Local adaptation to current but not future climate in seasonally tropical dry forests: population genomic evidence in a Neotropical legume tree
Neotropical seasonally dry biomes are amongst the most threatened ecosystems on earth and are predicted to lose more biodiversity with climate change. The capacity of natural populations to respond to these changes (i.e., their adaptive potential) depends on their genetic variation, but is poorly understood in most Neotropical dry forest species. Here, we used genome-wide single nucleotide polymorphism (SNP) data for 109 individuals across 12 Colombian populations of Enterolobium cyclocarpum, a widespread deciduous legume tree found in seasonally dry forests, human-disturbed and open landscapes from Central and Northern South America, to 1) explore population structure across the landscape, 2) determine local adaptation to heat and drought stress, and 3) assess the adaptive potential of populations in the face of climate change. Samples underwent ddRAD analysis following Peterson et al. (2012, https://doi.org/10.1371/journal.pone.0037135) as implemented in Durka et al. (2025, https://doi.org/10.1016/j.baae.2024.11.004) using EcoRI and MspI as restriction enzymes and a selected fragment length of 350-450 bp. Samples were sequenced on an Illumina Novaseq 6000 (PE150) , resulting in appr. 2 Mio. sequences per individual sample. Sequences were demultiplexed with process_radtags (--paired -i gzfastq -y gzfastq -b "$BCODESraw" --inline_index --renz_1 ecoRI --renz_2 mspI -cq --retain_header --rescue). Our results suggest clear genomic differentiation among regions and populations, and unevenly spatially distributed candidate SNPs putatively associated with drought and heat stress, together suggesting different degrees of local adaptation to climate across the landscape. Furthermore, all regions investigated (i.e., Caribbean, inter-Andean valleys, and Orinoquía) showed limited adaptive potential under future climate change scenarios. For some regions, gene flow may help buffer the effects of environmental change by bringing in adaptive alleles, however, this will likely be insufficient to counteract predicted mal-adaptation in certain regions, such as in the Orinoquía. Our results suggest that both barriers to gene flow (e.g., orography) and varying heat and drought stress conditions have shaped the genomic composition and adaptive potential of the species. Enterolobium cyclocarpum populations have adapted locally to current climate, but this adaptation may not be sufficient to cope with future climate change, particularly where population connectivity is low. Our findings have relevance for the conservation of species in highly threatened Neotropical biomes, such as dry forests, which are expected to experience rising temperatures and greater drought under future climate change.  Article DOI: 10.111/eva.70302  Sequencing was performed at the Molecular Ecology Laboratory - Helmholtz Centre for Environmental Research (UFZ), Halle, Germany.
Neotropical seasonally dry biomes are amongst the most threatened ecosystems on earth and are predicted to lose more biodiversity with climate change. The capacity of natural populations to respond to these changes (i.e., their adaptive potential) depends on their genetic variation, but is poorly understood in most Neotropical dry forest species. Here, we used genome-wide single nucleotide polymorphism (SNP) data for 109 individuals across 12 Colombian populations of Enterolobium cyclocarpum, a widespread deciduous legume tree found in seasonally dry forests, human-disturbed and open landscapes from Central and Northern South America, to 1) explore population structure across the landscape, 2) determine local adaptation to heat and drought stress, and 3) assess the adaptive potential of populations in the face of climate change. Samples underwent ddRAD analysis following Peterson et al. (2012, https://doi.org/10.1371/journal.pone.0037135) as implemented in Durka et al. (2025, https://doi.org/10.1016/j.baae.2024.11.004) using EcoRI and MspI as restriction enzymes and a selected fragment length of 350-450 bp. Samples were sequenced on an Illumina Novaseq 6000 (PE150) , resulting in appr. 2 Mio. sequences per individual sample. Sequences were demultiplexed with process_radtags (--paired -i gzfastq -y gzfastq -b "$BCODESraw" --inline_index --renz_1 ecoRI --renz_2 mspI -cq --retain_header --rescue). Our results suggest clear genomic differentiation among regions and populations, and unevenly spatially distributed candidate SNPs putatively associated with drought and heat stress, together suggesting different degrees of local adaptation to climate across the landscape. Furthermore, all regions investigated (i.e., Caribbean, inter-Andean valleys, and Orinoquía) showed limited adaptive potential under future climate change scenarios. For some regions, gene flow may help buffer the effects of environmental change by bringing in adaptive alleles, however, this will likely be insufficient to counteract predicted mal-adaptation in certain regions, such as in the Orinoquía. Our results suggest that both barriers to gene flow (e.g., orography) and varying heat and drought stress conditions have shaped the genomic composition and adaptive potential of the species. Enterolobium cyclocarpum populations have adapted locally to current climate, but this adaptation may not be sufficient to cope with future climate change, particularly where population connectivity is low. Our findings have relevance for the conservation of species in highly threatened Neotropical biomes, such as dry forests, which are expected to experience rising temperatures and greater drought under future climate change.  Article DOI: 10.111/eva.70302  Sequencing was performed at the Molecular Ecology Laboratory - Helmholtz Centre for Environmental Research (UFZ), Halle, Germany.