Biological Invasions, Climate Change, and Genomics

Abstract

The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.

Evolutionary pathways to invasive success: thermal adaptation, hybridisation and parallel evolution in a marine global invader

“…The diverse and high ecological costs of invasive species provide substantial incentives for minimising their spread and for gaining a deeper understanding of the ability of non-native species to survive and reproduce in introduced environments (Molnar et al 2008;Stewart et al 2009). While a large body of research has focused on the anthropogenic (Carlton and Geller 1993;Rius et al 2015a) and ecological factors (Carlton 1996;Branch and Steffani 2004;Lockwood et al 2009;Richardson 2011;Ibanez et al 2014) contributing to the spread of non-native species, understanding the evolutionary processes that create opportunities for some species to become invasive and the long-term outcomes of successful invasions remains a significant knowledge gap in evolutionary ecology (Stewart et al 2009;Chown et al 2015;Bock et al 2015).…”

“…Evolution through stochastic processes involving the demographic history of introduced populations is comparatively better understood than adaptive evolution both empirically (Roman and Darling 2007;Uller and Leimu 2011) and theoretically (Wright 1931;) and has been recently and extensively reviewed (e.g., Dlugosch and Parker 2008;Bock et al 2015;Dlugosch et al 2015;Estoup et al 2016). Now that high-throughput approaches are enabling genome-scale investigations in nonmodel organisms, including a variety of invasive species, biologists can make stronger inferences about the role of natural selection in invasive success and begin to identify the genetic changes that may predispose, accelerate or impede biological invasions (Prentis et al 2008;Rius et al 2015b;Chown et al 2015).…”

“…High-throughput genomic and transcriptomic approaches are becoming increasingly accessible methods to characterise and analyse genetic variation in introduced species adapting to new physiological and ecological conditions (Rius et al 2015a;Sherman et al 2016). Genomic outlier scans are widely used methods to identify loci with atypical patterns of genetic differentiation relative to the neutral genomic expectations, either by detecting reductions in genetic diversity (selective sweep; e.g., Puzey and Vallejo-Marín 2014;Messer and Petrov 2013), strong differences in allele frequencies between populations (e.g., Foll and Gaggiotti 2008) or allelic associations with the environment that may be indicative of natural selection acting on these genomic regions (e.g., reviewed in De Wit et al 2015;Chown et al 2015;Jeffery et al 2017). Other statistical methods for detecting selection involve neutrality tests based on allele frequency spectra (e.g., Tajima's D) or the variability of sequence data within and between species (e.g., HKA test; McDonald-Kreitman test) (reviewed in Anisimova and Liberles 2012).…”

“…This scenario, therefore, in its simplest form does not implicate evolution after the initial introduction of a population into the invaded range (Figure 1-1). Corroborative evidence of the 'pre-adaptation' hypothesis involves examining whether specific genetic changes associated with the evolutionary history of an invasive species have contributed to the evolution of invasiveness, or the potential for a species to become widespread following the initial introduction outside of its natural range (Bock et al 2015;Chown et al 2015). Bottom-up approaches such as genomic comparisons among closely related invasive and non-invasive species can reveal genetic changes that may predispose certain species or lineages to becoming successful invaders (Tepolt 2015).…”

“…Bottom-up approaches such as genomic comparisons among closely related invasive and non-invasive species can reveal genetic changes that may predispose certain species or lineages to becoming successful invaders (Tepolt 2015). Bottom-up approaches are particularly advantageous in that a priori identification of candidate genes or traits under selection is not required (Hodgins et al 2014;Renaut et al 2014;Chown et al 2015). Rather, this approach allows the examination of large numbers of genes to investigate whether changes in allele frequency, differences in gene expression, or signatures of positive selection between native and invasive taxa that may underlie adaptive variation (Hodgins et al 2014;Bock et al 2015).…”