Genetics and the Evolution of Prezygotic Isolation.

The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow? We address these questions by reviewing genetic features shared across plants and animals that influence prezygotic isolation.

Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation.

The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the species complex, there is evidence for widespread gene flow among members of this radiation.

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone.

Understanding the phenotypic and genetic architecture of reproductive isolation is a long-standing goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine "top-down" and "bottom-up" approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone.

Multiple evolutionary origins of glyphosate resistance in .

The multitude of herbicide resistance patterns that have evolved in different weed species is a remarkable example of the rapid adaptation to anthropogenic-driven disturbance. Recently, resistance to glyphosate was identified in multiple populations of in Oregon. We used phenotypic approaches, as well as population genomic and gene expression analyses, to determine whether known mechanisms were responsible for glyphosate resistance and whether resistance phenotypes evolved independently in different populations, and to identify potential loci contributing to resistance.

Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus.

Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M.

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers.

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers.

Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes of Mimulus aurantiacus.

Many forms of reproductive isolation contribute to speciation, and early-acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of intertaxon mating. Characterizing this form of isolation requires knowledge of both the geographic arrangement of suitable habitats in nature and the identification of phenotypes involved in shaping geographic distributions.

Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus).

Premise Of The Study: Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history.

Population genomics of divergence within an obligate pollination mutualism: Selection maintains differences between Joshua tree species.

Premise Of The Study: Speciation is a complex process that can be shaped by many factors, from geographic isolation to interspecific interactions. In Joshua trees, selection from pollinators on style length has been hypothesized to contribute to the maintenance of differentiation between two hybridizing sister species. We used population genomics approaches to measure the extent of genetic differentiation between these species, test whether selection maintains differences between them, and determine whether genetic variants associated with style length show signatures of selection.

Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower.

A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially explicit framework, but has not been used to study genome-wide patterns of divergence.

The geography of divergence with gene flow facilitates multitrait adaptation and the evolution of pollinator isolation in Mimulus aurantiacus.

Ecological adaptation is the driving force during divergence with gene flow and generates reproductive isolation early in speciation. Although gene flow opposes divergence, local adaptation can be facilitated by factors that prevent the breakup of favorable allelic combinations. We investigated how selection, genetic architecture, and geography have contributed to the maintenance of floral trait divergence and pollinator isolation between parapatric ecotypes of Mimulus aurantiacus.

Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers.

A primary goal in evolutionary biology is to identify the historical events that have facilitated the origin and spread of adaptations. When these adaptations also lead to reproductive isolation, we can learn about the evolutionary mechanisms contributing to speciation. We reveal the complex history of the gene MaMyb2 in shaping flower colour divergence within a recent radiation of monkey flowers.

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

Evolutionary biology is in an exciting era, in which powerful genomic tools make the answers accessible to long-standing questions about variation, adaptation and speciation. The availability of a suite of genomic resources, a shared knowledge base and a long history of study have made the phenotypically diverse plant genus Mimulus an important system for understanding ecological and evolutionary processes. An international Mimulus Research Meeting was held at Duke University in June 2014 to discuss developments in ecological and evolutionary genetic studies in Mimulus.

Strong premating reproductive isolation drives incipient speciation in Mimulus aurantiacus.

Determining which forms of reproductive isolation have the biggest impact on the process of divergence is a major goal of speciation research. These barriers are often divided into those that affect the potential for hybridization (premating isolation), and those that occur after mating (postmating isolation), and much debate has surrounded the relative importance of these categories. Within the species Mimulus aurantiacus, red- and yellow-flowered ecotypes occur in the southwest corner of California, and a hybrid zone occurs where their ranges overlap.

The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the repeatability of evolution.

A long-standing question in evolutionary biology asks whether the genetic changes contributing to phenotypic evolution are predictable. Here, we identify a genetic change associated with segregating variation in flower color within a population of Mimulus lewisii. To determine whether these types of changes are predictable, we combined this information with data from other species to investigate whether the spectrum of mutations affecting flower color transitions differs based on the evolutionary time-scale since divergence.

Flower color as a model system for studies of plant evo-devo.

Even though pigmentation traits have had substantial impacts on the field of animal evolutionary developmental biology, they have played only relatively minor roles in plant evo-devo. This is surprising given the often direct connection between flower color and fitness variation mediated through the effects of pollinators. At the same time, ecological and evolutionary genetic studies have utilized the molecular resources available for the anthocyanin pathway to generate several examples of the molecular basis of putatively adaptive transitions in flower color.

Divergent selection drives genetic differentiation in an R2R3-MYB transcription factor that contributes to incipient speciation in Mimulus aurantiacus.

Identifying the molecular genetic basis of traits contributing to speciation is of crucial importance for understanding the ecological and evolutionary mechanisms that generate biodiversity. Despite several examples describing putative "speciation genes," it is often uncertain to what extent these genetic changes have contributed to gene flow reductions in nature. Therefore, considerable interest lies in characterizing the molecular basis of traits that actively confer reproductive isolation during the early stages of speciation, as these loci can be attributed directly to the process of divergence.

Predictable patterns of constraint among anthocyanin-regulating transcription factors in Ipomoea.

• Transcription factors (TFs) may play a central role in plant morphological evolution. Variation in the nonsynonymous to synonymous nucleotide substitution rate (dN/dS) ratio among TFs can be attributed to either differences in constraint or the frequency of adaptive substitution. However, the relative contribution of these forces to the variation in dN/dS ratios is unknown.

Population genetics, pleiotropy, and the preferential fixation of mutations during adaptive evolution.

Ongoing debate centers on whether certain types of mutations are fixed preferentially during adaptive evolution. Although there has been much discussion, no quantitative framework currently exists to test for these biases. Here, we describe a method for distinguishing between the two processes that likely account for biased rates of substitution: variation in mutation rates and variation in the probability that a mutation becomes fixed once it arises.

Genetic changes contributing to the parallel evolution of red floral pigmentation among Ipomoea species.

The repeated, independent evolution of phenotypic traits reflects adaptation to similar selective pressures. In some circumstances, parallel phenotypic evolution has a common genetic basis. Here, we investigate the types of genetic change responsible for the repeated evolution of red flowers among Ipomoea species.

Altered trans-regulatory control of gene expression in multiple anthocyanin genes contributes to adaptive flower color evolution in Mimulus aurantiacus.

A fundamental goal in evolutionary biology is to identify the molecular changes responsible for adaptive evolution. In this study, we describe a genetic analysis to determine whether the molecular changes contributing to adaptive flower color divergence in Mimulus aurantiacus affect gene expression or enzymatic activity. High performance liquid chromatography analysis confirms that flower color differences are caused by the presence versus absence of anthocyanin pigments.

Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea.

Regulatory genes are believed to play a large role in morphological diversification and are often characterized by elevated rates of evolution. Whether this rapid evolution is primarily due to adaptive differentiation or relaxed selective constraint remains an open question. We attempted to distinguish between these alternative outcomes in 2 transcription factors known to regulate the expression of anthocyanin pigmentation genes in flowers.

Contrasting patterns of floral and molecular variation across a cline in Mimulus aurantiacus.

Steep clines in ecologically important traits may be caused by divergent natural selection. However, processes that do not necessarily invoke ongoing selection, such as secondary contact or restricted gene flow, can also cause patterns of phenotypic differentiation over short spatial scales. Distinguishing among all possible scenarios is difficult, but an attainable goal is to establish whether scenarios that imply selection need to be invoked.