Implications of land class and environmental factors on life cycle GHG emissions of Miscanthus as a bioenergy feedstock

Replacement of fossil fuels with sustainably produced biomass crops for energy purposes has the potential to make progress in addressing climate change concerns, nonrenewable resource use, and energy security. The perennial grass Miscanthus is a dedicated energy crop candidate being field tested in Ontario, Canada, and elsewhere. Miscanthus could potentially be grown in areas of the province that differ substantially in terms of agricultural land class, environmental factors and current land use. These differences could significantly affect Miscanthus yields, input requirements, production practices, and the types of crops being displaced by Miscanthus establishment. This study assesses implications on life cycle greenhouse gas (GHG) emissions of these differences through evaluating five Miscanthus production scenarios within the Ontario context. Emissions associated with electricity generation with Miscanthus pellets in a hypothetically retrofitted coal generating station are examined. Indirect land use change impacts are not quantified but are discussed. The net life cycle emissions for Miscanthus production varied greatly among scenarios (?90–170 kg CO₂eq per oven dry tonne of Miscanthus bales at the farm gate). In some cases, the carbon stock dynamics of the agricultural system offset the combined emissions of all other life cycle stages (i.e., production, harvest, transport, and processing of biomass). Yield and soil C of the displaced agricultural systems are key parameters affecting emissions. The systems with the highest potential to provide reductions in GHG emissions are those with high yields, or systems established on land with low soil carbon. All scenarios have substantially lower life cycle emissions (?20–190 g CO₂eq kWh^?1) compared with coal‐generated electricity (1130 g CO₂eq kWh^?1). Policy development should consider the implication of land class, environmental factors, and current land use on Miscanthus production.     

MHC class I expression dependent on bacterial infection and parental factors in whitefish embryos (Salmonidae)

Ecological conditions can influence not only the expression of a phenotype, but also the heritability of a trait. As such, heritable variation for a trait needs to be studied across environments. We have investigated how pathogen challenge affects the expression of MHC genes in embryos of the lake whitefish Coregonus palaea. In order to experimentally separate paternal (i.e. genetic) from maternal and environmental effects, and determine whether and how stress affects the heritable variation for MHC expression, embryos were produced in full‐factorial in vitro fertilizations, reared singly, and exposed at 208 degree days (late‐eyed stage) to either one of two strains of Pseudomonas fluorescens that differ in their virulence characteristics (one increased mortality, while both delayed hatching time). Gene expression was assessed 48 h postinoculation, and virulence effects of the bacterial infection were monitored until hatching. We found no evidence of MHC class II expression at this stage of development. MHC class I expression was markedly down‐regulated in reaction to both pseudomonads. While MHC expression could not be linked to embryo survival, the less the gene was expressed, the earlier the embryos hatched within each treatment group, possibly due to trade‐offs between immune function and developmental rate or further factors that affect both hatching timing and MHC expression. We found significant additive genetic variance for MHC class I expression in some treatments. That is, changes in pathogen pressures could induce rapid evolution in MHC class I expression. However, we found no additive genetic variance in reaction norms in our study population.     

Identification of a novel sperm class and its role in fertilization in Drosophila

In many species, males have evolved to produce a sterile sperm (parasperm) in conjunction with fertilizing sperm (eusperm). Here, we document evidence of males depositing two morphologically distinct types of parasperm (1 and 2) into the female reproductive tract in Drosophila pseudoobscura. These parasperm differ in length, shape, amount produced, amount in long‐term storage and may have separate roles in ensuring male fertilization success. Although both parasperm types protect eusperm from female spermicides, only parasperm 2, which has a corkscrew shape, is associated with sperm competition. Increased production of parasperm 2 is also negatively correlated with the eusperm and parasperm 1 production. Thus, selection may be acting on parasperm production in the presence of sperm competition. Our findings show how both sperm competition and cryptic female choice may be acting in conjunction to influence the evolution of ejaculate composition. Our identification and characterization of two distinct parasperm morphs will enhance the ability for further evaluation of parasperm's role in fertilization.     

Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus)

Host–pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1′665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen‐mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host–pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context.     

