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Abstract Traits that have lost function sometimes persist through evolutionary time. Persistence may occur if there is not enough standing genetic variation for the trait to allow a response to selection, if selection against the trait is weak relative to drift, or if the trait has a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in northeast Spain. A. thaliana is highly self-pollinating and prior work suggests short stamens do not contribute to self-pollination. We found a cline in short stamen number from retention of short stamens in high-elevation populations to incomplete loss in low-elevation populations. We did not find evidence that limited genetic variation constrains short stamen loss at high elevations, nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in northeast Spain that are different from loci associated with variation in short stamens across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms contributing to an elevational cline in short stamen number so further research is clearly warranted. 

{"Abstract":["Traits that have lost function sometimes persist through evolutionary\n time. Persistence may occur if there is not enough standing genetic\n variation for the trait to allow a response to selection, if selection\n against the trait is weak relative to drift, or if the trait has a\n residual function. To determine the evolutionary processes shaping whether\n nonfunctional traits are retained or lost, we investigated short stamens\n in 16 populations of Arabidopsis thaliana along an elevational cline in\n northeast Spain. A. thaliana is highly self-pollinating and prior work\n suggests short stamens do not contribute to self-pollination. We found a\n cline in short stamen number from retention of short stamens in high\n elevation populations to incomplete loss in low elevation populations. We\n did not find evidence that limited genetic variation constrains short\n stamen loss at high elevations, nor evidence for divergent selection on\n short stamens between high and low elevations. Finally, we identified loci\n associated with short stamens in northeast Spain that are different from\n loci associated with variation in short stamens across latitudes from a\n previous study. Overall, we did not identify the evolutionary mechanisms\n contributing to an elevational cline in short stamen number so further\n research is clearly warranted. This dryad dataset includes the GWAS output\n results. See the github for phenotypic data and SRA for genotypic data."],"TechnicalInfo":["# Evaluating the roles of drift and selection in trait loss along an\n elevational gradient Dataset DOI:\n [10.5061/dryad.8sf7m0d0z](10.5061/dryad.8sf7m0d0z) ## Description of the\n data and file structure These files are the relatedness matrices and GWAS\n output files for a GWAS on short stamen number in *A.\n thaliana* from an elevation gradient across the Pyrenees. The\n associated paper is "Evaluating the Roles of Drift and Selection in\n Trait Loss along an Elevational Gradient" by Buysse et al. The code\n used to generate the files can be found on\n github: [https://github.com/sfbuysse/A_thaliana_StamenLoss_2025](https://github.com/sfbuysse/A_thaliana_StamenLoss_2025).  The input data is SNP information for 61 genotypes from 16 native populations of *A. thaliana*. ### Files and variables #### File: RelatednessMatrices.zip **Description:** **RelatednessMatrices.zip** contains centered Relatedness Matrices made with GEMMA v0.98.4. Relatedness matrices are *.cXX.txt and *.log.txt show the code and run log information. allSNPs.PlinkFiltering_Asin, allSNPs.PlinkFiltering_Binary, allSNPs.PlinkFiltering_raw : identical relatedness matrices made using all SNPs in the dataset after filtering with Plink. Names were changed to match the phenotype files to run the GWAS.  allSNPs.PlinkFiltering*_*raw_subset : centered relatedness matrix made with all SNPs after plink filtering but only the individuals with some short stamen loss (mean short stamen number < 2). NoCent.PlinkFiltering_Asin, NoCent.PlinkFiltering_Binary, NoCent.PlinkFiltering_raw  : identical relatedness matrices made after excluding the centromere region and filtering with Plink. Names were changed to match the phenotype files to run the GWAS.  NoCent.PlinkFiltering_raw_subset. : centered relatedness matrix made after excluding the centromere and plink filtering but only the individuals with some short stamen loss (mean short stamen number < 2). #### File: GWAS.zip **Description:** **GWAS.zip** contains GWAS output files. The GWAS output files are  *.assoc.txt and the code information is  *.log.txt. GWAS were run in GEMMA v0.98.4. Within each .assoc.txt file the columns are as follows: * chr = chromosome * rs = snp id (chromosome:base pair position) * ps = base pair position * n_miss = number of genotypes missing genetic information at that SNP * allele1 = minor allele * allele2 = major allele * af = minor allele frequency * beta = affect size * se = standard error for beta * log_lH1 = log liklihood of alternative hypothesis that beta does not equal 0 (H0 is that beta =0) * l_remle = restricted maximum liklihood estimates for lambda * l_mle = maximum liklihood estimates for lambda * p_wald = p value from the Wald test * p_lrt = p value from liiklihood ratio test * p_score = p value from score test allSNPs.PlinkFiltering_Asin.c : include allSNPs after filtering with plink. phenotypes were arcsine transformed before GWAS. Centered relatedness matrix used. allSNPs.PlinkFiltering_Binary.c : include allSNPs after filtering with plink. phenotypes were transformed to a binary trait before GWAS - no short stamen loss = 0, any short stamen loss = 1. Centered relatedness matrix used. allSNPs.PlinkFiltering_raw.c : include allSNPs after filtering with plink. phenotypes were not transformed before GWAS. Centered relatedness matrix used. allSNPs.PlinkFiltering*_*raw_subset.c : include allSNPs after filtering with plink. phenotypes were not transformed before GWAS but the individuals used were subset down to only those that had some short stamen loss (mean short stamen number < 2). Centered relatedness matrix used. NoCent.PlinkFiltering_Asin.c : Centromere excluded. Plink Filtering as before. Arcsine transformed phenotypes. Centered relatedness matrix. NoCent.PlinkFiltering_Binary.c : Centromere excluded. Plink Filtering as before. Phenotypes converted to a binary trait. Centered relatedness matrix. NoCent.PlinkFiltering_raw.c : Centromere excluded. Plink Filtering as before. Phenotypes not transformed. Centered relatedness matrix. NoCent.PlinkFiltering_raw_subset.c : Centromere excluded. Plink Filtering as before. Individuals subset to only those that had some short stamen loss. Centered relatedness matrix. ## Code/software We used GEMMA v0.98.4 to create the files. ## Access information Other publicly accessible locations of the data: * [https://github.com/sfbuysse/A_thaliana_StamenLoss_2025](https://github.com/sfbuysse/A_thaliana_StamenLoss_2025) : scripts and information for creation of input files and use of output files after generation. * Genotypic data used is submitted to NCBI SRA as accession PRJNA1246133."]} 

