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1. The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex

   https://doi.org/10.1111/mec.13763  

   Ferris, Kathleen G. ; Barnett, Laryssa L. ; Blackman, Benjamin K. ; Willis, John H. ( August 2016 , Molecular Ecology)

   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 betweenMimulus laciniatusand 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 denseSNPmarkers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to fewQTLof large effect including a highly pleiotropicQTLon chromosome 8. ThisQTLregion contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in otherMimulusspecies. 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.

    

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2. Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning

   https://doi.org/10.1111/mec.13542  

   Brock, Marcus T. ; Lucas, Lauren K. ; Anderson, Nickolas A. ; Rubin, Matthew J. ; Cody Markelz, R. J. ; Covington, Michael F. ; Devisetty, Upendra K. ; Chapple, Clint ; Maloof, Julin N. ; Weinig, Cynthia ( February 2016 , Molecular Ecology)

   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 floralUVpatterning (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 inUVpatterning between wild (commonly lackingUVpatterns) and crop (commonly exhibitingUVpatterns) accessions. Similar to the majority of crops, recombinant inbred lines (RILs) derived from an oilseed crop × WIfast‐plant^®cross exhibitUVpatterns, the size of which varies extensively among genotypes. InRILs, we further observe strong statistical‐genetic andQTLcorrelations within petal morphological traits and within measurements of petalUVpatterning; however, correlations between morphology andUVpatterning are weak or nonsignificant, suggesting thatUVpatterning is regulated and may evolve independently of overall petal size.HPLCanalyses reveal a high concentration of sinapoyl glucose inUV‐absorbing petal regions, which, in concert with physical locations ofUV‐traitQTLs, suggest a regulatory and structural gene as candidates underlying observed quantitative variation. Finally, insects prefer flowers withUVbulls‐eye patterns over those that lack patterns, validating the importance ofUVpatterning in pollen‐limited populations ofB. rapa.

    

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3. Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials

   https://doi.org/10.1111/mec.13522  

   Foust, C. M. ; Preite, V. ; Schrey, A. W. ; Alvarez, M. ; Robertson, M. H. ; Verhoeven, K. J. F. ; Richards, C. L. ( February 2016 , Molecular Ecology)

   While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. UsingAFLPand methylation‐sensitiveAFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat inSpartina alterniflora. InBorrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site‐specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation andDNAmethylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients.

    

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4. Convergent evolution of root system architecture in two independently evolved lineages of weedy rice

   https://doi.org/10.1111/nph.15791  

   Wedger, Marshall J. ; Topp, Christopher N. ; Olsen, Kenneth M. ( April 2019 , New Phytologist)

   Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de‐domesticated form of rice, to study the evolution of weed‐associatedRSAtraits and the extent to which they evolve through shared or different genetic mechanisms.

   We characterised 98 two‐dimensional and three‐dimensionalRSAtraits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL)mapping to compare genetic architecture between the weed strains.

   The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a ‘weedy’RSAphenotype. Notably, comparativeQTLmapping revealed little evidence for shared underlying genetic mechanisms.

   Our findings suggest that despite the double bottlenecks of domestication and de‐domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedyRSAtraits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below‐ground contact as a competitive strategy.

    

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5. A simple genetic architecture and low constraint allow rapid floral evolution in a diverse and recently radiating plant genus

   https://doi.org/10.1111/nph.15844  

   Kostyun, Jamie L. ; Gibson, Matthew J. S. ; King, Christian M. ; Moyle, Leonie C. ( May 2019 , New Phytologist)

   Genetic correlations among different components of phenotypes, especially those resulting from pleiotropy, can constrain or facilitate trait evolution. These factors could especially influence the evolution of traits that are functionally integrated, such as those comprising the flower. Indeed, pleiotropy is proposed as a main driver of repeated convergent trait transitions, including the evolution of phenotypically similar pollinator syndromes.

   We assessed the role of pleiotropy in the differentiation of floral and other reproductive traits between two species –Jaltomata sinuosaandJ. umbellata(Solanaceae) – that have divergent suites of floral traits consistent with bee and hummingbird pollination, respectively. To do so, we generated a hybrid population and examined the genetic architecture (trait segregation and quantitative trait locus (QTL) distribution) underlying 25 floral and fertility traits.

   We found that most floral traits had a relatively simple genetic basis (few, predominantly additive,QTLs of moderate to large effect), as well as little evidence of antagonistic pleiotropy (few trait correlations andQTLcolocalization, particularly between traits of different classes). However, we did detect a potential case of adaptive pleiotropy among floral size and nectar traits.

   These mechanisms may have facilitated the rapid floral trait evolution observed withinJaltomata, and may be a common component of rapid phenotypic change more broadly.

    

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