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

Animals harbour diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge: distinguishing between mutualistic and pathogenic members of diverse and host‐specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus, MHC polymorphism contributes to microbial variation among hosts. Here, we show that MHC IIb polymorphism is associated with among‐individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. We sampled stickleback from Cedar Lake, on Vancouver Island, and used next‐generation sequencing to genotype the sticklebacks’ gut microbiota (16S sequencing) and their MHC class IIb exon 2 sequences. The presence of certain MHC motifs was associated with altered relative abundance (increase or decrease) of some microbial Families. The effect sizes are modest and entail a minority of microbial taxa, but these results represent the first indication that MHC genotype may affect gut microbiota composition in natural populations (MHC‐microbe associations have also been found in a few studies of lab mice). Surprisingly, these MHC effects were frequently sex‐dependent. Finally, hosts with more diverse MHC motifs had less diverse gut microbiota. One implication is that MHC might influence the efficacy of therapeutic strategies to treat dysbiosis‐associated disease, including the outcome of microbial transplants between healthy and diseased patients. We also speculate that macroparasite‐driven selection on MHC has the potential to indirectly alter the host gut microbiota, and vice versa.     

Description of bovine major histocompatibility complex class IIa haplotypes using parthenogenetic embryo‐derived cells

In this study, we report an approach to characterize individual BoLA haplotypes using cells from parthenogenetic bovine embryos derived from slaughterhouse ovaries. Eight of the 15 parthenogenetic embryos so obtained had not undergone meiotic recombination on the BoLA region and were suitable to describe BoLA haplotypes. Detailed analysis of the BoLA class IIa region identified seven different class IIa haplotypes, including six not previously described and two new alleles of BoLA‐DQA and one BoLA‐DQB. Our method provided reliable sources of homozygous DNA to describe BoLA haplotypes.     

Molecular cloning and characterization of a sigma‐class glutathione S‐Transferase from the freshwater mussel Hyriopsis cumingii

A full‐length cDNA of a sigma‐like glutathione S‐transferase (GST) was identified from Hyriopsis cumingii (HcGSTS). The deduced amino acid sequence of HcGSTS was found to comprise 203 amino acid residues and to contain the distinct highly conserved glutathione binding site of N‐terminal and the relatively diverse substrate binding site of C‐terminal. Alignment analysis and phylogenetic relationship suggested that the HcGSTS is a sigma‐class GST. The mRNA of HcGSTS was constitutively expressed in all tested tissues, the strongest expression being in the hepatopancreas. The mRNA expression of HcGSTS was significantly up‐regulated (P < 0.05) in all assessed tissues after stimulation of the mussels with peptidoglycan (PGN) and LPS, the only exception being when the gills were challenged with PGN. The expression of HcGSTS mRNA in kidney and foot was also significantly up‐regulated (P < 0.05) by microcystin‐LR. Recombinant HcGSTS exhibited high activity towards the substrate 1‐chloro‐2,4‐dinitrobenzene. The optimal pH was 8.0 and temperature 35 °C.     

Evolution of major histocompatibility complex class I genes in the sable Martes zibellina (Carnivora,Mustelidae)

The molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immune response among vertebrates. We investigated the molecular evolution of MHC class I genes in the sable Martes zibellina. We isolated 26 MHC class I sequences, including 12 putatively functional sequences and 14 pseudogene sequences, from 24 individuals from two geographic areas of northeast China. The number of putatively functional sequences found in a single individual ranged from one to five, which might be at least 1–3 loci. We found that both balancing selection and recombination contribute to evolution of MHC class I genes in M. zibellina. In addition, we identified a candidate nonclassical MHC class I lineage in Carnivora, which may have preceded the divergence (about 52–57 Mya) of Caniformia and Feliformia. This may contribute to further understanding of the origin and evolution of nonclassical MHC class I genes. Our study provides important immune information of MHC for M. zibellina, as well as other carnivores.     

Mutants in the imprinted PICKLE RELATED 2 gene suppress seed abortion of fertilization independent seed class mutants and paternal excess interploidy crosses in Arabidopsis

Endosperm cellularization is essential for embryo development and viable seed formation. Loss of function of the FERTILIZATION INDEPENDENT SEED (FIS) class Polycomb genes, which mediate trimethylation of histone H3 lysine27 (H3K27me3), as well as imbalanced contributions of parental genomes interrupt this process. The causes of the failure of cellularization are poorly understood. In this study we identified PICKLE RELATED 2 (PKR2) mutations which suppress seed abortion in fis1/mea by restoring endosperm cellularization. PKR2, a paternally expressed imprinted gene (PEG), encodes a CHD3 chromatin remodeler. PKR2 is specifically expressed in syncytial endosperm and its maternal copy is repressed by FIS1. Seed abortion in a paternal genome excess interploidy cross was also partly suppressed by pkr2. Simultaneous mutations in PKR2 and another PEG, ADMETOS (ADM), additively rescue the seed abortion in fis1 and in the interploidy cross, suggesting that PKR2 and ADM modulate endosperm cellularization independently and reproductive isolation between plants of different ploidy is established by imprinted genes. Genes upregulated in fis1 and downregulated in the presence of pkr2 are enriched in glycosyl‐hydrolyzing activity, while genes downregulated in fis1 and upregulated in the presence of pkr2 are enriched with microtubule motor activity, consistent with the cellularization patterns in fis1 and the suppressor line. The antagonistic functions of FIS1 and PKR2 in modulating endosperm development are similar to those of PICKLE (PKL) and CURLY LEAF (CLF), which antagonistically regulate root meristem activity. Our results provide further insights into the function of imprinted genes in endosperm development and reproductive isolation.     

