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In an effort to reduce nitrogen oxide (NOx) emissions and other pollutants from heavy-duty vehicles (HDVs), regulators have been implementing more stringent regulations that have included a combination of significantly more stringent emissions standards with the introduction of battery electric vehicles (BEVs). This study analyzed in-use NOx emissions data from 63 HDVs across various vocations, model years, and engine technologies/fuels to assess which current technologies offer a realistic path toward reducing NOx emissions without significantly burdening fleet operators or electrical infrastructure. All 63 HDVs were equipped with portable emissions measurement systems when they were tested for in-use NOx emissions during their routine operation on California roadways. The data was analyzed using the moving average window method proposed by the Environmental Protection Agency (EPA) in which the in-use emissions are broken up into two bins dependent on the engine load: ≤6 % (idle) and >6 % of maximum rated power. It was found that diesel engines manufactured after 2020 and natural gas engines certified to the 0.02 g/bhp-h NOx standard met the 2027 and 2035 EPA in-use NOx standards for both bins even though the future standards do not apply to these older engines. In addition, over an 80 % reduction in average NOx emissions is seen in both bins and fuels as modern NOx and greenhouse gas standards were implemented in 2017. With the implementation of ultralow NOx diesel technology engines, capable of meeting 0.035 g/bhp-h NOx limits, it was found that reductions in the NOx emissions inventories from 90.0 to 91.9 % could be achieved by 2050, depending on the deployment of BEVs. In conclusion, current and upcoming engine technologies can serve as benchmark powertrain solutions for emissions inventory reductions in the near and intermediate terms solutions even to the extent that the transition to battery electric HDVs becomes more gradual. 

Abstract The duplication of genes has long been recognized as a substrate for evolutionary novelty and adaptation, but the factors that govern fixation of paralogs soon after duplication are only partially understood. Duplication often leads to an increase in gene dosage, or the amount of functional gene product. For genes with which an increased dosage is harmful (i.e., triplosensitive genes), a dosage balancing mechanism needs to be present immediately after duplication if it is to evade negative selection. Previous research in vertebrates has demonstrated a potential role for epigenetic factors in allowing triplosensitive genes to increase in copy number by regulating their expression post-duplication. Here we expand this research by investigating the epigenetic landscape of duplicate genes inD. discoideum, a basal lineage separated from humans by over a billion years. We found that activating histone modifications are quickly lost in duplicate genes before gradually increasing in enrichment as paralogs age. For the repressive modification H3K9me3, we found it was enriched in the youngest paralogs, and that this enrichment was likely mediated by heterochromatin spread from transposable elements. We similarly found enrichment of H3K9me3 in young human duplicates, and again found transposable elements as a potential mediator. Finally, we leveraged recent genome-wide estimates of triplosensitivity in human genes to directly examine the relationship between this kind of dosage sensitivity and enrichment for repressive histone modifications. Interestingly, while we found no significant link between enrichment for the repressive mark H3K9me3 and triplosensitivity in human paralogs, we did find a significant association between triplosensitivity and transposon proximity. Our findings suggest that transposons may contribute to the epigenetic regulatory environment associated with dosage balancing of young duplicates in both protists and humans. 

Abstract Sex chromosome replacement is frequent in many vertebrate clades, including fish, frogs, and lizards. In order to understand the mechanisms responsible for sex chromosome turnover and the early stages of sex chromosome divergence, it is necessary to study lineages with recently evolved sex chromosomes. Here we examine sex chromosome evolution in a group of African cichlid fishes (tribe Tropheini) which began to diverge from one another less than 4 MYA. We have evidence for a previously unknown sex chromosome system, and preliminary indications of several additional systems not previously reported in this group. We find a high frequency of sex chromosome turnover and estimate a minimum of 14 turnovers in this tribe. We date the origin of the most common sex determining system in this tribe (XY-LG5/19) near the base of one of two major sub-clades of this tribe, about 3.4 MY ago. Finally, we observe variation in the size of one sex-determining region that suggests independent evolution of evolutionary strata in species with a shared sex-determination system. Our results illuminate the rapid rate of sex chromosome turnover in the tribe Tropheini and set the stage for further studies of the dynamics of sex chromosome evolution in this group. 

ABSTRACT Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important effects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved. 

Advances in genome sequencing have greatly accelerated the identification of sex chromosomes in a variety of species. Many of these species have experienced structural rearrangements that reduce recombination between the sex chromosomes, allowing the accumulation of sequence differences over many megabases. Identification of the genes that are responsible for sex determination within these sometimes large regions has proved difficult. Here, we identify an XY sex chromosome system on LG19 in the West African cichlid fishChromidotilapia guntheriin which the region of differentiation extends over less than 400 kb. We develop high-quality male and female genome assemblies for this species, which confirm the absence of structural variants, and which facilitate the annotation of genes in the region. The peak of differentiation lies withinrin3, which has experienced several debilitating mutations on the Y chromosome. We suggest two hypotheses about how these mutations might disrupt endocytosis, leading to Mendelian effects on sexual development.