Life on the edge: A new toolbox for population-level climate change vulnerability assessments

Global change is impacting biodiversity across all habitats on earth. New
selection pressures from changing climatic conditions and other
anthropogenic activities are creating heterogeneous ecological and
evolutionary responses across many species’ geographic ranges. Yet we
currently lack standardised and reproducible tools to effectively predict
the resulting patterns in species vulnerability to declines or range
changes. We developed an informatic toolbox that integrates ecological,
environmental and genomic data and analyses (environmental dissimilarity,
species distribution models, landscape connectivity, neutral and adaptive
genetic diversity, genotype-environment associations and genomic offset)
to estimate population vulnerability. In our toolbox, functions and data
structures are coded in a standardised way so that it is applicable to any
species or geographic region where appropriate data are available, for
example individual or population sampling and genomic datasets (e.g.
RAD-seq, ddRAD-seq, whole genome sequencing data) representing
environmental variation across the species geographic range. To
demonstrate multi-species applicability, we apply our toolbox to three
georeferenced genomic datasets for co-occurring East African spiny reed
frogs (Afrixalus fornasini, A. delicatus and A. sylvaticus) to predict
their population vulnerability, as well as demonstrating that range loss
projections based on adaptive variation can be accurately reproduced from
a previous study using data for two European bat species (Myotis
escalerai, and M. crypticus). Our framework sets the stage for large
scale, multi-species genomic datasets to be leveraged in a novel climate
change vulnerability framework to quantify intraspecific differences in
genetic diversity, local adaptation, range shifts and population
vulnerability based on exposure, sensitivity, and landscape barriers.