The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human‐altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments.
Atlantic killifish (
- PAR ID:
- 10247311
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 25
- Issue:
- 21
- ISSN:
- 0962-1083
- Format(s):
- Medium: X Size: p. 5467-5482
- Size(s):
- p. 5467-5482
- Sponsoring Org:
- National Science Foundation
More Like this
-
Abstract Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype–phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD‐seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB‐126. We found that one to two large‐effect QTL loci accounted for resistance to PCB‐mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB‐126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB‐126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex. -
Abstract Floral attraction traits can significantly affect pollinator visitation patterns, but adaptive evolution of these traits may be constrained by correlations with other traits. In some cases, molecular pathways contributing to floral attraction are well characterized, offering the opportunity to explore loci potentially underlying variation among individuals. Here, we quantify the range of variation in floral
UV patterning (i.e.UV ‘bulls‐eye nectar guides) among crop and wild accessions ofBrassica rapa . We then use experimental crosses to examine the genetic architecture, candidate loci and biochemical underpinnings of this patterning as well as phenotypic manipulations to test the ecological impact. We find qualitative variation inUV patterning between wild (commonly lackingUV patterns) and crop (commonly exhibitingUV patterns) accessions. Similar to the majority of crops, recombinant inbred lines (RIL s) derived from an oilseed crop ×WI fast‐plant®cross exhibitUV patterns, the size of which varies extensively among genotypes. InRIL s, we further observe strong statistical‐genetic andQTL correlations within petal morphological traits and within measurements of petalUV patterning; however, correlations between morphology andUV patterning are weak or nonsignificant, suggesting thatUV patterning is regulated and may evolve independently of overall petal size.HPLC analyses reveal a high concentration of sinapoyl glucose inUV ‐absorbing petal regions, which, in concert with physical locations ofUV ‐traitQTL s, suggest a regulatory and structural gene as candidates underlying observed quantitative variation. Finally, insects prefer flowers withUV bulls‐eye patterns over those that lack patterns, validating the importance ofUV patterning in pollen‐limited populations ofB. rapa . -
Abstract The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype‐by‐environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (
IBM ) recombinant inbred populations grown in 10 environments. Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads theionome , the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. We compared quantitative trait loci (QTL ) determining single‐element variation toQTL that predict variation in principal components (PC s) of multiple‐element covariance. Single‐element and multivariate approaches detected partially overlapping sets of loci.QTL influencing trait covariation were detected at loci that were not found by mapping single‐element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi‐element traits that were determined by both genetic and environmental factors as well as genotype‐by‐environment interactions. Growth environment had a profound effect on the elemental profiles and multi‐element phenotypes were significantly correlated with specific environmental variables. -
Abstract The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system‐related traits, and leaf shape between
Mimulus laciniatus and a sympatric population of its close relativeM. guttatus . These three traits are probably involved inM. laciniatus’ adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them ‘magic traits’. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next‐generation sequencing, we generate denseSNP markers across the genome and map quantitative trait loci (QTL s) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to fewQTL of large effect including a highly pleiotropicQTL on chromosome 8. ThisQTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in otherMimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects. -
Abstract Steep genetic clines resulting from recent secondary contact between previously isolated taxa can either gradually erode over time or be stabilized by factors such as ecological selection or selection against hybrids. We used patterns of variation in 30 nuclear and two mitochondrial
SNP s to examine the factors that could be involved in stabilizing clines across a hybrid zone between two subspecies of the Atlantic killifish,Fundulus heteroclitus . Increased heterozygote deficit and cytonuclear disequilibrium in populations near the center of the mtDNA cline suggest that some form of reproductive isolation such as assortative mating or selection against hybrids may be acting in this hybrid zone. However, only a small number of loci exhibited these signatures, suggesting locus‐specific, rather than genomewide, factors. Fourteen of the 32 loci surveyed had cline widths inconsistent with neutral expectations, with twoSNP s in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non‐neutral nuclear clines were forSNP s in genes related to oxidative metabolism. Among these putatively non‐neutral nuclear clines,SNP s in two nuclear‐encoded mitochondrial genes (SLC 25A3 andHDDC 2), as well asSNP s in the myoglobin, 40S ribosomal protein S17, and actin‐bindingLIM protein genes, had clines that were coincident and concordant with the mitochondrial clines. When hybrid index was calculated using this subset of loci, the frequency distribution of hybrid indices for a population located at the mtDNA cline center was non‐unimodal, suggesting selection against advanced‐generation hybrids, possibly due to effects on processes involved in oxidative metabolism.