Genomic studies on the nature of species: adaptation and speciation in <i>Mimulus</i>

Twyford, Alex D.; Streisfeld, Matthew A.; Lowry, David B.; Friedman, Jannice

doi:10.1111/mec.13190

Cited by 33 publications

(24 citation statements)

References 123 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nesom). Mimulus guttatus is a model system for understanding the genetic underpinnings of evolutionary adaptations (reviewed in Wu et al, ; Twyford, Streisfeld, Lowry, & Friedman, ). Both annual and perennial populations are found throughout much of the range of M. guttatus (Friedman & Willis, ; van Kleunen, ; Lowry & Willis, ; Oneal, Lowry, Wright, Zhu, & Willis, ; Twyford et al., ).…”

Section: Introductionmentioning

confidence: 99%

Gene regulatory divergence between locally adapted ecotypes in their native habitats

2018

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

Gene regulatory divergence between locally adapted ecotypes in their native habitats

2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mimulus has become a widely used model for evolutionary genetic studies because of its phenotypic, ecological, and genetic variation, with centers of species diversity in both North and South America (Wu et al 2008; Sobel and Streisfeld 2013; Beardsley and Olmstead 2002; Twyford et al 2015). Mimulus is a powerful system for genetic studies due to the interfertility of diverse species and the availability of genomic resources, including the genome sequence of Mimulus guttatus , M. cardinalis , M. lewisii , and M. luteus (Hellsten et al 2013; Yuan et al 2013; Edger et al 2016).…”

mentioning

confidence: 99%

A Whole-Transcriptome Approach to Evaluating Reference Genes for Quantitative Gene Expression Studies: A Case Study in Mimulus

Stanton

Edger

Puzey

et al. 2017

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional “housekeeping” reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.

show abstract

“…When we look for traits involved in speciation, we tend to focus on differences between ecotypes or between populations of a wide variety of taxa. This has certainly been fruitful, we have learned a lot about the processes and genes involved in divergence from focusing on ecotypes and species pairs in sticklebacks (Peichel & Marques, ), Heliconius butterflies (Nadeau et al., ) and Mimulus monkey flowers (Twyford, Streisfeld & Friedman, ), among many others. However, this approach means we likely overlook important variation in traits or genes at transition zones between habitats.…”

Section: Surfing On Cline Waves—spatial Variation In Genes and Phenotmentioning

confidence: 99%

Notes from a snail island: Littorinid evolution and adaptation

Ravinet

2018

Molecular Ecology

View full text Add to dashboard Cite

The most successful study systems are built on a foundation of decades of research on the basic biology, ecology and life history of the organisms in question. Combined with new technologies, this can provide a formidable means to address important issues in evolutionary biology and molecular ecology. Littorinid marine snails are a good example of this, with a rich literature on their taxonomy, speciation, thermal tolerance and behavioural adaptations. In August 2017, an international meeting on Littorinid evolution was held at the Tj€ arn€ o Marine Research Laboratory in Western Sweden. In this meeting review, I provide a summary of some of the exciting work on parallel evolution, sexual selection and adaptation to environmental stress presented there. I argue that newly available genomic resources present an opportunity for integrating the traditionally divergent fields of speciation and environmental adaptation in Littorinid research.

show abstract

Genomic studies on the nature of species: adaptation and speciation in Mimulus

Cited by 33 publications

References 123 publications

Gene regulatory divergence between locally adapted ecotypes in their native habitats

Gene regulatory divergence between locally adapted ecotypes in their native habitats

A Whole-Transcriptome Approach to Evaluating Reference Genes for Quantitative Gene Expression Studies: A Case Study in Mimulus

Notes from a snail island: Littorinid evolution and adaptation

Contact Info

Product

Resources

About