Ecological Genomics Meets Community-Level Modelling of Biodiversity: Mapping the Genomic Landscape of Current and Future Environmental Adaptation

Ecol Lett. 2015 Jan;18(1):1-16. doi: 10.1111/ele.12376. Epub 2014 Sep 30.

Abstract

Local adaptation is a central feature of most species occupying spatially heterogeneous environments, and may factor critically in responses to environmental change. However, most efforts to model the response of species to climate change ignore intraspecific variation due to local adaptation. Here, we present a new perspective on spatial modelling of organism-environment relationships that combines genomic data and community-level modelling to develop scenarios regarding the geographic distribution of genomic variation in response to environmental change. Rather than modelling species within communities, we use these techniques to model large numbers of loci across genomes. Using balsam poplar (Populus balsamifera) as a case study, we demonstrate how our framework can accommodate nonlinear responses of loci to environmental gradients. We identify a threshold response to temperature in the circadian clock gene GIGANTEA-5 (GI5), suggesting that this gene has experienced strong local adaptation to temperature. We also demonstrate how these methods can map ecological adaptation from genomic data, including the identification of predicted differences in the genetic composition of populations under current and future climates. Community-level modelling of genomic variation represents an important advance in landscape genomics and spatial modelling of biodiversity that moves beyond species-level assessments of climate change vulnerability.

Keywords: Biodiversity; Populus balsamifera; Single-nucleotide polymorphism; climate change; generalised dissimilarity modelling; gradient forests; intraspecific variation; landscape genetics; local adaptation; species distribution modelling.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Physiological / genetics*
  • Biodiversity*
  • CLOCK Proteins / genetics
  • Climate Change*
  • Genetic Variation
  • Genomics / methods*
  • Models, Biological*
  • Models, Statistical
  • Plant Proteins / genetics
  • Polymorphism, Single Nucleotide
  • Populus / genetics
  • Spatial Analysis

Substances

  • Plant Proteins
  • CLOCK Proteins