Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet Process Prior (DPP) model. Among the parameters jointly inferred are the population-wide rate of self-fertilization, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual

Effects of Short-Term Exposure to Diesel Exhaust on the Ecophysiology, Growth, and Fecundity of Soybean (Glycine max (L.) Merr.) and Chicory (Cichorium intybus L.)

Plants growing along roadways are often exposed to vehicle exhaust containing both particulate matter (PM) and various gases that could affect gas exchange and thus plant reproduction. To investigate effects of diesel exhaust exposure on plant ecophysiology, growth, and fecundity, individuals of soybean (Glycine max (L.) Merr.) and chicory (Cichorium intybus L.) were exposed to either exhaust from a diesel generator or ambient air. Exposure occurred daily over a 5-day period (beginning 18 June 2013) using open-top chambers in an agricultural field in southwestern Ohio, United States. Plants were evaluated at 3 times (before, directly after exposure, and following a 5.5-week post-treatment recovery period) for photosynthetic rate (A), stomatal conductance (g), water use efficiency (WUE), stomatal clogging due to PM deposition, and number of nodes. Aboveground biomass, fruit number, mean seed number, and seed mass were measured for soybean after the recovery period. In soybean, A minimally decreased with exposure to diesel exhaust (compared to the control), but an increase in g and a decrease in WUE were detected after the exhaust treatment. Chicory exhibited a relatively low increase in A after the treatment, but there were no clear differences in g or WUE. Growth and fecundity were similar among all soybean plants directly after treatment, but after 5.5 weeks plants exposed to diesel exhaust had increased vegetative biomass while exhibiting no difference in fecundity. These plant species reacted differently to short-term diesel exhaust exposure, suggesting that the impact of diesel exhaust will depend on both the plant species and its physiology

Research inequity in the plant sciences

Do all plant biologists worldwide have equal access to novel methods, enabling them to be equally productive, publish, and receive credit for their research? Or does reduced access to cutting-edge techniques in countries with lower financial resources create an inequity for researchers located there? Such disparities and biases do exist within our discipline and must be addressed if we are to move forward as a more just society. Applications in Plant Sciences has taken steps to address this important issue of research inequity, as outlined below. We now call upon the entire botanical community—researchers, editors and reviewers, funding agencies, and publishers—to work together toward a more equitable environment for all researchers around the world

A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens sampling formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet process prior model. Our sampler is designed to accommodate additional information, including observations pertaining to the sex ratio, the intensity of inbreeding depression, and other aspects of reproduction. It can provide joint posterior distributions for the population-wide proportion of uniparental individuals, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual. Further, estimation of all basic parameters of a given model permits estimation of functions of those parameters, including the proportion of the gene pool contributed by each sex and relative effective numbers

Asymmetrical Gene Flow in a Hybrid Zone of Hawaiian Schiedea (Caryophyllaceae) Species with Contrasting Mating Systems

Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1) putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2) gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3) in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s) of S. menziesii

Why Vouchers Matter in Botanical Research

What is a voucher and why is it important in research? As a preserved specimen of an identified taxon deposited in a permanent and accessible storage facility, the voucher serves as the supporting material for published studies of the taxon and ensures that the science is repeatable. Vouchers are crucial in authenticating the taxonomy of an organism, as a tool for identifying localities of the taxon, and for additional taxonomic, genetic, ecological, and/or environmental research

Changing Technologies Offer New Opportunities in the Plant Sciences

The plant sciences are now facing an unprecedented time in our history in which technology is advancing at a rapid pace, creating a wide variety of novel opportunities for our field. <i>Applications in Plant Sciences</i> is a new source for sharing exciting and innovative applications of new technologies that have the potential to propel plant research forward into the future