Structural basis for decreased induction of class IB PI3‐kinases expression by MIF inhibitors

Macrophage migration inhibitory factor (MIF) is a master regulator of proinflammatory cytokines and plays pathological roles when not properly regulated in rheumatoid arthritis, lupus, atherosclerosis, asthma and cancer. Unlike canonical cytokines, MIF has vestigial keto‐enol tautomerase activity. Most of the current MIF inhibitors were screened for the inhibition of this enzymatic activity. However, only some of the enzymatic inhibitors inhibit receptor‐mediated biological functions of MIF, such as cell recruitment, through an unknown molecular mechanism. The goal of this study was to understand the molecular basis underlying the pharmacological inhibition of biological functions of MIF. Here, we demonstrate how the structural changes caused upon inhibitor binding translate into the alteration of MIF‐induced downstream signalling. Macrophage migration inhibitory factor activates phosphoinositide 3‐kinases (PI3Ks) that play a pivotal role in immune cell recruitment in health and disease. There are several different PI3K isoforms, but little is known about how they respond to MIF. We demonstrate that MIF up‐regulates the expression of Class IB PI3Ks in leucocytes. We also demonstrate that MIF tautomerase active site inhibitors down‐regulate the expression of Class IB PI3Ks as well as leucocyte recruitment in vitro and in vivo. Finally, based on our MIF:inhibitor complex crystal structures, we hypothesize that the reduction in Class IB PI3K expression occurs because of the displacement of Pro1 towards the second loop of MIF upon inhibitor binding, which results in increased flexibility of the loop 2 and sub‐optimal MIF binding to its receptors. These results will provide molecular insights for fine‐tuning the biological functions of MIF.     

Many loci make light work: High individual diversity despite low population diversity and random mating at class I MHC in a Critically Endangered island songbird

Multi‐cellular organisms are under constant attack from parasites, making immune defence a critical aspect of fitness. In vertebrate animals, genes of the major histocompatibility complex (MHC) determine the breadth of pathogens to which individuals can respond. Having many MHC alleles can confer better protection against infectious disease, and balancing selection at MHC is widespread. Indeed, MHC loci are famously variable, with some populations harbouring thousands of alleles (Biedrzycka et al., 2018; Robinson, Soormally, Hayhurst, & Marsh, 2016). MHC has also long fascinated behavioural ecologists because mate choice—for example, preferring MHC‐dissimilar partners—may amplify the effects of natural selection (Penn & Potts, 1999). But despite keen interest in the evolutionary ecology of MHC, extensive duplication (Minias, Pikus, Whittingham, & Dunn, 2019) has made these genes challenging to study. In a From the Cover article in this issue of Molecular Ecology, Stervander, Dierickx, Thorley, Brooke, and Westerdahl (2020) characterizes class I MHC in a Critically Endangered songbird, relating genotype to mate choice and survivorship. By inferring copy number and patterns of allelic co‐segregation, the authors pave the way to elucidating the genomic architecture of MHC in this bottlenecked population. These insights help reconcile apparently counterintuitive findings: no effect of MHC genotype on mate choice or survival, and high MHC diversity within individuals despite low diversity at the population level. The latter finding is cause for optimism regarding conservation prospects. Moreover, these results suggest that ancient duplication events can have longstanding effects on the adaptive landscapes of natural and sexual selection.     

