Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

PREMISE OF THE STUDY: Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for maternal-excess crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins of Mimulus peregrinus, an allohexaploid recently derived from the triploid M. xrobertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. METHODS: We used reciprocal crosses between the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to determine the viability of triploid M. xrobertsii hybrids resulting from paternal-vs. maternal-excess crosses. To investigate whether experimental results predict patterns seen in the field, we performed parentage analyses comparing natural populations of M. peregrinus to its diploid, tetraploid, and triploid progenitors. Organellar sequences obtained from pre-existing genomic data, supplemented with additional genotyping was used to establish the maternal ancestry of multiple M. peregrinus and M. xrobertsii populations. KEY RESULTS: We found strong evidence for asymmetric origins of M. peregrinus, but opposite to the common pattern, with paternal-excess crosses significantly more successful than maternal-excess crosses. These results successfully predicted hybrid formation in nature: 111 of 114 M. xrobertsii individuals, and 27 of 27 M. peregrinus, had an M. guttatus maternal haplotype. CONCLUSION: This study, which includes the first Mimulus chloroplast genome assembly, demonstrates the utility of parentage analysis through genome skimming. We highlight the benefits of complementing genomic analyses with experimental approaches to understand asymmetry in allopolyploid speciation

Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

PREMISE OF THE STUDY:Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for “maternal-excess” crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins ofMimulus peregrinus, an allohexaploid recently derived from the triploidM. ×robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species.  METHODS:We used reciprocal crosses between the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to determine the viability of triploidM. ×robertsiihybrids resulting from paternal- vs. maternal-excess crosses. To investigate whether experimental results predict patterns seen in the field, we performed parentage analyses comparing natural populations ofM. peregrinusto its diploid, tetraploid, and triploid progenitors. Organellar sequences obtained from pre-existing genomic data, supplemented with additional genotyping was used to establish the maternal ancestry of multipleM. peregrinusandM. ×robertsiipopulations.  KEY RESULTS:We found strong evidence for asymmetric origins ofM. peregrinus, but opposite to the common pattern, with paternal-excess crosses significantly more successful than maternal-excess crosses. These results successfully predicted hybrid formation in nature: 111 of 114M. ×robertsiiindividuals, and 27 of 27M. peregrinus, had anM. guttatusmaternal haplotype.  CONCLUSION:This study, which includes the firstMimuluschloroplast genome assembly, demonstrates the utility of parentage analysis through genome skimming. We highlight the benefits of complementing genomic analyses with experimental approaches to understand asymmetry in allopolyploid speciation

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

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

The case for the continued use of the genus name Mimulus for all monkeyflowers

The genus Mimulus is a well-studied group of plant species, which has for decades allowed researchers to address a wide array of fundamental questions in biology (Wu & al. 2008; Twyford & al. 2015). Linnaeus named the type species of Mimulus (ringens L.), while Darwin (1876) used Mimulus (luteus L.) to answer key research questions. The incredible phenotypic diversity of this group has made it the focus of ecological and evolutionary study since the mid-20th century, initiated by the influential work of Clausen, Keck, and Hiesey as well as their students and collaborators (Clausen & Hiesey 1958; Hiesey & al. 1971, Vickery 1952, 1978). Research has continued on this group of diverse taxa throughout the 20th and into the 21st century (Bradshaw & al. 1995; Schemske & Bradshaw 1999; Wu & al. 2008; Twyford & al. 2015; Yuan 2019), and Mimulus guttatus was one of the first non-model plants to be selected for full genome sequencing (Hellsten & al. 2013). Mimulus has played a key role in advancing our general understanding of the evolution of pollinator shifts (Bradshaw & Schemske 2003; Cooley & al. 2011; Byers & al. 2014), adaptation (Lowry & Willis 2010; Kooyers & al. 2015; Peterson & al. 2016; Ferris & Willis 2018; Troth & al. 2018), speciation (Ramsey & al. 2003; Wright & al. 2013; Sobel & Streisfeld 2015; Zuellig & Sweigart 2018), meiotic drive (Fishman & Saunders 2008), polyploidy (Vallejo-Marín 2012; Vallejo-Marín & al. 2015), range limits (Angert 2009; Sexton et al. 2011; Grossenbacher & al. 2014; Sheth & Angert 2014), circadian rhythms (Greenham & al. 2017), genetic recombination (Hellsten & al. 2013), mating systems (Fenster & Ritland 1994; Dudash & Carr 1998; Brandvain & al. 2014) and developmental biology (Moody & al. 1999; Baker & al. 2011, 2012; Yuan 2019). This combination of a rich history of study coupled with sustained modern research activity is unparalleled among angiosperms. Across many interested parties, the name Mimulus therefore takes on tremendous biological significance and is recognizable not only by botanists, but also by zoologists, horticulturalists, naturalists, and members of the biomedical community. Names associated with a taxonomic group of this prominence should have substantial inertia, and disruptive name changes should be avoided. As members of the Mimulus community, we advocate retaining the genus name Mimulus to describe all monkeyflowers. This is despite recent nomenclature changes that have led to a renaming of most monkeyflower species to other genera.Additional co-authors: Jannice Friedman, Dena L Grossenbacher, Liza M Holeski, Christopher T Ivey, Kathleen M Kay, Vanessa A Koelling, Nicholas J Kooyers, Courtney J Murren, Christopher D Muir, Thomas C Nelson, Megan L Peterson, Joshua R Puzey, Michael C Rotter, Jeffrey R Seemann, Jason P Sexton, Seema N Sheth, Matthew A Streisfeld, Andrea L Sweigart, Alex D Twyford, John H Willis, Kevin M Wright, Carrie A Wu, Yao-Wu Yua

