty &gt; 100 km. Finally, we removed
 duplicate coordinates, coordinates inconsistent with the country
 assignment of the record or falling outside the native distribution range
 of the species and those recorded before 1945.  Based
 on this refined occurrence dataset, we downloaded environmental data from
 WorldClim for all 472 species with genome size estimates using the R
 package raster (Hijmans & van Etten 2012). Data were extracted for
 each individual in the occurrence dataset for all palm species, comprising
 all nineteen bioclimatic variables from the WorldClim dataset, which
 detail biologically significant measures of temperature and precipitation
 (BIO1 to BIO19), as well as elevation data. From this we calculated a
 ‘per-species’ mean for each variable by averaging every value for all
 individuals of a species.