Ecology and the Evolution of Sex Chromosomes

This article reviews and discusses ecological factors that affect sex chromosome evolution. Sex chromosomes are common features of animal genomes, and are often the location where master sex determination genes are found. Many important aspects of sex chromosome evolution are thought to be driven by sex-specific selection pressures, such as sexual antagonism and sexual selection. Sex-specific selection affects both the formation of sex chromosomes from autosomes and differences in the evolutionary trajectories between sex chromosomes and autosomes. Most population genetic models are agnostic as to whether the sex-specific selection pressures arise from intrinsic features of organismal biology or extrinsic factors that depend on environment. Here, I review the evidence that extrinsic, or ecological, factors are important determinants of sex-specific selection pressures that shape sex chromosome evolution.

Behaviors of Homologous Antibiotic Resistance Genes in a Cephalosporin WWTP, Subsequent WWTP and the Receiving River

High concentrations of antibiotics in antibiotic production wastewater can cause the widespread transmission of antibiotic resistance genes (ARGs). Here, we collected a set of time series samples from a cephalosporin production wastewater treatment plant (X-WWTP), the subsequent municipal WWTP (Y-WWTP) and the receiving stream. Using a functional gene microarray, GeoChip 5.0, which contains multiple homologous probes for 18 ARG and 13 antibiotic metabolism gene (AMG) families, we found that more than 50% of homologous probes for 20 gene families showed a relative abundance higher in X-WWTP, while only 10–20% showed lower relative abundance. The different response patterns of homologous ARG (hARGs) within the same ARG family imply environmental selection pressures are only responsible for the ARG enrichment and spread of some specific instead of all ARG-containing microorganisms, which contradicted the traditionally held belief that environmental selection pressures, especially antibiotic concentration, select for all ARG-containing microorganisms thereby selecting different hARGs in the same ARG family in an undifferentiated way. Network results imply that hARGs from three β_lactamase families enriched under the selection pressure of high cephalosporin antibiotic concentrations in X-WWTP formed positively correlated homologous ARG clusters (pohARGCs). The pohARGCs were also enhanced in the sediment of the receiving stream. The enrichment of hARGs from three β_lactamase families was likely through microorganisms belonging to the Betaproteobacteria genus.

The recalibrational theory: Anger as a bargaining emotion

This chapter uses the adaptationist program (Williams, 1966) - to predict and explain the major features of anger. According to this approach, anger evolved by natural selection to bargain for better treatment. Thus, the major triggers of anger (e.g. cost impositions, cues of disrespect) all indicate an increased willingness (on the part of the offender) to impose costs on the angry individual. Once triggered, the anger system bargains using the two primary incentives that humans have available to modify others’ behavior in favor of the focal individual: the imposition of costs and the denial of benefits. This simple functional sketch of anger is then supplemented with additional considerations needed to address the resultant selection pressures created by bargaining. This process offers functionally sound and theoretically justified explanations for: anger in aggressive and cooperative contexts, the role of apologies and their sincerity, the content of sex-specific insults, the computational structure of “intentionality” in the context of anger, and the origin of the implicit rules of combat.

Genome reorganization during emergence of host-associated Mycobacterium abscessus

Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.

Iterative mutagenesis induced by atmospheric and room temperature plasma treatment under multiple selection pressures for the improvement of coenzyme Q10 production by Rhodobacter sphaeroides

CoQ10, which has been widely applied in medicine by dietary supplement, possesses important functions in antioxidant process and bioenergy generation. Iterative mutagenesis introduced by atmospheric and room temperature plasma (ARTP) treatment was studied to improve the coenzyme Q10 (CoQ10) production of Rhodobacter sphaeroides (R. sphaeroides), and multiple selection pressures including vitamin K3 (VK3), Na2S and benzoic acid (BA) were adopted for the first time. After two rounds of mutation and screening, a mutant strain R.S 17 was obtained, and the product titer was increased by 80.37%. The CoQ10 titer and cell density reached 236.7 mg L−1 and 57.09 g L−1, respectively, in the fed-batch fermentation, and the CoQ10 content was 22.1% higher than that of the parent strain. In addition, the spectral scanning results indicated the metabolic flux improvement contributing to the CoQ10 production in R.S 17, and the genetic stability was validated. Based on the iterative mutagenesis introduced by ARTP under multiple selection pressures, the promotion of CoQ10 production by R. sphaeroides was achieved. The significant improvement in fermentation performances and the good genetic stability of R.S 17 indicate a potential way for the efficient biosynthesis of CoQ10.