Effects of burial and substrate characteristics on the germination ecology of a rare coastal pioneer species, Amaranthus pumilus.

The limited information available regarding the germination ecology of the federally threatened coastal pioneer, Amaranthus pumilus (Raf. Amaranthaceae), may be an obstacle to the development of sound species management and conservation plans. We investigated the effects of seed burial depth, sand versus shell substrate, and the presence or absence of soil microorganisms on seed germination and seedling emergence of A. pumilus in a controlled, growth chamber environment. Burial treatments consisted of forty seeds each, planted at 0, 2, 4, and 6 cm and incubated for 26 days. Effects of substrate and soil microorganisms were tested using a factorial combination of sand versus shell with sterilized versus unsterilized substrate. Each treatment consisted of 35 seeds, planted in petri dishes and incubated for 18 days. Germination and emergence decreased with increasing burial depth. At 4 cm of burial, above-ground emergence was delayed approximately six days relative to 0 and 2 cm of burial. At 6 cm of burial, few seeds germinated and none emerged. Viability of seeds that niether emerged nor germinated was reduced relative to that of other treatments. Substrate type and sterilization had no observable effects of seed germination or emergence of seedlings. Long-term studies will be required to determine the effects of these factors on seedling development and survival to adulthood. The equivalence of germination and emergence on sand versus shell substrate conflicts with field observations that indicate preferential establishmnet of A. pumilus on sand. Differences noted in the field may be due to the lower water retention capacity of shell substrate, a factor that was not tested in this experiment. Ecosystem-level issues, such as habitat degradation and loss, are of critical and immediate importance to species persistance. However, conservation and restoration efforts will be facilitated by an improved understanding of the environmental factors that influence individual growth and survival.http://deepblue.lib.umich.edu/bitstream/2027.42/54874/1/3315.pdfDescription of 3315.pdf : Access restricted to on-site users at the U-M Biological Station

Evolution of Floral Color Patterning in Chilean <em>Mimulus</Em>

<p>Evolution can be studied at many levels, from phenotypic to molecular, and from a variety of disciplines. An integrative approach can help provide a more complete understanding of the complexities of evolutionary change. This dissertation examines the ecology, genetics, and molecular mechanisms of the evolution of floral anthocyanin pigmentation in four species of <em>Mimulus</em> native to central Chile. Anthocyanins, which create red and purple colors in many plants, are a valuable model for studying evolutionary processes. They are ecologically important and highly variable both within and between species, and the underlying biosynthetic pathway is well characterized. The focus of this dissertation is dramatic diversification in anthocyanin coloration, in four taxa that are closely related to the genomic model system <em>M. guttatus</em>. I posed three primary questions: (1) Is floral diversification associated with pollinator divergence? (2) What is the genetic basis of the floral diversification? (3) What is the molecular mechanism of the increased production of anthocyanin pigment? The first question was addressed by evaluating patterns of pollinator visitation in natural populations of all four study taxa. The second question was explored using segregation analysis for a series of inter- and intraspecific crosses. One trait, increased petal anthocyanins in <em>M. cupreus</em>, was further dissected at the molecular level, using candidate gene testing and quantitative gene expression analysis. Pollinator studies showed little effect of flower color on pollinator behavior, implying that pollinator preference probably did not drive pigment evolution in this group. However, segregation analyses revealed that petal anthocyanin pigmentation has evolved three times independently in the study taxa, suggesting an adaptive origin. In addition to pollinator attraction, anthocyanins and their biochemical precursors protect against a variety of environmental stressors, and selection may have acted on these additional functions. Molecular analysis of petal anthocyanins in <em>M. cupreus</em> revealed that this single-locus trait maps to a transcription factor, <em>McAn1</em>, which is differentially expressed in high- versus low-pigmented flowers. Expression of the anthocyanin structural genes is tightly correlated with <em>McAn1</em> expression. The results suggest that <em>M. cupreus</em> pigmentation evolved by a mutation cis to <em>McAn1</em> that alters the intensity of anthocyanin biosynthesis.</p>Dissertatio

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M. luteus var. luteus inbred line EY7 - calyx transcriptome "T2" - sample JS

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M. luteus var. luteus inbred line EY7 - leaf transcriptome "T2" - sample JS