Gene regulatory divergence between locally adapted ecotypes in their native habitats

Abstract

Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.

Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

“…Besides genetic changes, we also identified transcripts expression differences between seedlings from PA-arid and PA-humid sites after acclimatization in pots under shaded, well-watered conditions (Figure 2c, Figure 5), indicating an additional molecular basis for phenotypic divergences. Because differential gene expression influence trait variation (Wolf, Lindell, & Backstrom, 2010), it can be substantial between distinct locally adapted populations (Akman, Carlson, Holsinger, & Latimer, 2016; Gould, Chen, & Lowry, 2018). Differential expression was observed mainly in roots and stems of A. germinans seedlings, which are the first organs exposed to increased salinity and water deficits in mangroves, thus where osmotic stress sensing and signaling to the whole plant are triggered (Chaves, Maroco, & Pereira, 2003; Janiak, Kwas niewski, & Szarejko, 2016).…”

Genomics of clinal local adaptation inPinus sylvestrisunder continuous environmental and spatial genetic setting

“…Inversions can create large areas of restricted recombination as they prevent proper chromatid pairing, although gene conversion and double cross-overs may allow some genetic exchange between inverted and non-inverted haplotypes (Andoflatto, Depaulis, & Navarro, 2001). Empirical studies have inversions contributing to local adaptation for instance in D. melanogaster (Kapun & Flatt, 2018), sticklebacks (Jones et al, 2012), yellow monkeyflower (Gould, Chen, & Lowry, 2018), teosinte (Tanja Pyhäjärvi, Hufford, Mezmouk, & Ross-Ibarra, 2013), humans (Puig, Casillas, Villatoro, & Cáceres, 2015) and in many others (Wellenreuther & Bernatchez, 2018).…”

“…melanogaster (Kapun & Flatt, 2018), sticklebacks (Jones et al, 2012), yellow monkeyflower (Gould, Chen, & Lowry, 2018), teosinte (Pyhäjärvi, Hufford, Mezmouk, & Ross-Ibarra, 2013) and in butterfly mimicry (Kunte, 2014).…”

Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

“…In addition to genetic changes, we also identified transcript expression differences between seedlings from PA-arid and PA-humid sites after acclimatization in pots under shaded, well-watered conditions (Figures 2c and 5), indicating an additional molecular basis for phenotypic divergences. Because differential gene expression influences trait variation (Wolf, Lindell, & Backstrom, 2010), it can be substantial between distinct locally adapted populations (Akman, Carlson, Holsinger, & Latimer, 2016;Gould, Chen, & Lowry, 2018).…”