Abstract The origin of phenotypic novelty is a perennial question of genetics and evolution. To date, few studies of biological pattern formation specifically address multi-generational aspects of inheritance and phenotypic novelty. For quantitative traits influenced by many segregating alleles, offspring phenotypes are often intermediate to parental values. In other cases, offspring phenotypes can be transgressive to parental values. For example, in the model organismMimulus(monkeyflower), the offspring of parents with solid-colored petals exhibit novel spotted petal phenotypes. These patterns are controlled by an activator-inhibitor gene regulatory network with a small number of loci. Here we develop and analyze a model of hybridization and pattern formation that accounts for the inheritance of a diploid gene regulatory network composed of either homozygous or heterozygous alleles. We find that the resulting model of multi-generational Turing-type pattern formation can reproduce transgressive petal phenotypes similar to those observed inMimulus. The model gives insight into how non-patterned parent phenotypes can yield phenotypically transgressive, patterned offspring, aiding in the development of empirically testable hypotheses. 

Abstract 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. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments. 

Abstract Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers. 

Abstract Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use sequence and expression analysis, followed by transgenic manipulation of gene expression, to identify MYB5a—orthologous to the NEGAN transcriptional activator from M. lewisii—as the gene responsible for the transition to anthocyanin-pigmented petals in M. l. variegatus. In other monkeyflower taxa, MYB5a/NEGAN is part of a reaction-diffusion network that produces semi-repeating spotting patterns, such as the array of spots in the nectar guides of both M. lewisii and M. guttatus. Its co-option for the evolution of an apparently non-patterned trait—the solid petal lobe pigmentation of M. l. variegatus—illustrates how reaction-diffusion can contribute to evolutionary novelty in non-obvious ways. Transcriptome sequencing of a MYB5a RNAi line of M. l. variegatus reveals that this genetically simple change, which we hypothesize to be a regulatory mutation in cis to MYB5a, has cascading effects on gene expression, not only on the enzyme-encoding genes traditionally thought of as the targets of MYB5a but also on all of its known partners in the anthocyanin regulatory network.