The role of a class III gibberellin 2‐oxidase in tomato internode elongation

A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth‐promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. The use of tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode‐specific elongation in a eudicot species with a sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild‐type petioles was identified through a forward genetic screen. In addition to stem‐specific elongation, this mutant, named tomato internode elongated ‐1 (tie‐1) is more sensitive to the GA biosynthetic inhibitor paclobutrazol and has altered levels of intermediate and bioactive GAs compared with wild‐type plants. The mutation responsible for the internode elongation phenotype was mapped to GA2oxidase 7, a class III GA 2‐oxidase in the GA biosynthetic pathway, through a bulked segregant analysis and bioinformatic pipeline, and confirmed by transgenic complementation. Furthermore, bacterially expressed recombinant TIE protein was shown to have bona fide GA 2‐oxidase activity. These results define a critical role for this gene in internode elongation and are significant because they further the understanding of the role of GA biosynthetic genes in organ‐specific elongation.     

Ichnodiversity and ichnodisparity: significance and caveats

Ichnodiversity has been used as a proxy for environmental stress and stability in facies interpretations and to reconstruct evolutionary radiations and colonization histories in evolutionary palaeoecology. The three components of global diversity are exported from ecology and adapted for ichnology. Alpha ichnodiversity is used for palaeoenvironmental characterization, being assessed for individual facies. Beta ichnodiversity is commonly overlooked, although it may provide information about degree of similarity between ichnofaunas formed along environmental gradients. Gamma ichnodiversity may provide clues to detect ichnofossil provincialism. The concept of disparity may also prove to be significant in ichnological studies. Whereas ichnodiversity refers to ichnotaxonomic richness, ichnodisparity provides a measure of the variability of morphological plans in biogenic structures. Changes in global ichnodiversity do not necessarily parallel changes in ichnodisparity. For example, while the Cambrian explosion involved a dramatic increase in both, the Ordovician radiation essentially reflects an increase only in the former. Ichnodiversity and ichnodisparity should be used with caution because they are both affected by taphonomic processes. High diversity of superficial to shallow‐tier trace fossils may result from enhanced preservation due a poorly developed mixed layer, rather than a true reflection of ecosystem performance, as shown by underexploited infaunal ecospace after biotic crises (e.g. end‐Permian mass extinction).     

Evolution of MHC class II SLA‐DRB1 locus in the Croatian wild boar (Sus scrofa) implies duplication and weak signals of positive selection

The wild boar is an ancestor of the domestic pig and an important game species with the widest geographical range of all ungulates. Although a large amount of data are available on major histocompatibility complex (MHC) variability in domestic pigs, only a few studies have been performed on wild boars. Due to their crucial role in appropriate immune responses and extreme polymorphism, MHC genes represent some of the best candidates for studying the processes of adaptive evolution. Here, we present the results on the variability and evolution of the entire MHC class II SLA‐DRB1 locus exon 2 in 133 wild boars from Croatia. Using direct sequencing and cloning methods, we identified 20 SLA‐DRB1 alleles, including eight new variants, with notable divergence. In some individuals, we documented functional locus duplication, and SLA‐DRB1*04:10 was identified as the allele involved in the duplication. The expression of a duplicated locus was confirmed by cloning and sequencing cDNA‐derived amplicons. Based on individual genotypes, we were able to assume that alleles SLA‐DRB1*04:10 and SLA‐DRB1*06:07 are linked as an allelic combination that co‐evolves as a two‐locus haplotype. Our investigation of evolutionary processes at the SLA‐DRB1 locus confirmed the role of intralocus recombination in generating allelic variability, whereas tests of positive selection based on the dN/dS (non‐synonymous/synonymous substitution rate ratio) test revealed atypically weak and ambiguous signals.     

Interactions Between Rhizoctonia Root Rot and the Foliar Common Bean Diseases Anthracnose and Rust

The effects of co‐inoculation of Rhizoctonia solani and Colletotrichum lindemuthianum or Uromyces appendiculatus at different inoculum levels were studied on the disease dynamics and on the growth of bean plants under greenhouse conditions. Bean seeds were sown in R. solani‐infested soil. Additional experiments in which seedlings were transplanted to infested soil were also carried out. Conidial suspensions of C. lindemuthianum or uredospores of U. appendiculatus were inoculated onto leaves at plant developmental stages V2 and V3, respectively. Interactions between root rot and the aerial diseases were observed depending on the inoculum levels and on the timing of R. solani inoculation. Anthracnose severity tended to be higher on R. solani‐infected plants. Conversely, R. solani infection significantly reduced diameter of pustules and rust severity. When seedlings were transplanted to soil infested with low levels of R. solani, root rot severity and density of R. solani in the soil were magnified at high levels of C. lindemuthianum or U. appendiculatus. In these experiments, a synergistic interaction between root rot and anthracnose was observed to affect the plant dry weight. Antagonistic effects on the plant dry weight were found for the combination root rot/rust only when seeds were sown in infested soil.