RAD sequencing reveals within‐generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

Abstract

Measuring the effects of selection on the genome imposed by human-altered environment is currently a major goal in ecological genomics. Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection is expected to cause subtle allelic changes among covarying loci rather than pronounced changes at few loci of large effects. The goal of this study was to test for the occurrence of polygenic selection in both North Atlantic eels (European Eel, Anguilla anguilla and American Eel, A. rostrata), using a method that searches for covariation among loci that would discriminate eels from 'control' vs. 'polluted' environments and be associated with specific contaminants acting as putative selective agents. RAD-seq libraries resulted in 23 659 and 14 755 filtered loci for the European and American Eels, respectively. A total of 142 and 141 covarying markers discriminating European and American Eels from 'control' vs. 'polluted' sampling localities were obtained using the Random Forest algorithm. Distance-based redundancy analyses (db-RDAs) were used to assess the relationships between these covarying markers and concentration of 34 contaminants measured for each individual eel. PCB153, 4'4'DDE and selenium were associated with covarying markers for both species, thus pointing to these contaminants as major selective agents in contaminated sites. Gene enrichment analyses suggested that sterol regulation plays an important role in the differential survival of eels in 'polluted' environment. This study illustrates the power of combining methods for detecting signals of polygenic selection and for associating variation of markers with putative selective agents in studies aiming at documenting the dynamics of selection at the genomic level and particularly so in human-altered environments.

Recent advances in conservation and population genomics data analysis

“…A simple visualization of expected and observed frequencies of homozygote genotypes across single nucleotide polymorphisms (SNPs) can be effective in identifying data problems (Figure 1). A simple model for estimating the heterozygote miscall (dropout) rate was applied to 12 publicly available RAD‐seq datasets (Fernández et al., 2016; Hecht, Matala, Hess, & Narum, 2015; Laporte et al., 2016; Larson et al., 2014; Le Moan, Gagnaire, & Bonhomme, 2016; Portnoy et al., 2015; Prince et al., 2017; Puritz, Gold, & Portnoy, 2016; Ravinet et al., 2016; Swaegers et al., 2015). While a few had low genotyping error rates (<5%), in others, allelic dropout, low read depth, PCR duplicates, erroneous assembly, and/or poor filtering resulted in much higher estimated error rates, with between 5% and 72% of heterozygotes apparently being miscalled as homozygotes.…”

Assessing pre- and post-zygotic barriers between North Atlantic eels (Anguilla anguilla and A. rostrata)

“…In this sense, both European and American eel have experienced drastic declines in the past ca. 30 years (Åström and Dekker, 2007), possibly linked to inland pollution, dams and fisheries (Busch and Braun, 2014;Laporte et al, 2016). This decline suggests possible reduced densities of spawning eels that could lead to a reduced spatial overlap and hybridization (Albert et al, 2006;Jacobsen et al, 2014b).…”

Mechanisms of Thermal Tolerance in Reef-Building Corals across a Fine-Grained Environmental Mosaic: Lessons from Ofu, American Samoa

“…Data from Ofu indicate that thermal tolerance is a polygenic trait, where a number of alleles of small effect across many different cellular pathways are responsible for elevated thermal tolerance of the HV pool corals Palumbi et al, 2014). Polygenic traits are a common feature of high gene flow species and occur widely in marine populations (Limborg et al, 2012;Hale et al, 2013;Pespeni et al, 2013;Laporte et al, 2015;Barney et al, 2017).…”