DOI: 10.5061/dryad.cc2fqz6d3
title: Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity

description: Urbanisation is rapidly altering ecosystems, leading to profound
 biodiversity loss. To mitigate these effects, we need a better
 understanding of how urbanisation impacts dispersal and reproduction. Two
 contrasting population demographic models have been proposed that predict
 that urbanisation either promotes (facilitation model) or constrains
 (fragmentation model) gene flow and genetic diversity. Which of these
 models prevails likely depends on the strength of selection on specific
 phenotypic traits that influence dispersal, survival, or reproduction.
 Here, we a priori examined the genomic impact of urbanisation on the
 Neotropical túngara frog (Engystomops pustulosus), a species known to
 adapt its reproductive traits to urban selective pressures. Using
 whole-genome resequencing for multiple urban and forest populations we
 examined genomic diversity, population connectivity and demographic
 history. Contrary to both the fragmentation and facilitation models, urban
 populations did not exhibit substantial changes in genomic diversity or
 differentiation compared to forest populations, and genomic variation was
 best explained by geographic distance rather than environmental factors.
 Adopting an a posteriori approach, we additionally found both urban and
 forest populations to have undergone population declines. The timing of
 these declines appears to coincide with extensive human activity around
 the Panama Canal during the last few centuries rather than recent
 urbanisation. Our study highlights the long-lasting legacy of past
 anthropogenic disturbances in the genome and the importance of considering
 the historical context in urban evolution studies as anthropogenic effects
 may be extensive and impact non-urban areas on both recent and older
 timescales. 
description: Full Methods description provided in manuscript: Moran et al.,
 2023 Genomic data: Whole genome resequencing data used
 in this study is available from the European Nucleotide Archive (ENA)
 (PRJEB60348). Environmental data: The collection of
 light (in Lux), noise (in dB SPL, fast, max, A-weighted) and canopy cover
 data (percentage canopy cover estimated from pictures) data was previously
 described and published in Halfwerk et al., 2019. The level of
 urbanisation (Urban_score) was calculated based on the type of
 landscape-cover for each sampling location using ‘Urbanisation Score’
 software (Lipovits et al., 2015; Seress et al., 2014). This program
 accesses satellite images via GoogleMaps and applies a semi-automated
 approach to quantify the relative abundance of vegetation and impervious
 surfaces within a 1 km<sup>2</sup> area around each sampling
 location. These values were then combined using principal component
 analysis (PCA) and an urbanisation score retained (PC1) for each
 location.
description: # Genomic footprints of (pre) colonialism: population declines in urban
 and forest túngara frogs coincident with historical human activity
 <br> ## Description
 of the data and file structure The metadata file encompasses sampling
 location, corresponding population code (pop), and environmental data for
 forest (F) and urban (U) sites. The collection of light (in Lux), noise
 (in dB SPL, fast, max, A-weighted) and canopy cover data (percentage
 canopy cover estimated from pictures) was previously described and
 published in Halfwerk et al., 2019. The level of urbanisation
 (Urban_score) was calculated based on the type of landscape-cover for each
 sampling location using ‘Urbanisation Score’ software (Lipovits et al.,
 2015; Seress et al., 2014). This program accesses satellite images via
 GoogleMaps and applies a semi-automated approach to quantify the relative
 abundance of vegetation and impervious surfaces within a 1
 km<sup>2</sup> area around each sampling location. These
 values were then combined using principal component analysis (PCA) and an
 urbanisation score retained (PC1) for each location. ## Sharing/Access
 information Related data: Whole genome resequencing data used in this
 study is available from the European Nucleotide Archive (ENA)
 (PRJEB60348). ## Code/Software Main bash scripts for running software and
 R code used for analyses. Additional custom scripts are available from the
 corresponding authors upon request.