Genetic Diversity of the Symbiotic Fungus Epichloë festucae in Naturally Occurring Host Grass Populations

Epichloë festucae is a common symbiont of the perennial and widely distributed cool season grass, Festuca rubra. The symbiosis is highly integrated involving systemic growth of the fungus throughout above-ground host parts and vertical transmission from plant to its offspring via host seeds. However, the nature of symbiosis is labile ranging from antagonistic to mutualistic depending on prevailing selection pressures. Both the loss of fungus in the maternal host lineage and horizontal transmission through sexual spores within the host population may partly explain the detected variation in symbiosis in wild grass populations. Epichloë species are commonly considered as pathogens when they produce sexual spores and partly castrate their host plant. This is the pathogenic end of the continuum from antagonistic to mutualistic interactions. Here we examined the population genetic structure of E. festucae to reveal the gene flow, importance of reproduction modes, and alkaloid potential of the symbiotic fungus in Europe. Epichloë-species are highly dependent on the host in survival and reproduction whilst benefits to the host are largely linked to defensive mutualism attributable to fungal-origin bioactive alkaloids that negatively affect vertebrate and/or invertebrate herbivores. We detected decreased genetic diversity in previously glaciated areas compared to non-glaciated regions during the last glacial maximum period and found three major genetic clusters in E. festucae populations: southern, northeastern and northwestern Europe. Sexual reproduction may have a higher role than expected in Spanish E. festucae populations due to the predominance of unique genotypes and presence of both mating types in the region. In contrast, asexual reproduction via host seeds predominates in the Faroe Island and Finland in northern Europe due to the presence of biased mating-type ratios and large dominant genotypes in the E. festucae populations within the region. A substantially larger variation of alkaloid genotypes was observed in the fungal populations than expected, although the variability of the alkaloid genotypes within populations is considerably lower in northern than Spanish populations in southern Europe. E. festucae populations consist of different combinations of alkaloid classes from the gene clusters of ergot alkaloid and indole-terpenes, and from pyrrolopyrazine alkaloid gene. We suggest that the postglacial distribution history of the host grass, prevailing reproduction strategies of E. festucae, and local selection pressures likely explain a large part of the genetic variation observed in fungal populations among geographic regions. The identified alkaloid genotypes can be used by turfgrass breeders to improve resistance against herbivores in red fescue varieties and to develop new sustainable cultivars in Europe.

Myrmecovory in Neotropical primates

Ants are the dominant group of animals in many habitats, particularly in tropical rainforests. High abundance and formation of large colonies convert them into a potential food source for a broad spectrum of animals. In this paper we review myrmecovory (consumption of ants) in Neotropical primates. Myrmecovory has been reported from 57 taxa (species + subspecies) out of 217 species of Neotropical primates, representing 18 out of 22 genera. The proportion of ants in the animal portion of the diet is highest amongst members of the genera Cebus, Sapajus, Cheracebus and Plecturocebus, but generally low in callitrichids, large pitheciids (Cacajao, Chiropotes) and atelids. Ants from seven subfamilies of Formicidae (out of 13 subfamilies found in the Neotropics) are consumed, including taxa with and without functional sting and with varying other defences. Foraging technics employed in myrmecovory range from picking ants from open substrates to extractive foraging involving the destruction of ant nests or shelters, but tool use has not been reported. We conclude that myrmecovory is widespread amongst Neotropical primates but on average contributes only a minor proportion of the diet. The diversity of foraging technics employed and lack of tool use in Neotropical primate myrmecovory, even for ants with functional stings and aggressive biting, suggests that tool use for myrmecovory in hominids has not evolved in response to ant defences but is a consequence of enhanced cognitive skills that evolved under other selection pressures.

Large-scale comparative small RNA analyses reveal genomic structural variants in driving expression dynamics and differential selection pressures on distinct small RNA classes during tomato domestication

Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, through comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions, we demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nt heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nt hc-siRNAs likely contribute to the alteration of mRNA gene expression during recent evolution of tomato, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families, highlighting different selection pressures on miRNAs compared to phasiRNAs and 24-nt hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.

StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication

The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.

Ecology dictates the value of memory for foraging bees

Summary“Ecological intelligence” hypotheses posit that the benefits of cognitive investment vary with foraging ecology, and provide a key framework for understanding the evolution of animal learning and memory1–4. However, although certain ecological selection pressures have been found to correlate with brain or neural region size5–8, empirical evidence to show that any specific cognitive trait is useful in certain environments but not others is currently lacking. Here, we assay the short-term memory of bumblebee (Bombus terrestris audax) workers from 25 identically reared colonies, before allowing each colony to forage in a landscape where forage availability varies seasonally. Through analysis of the bees’ lifetime foraging careers, comprising >1700 foraging trips over two years, we show that performance on a task designed to test short-term memory predicts individual foraging efficiency – a fitness proxy that is key to colony reproductive output – in plentiful spring foraging conditions. However, this relationship is reversed during the summer floral dearth, when the costs of cognitive investment may outweigh the benefits. Our results provide evidence that the value of a cognitive trait depends upon the prevailing ecological conditions and suggest that temporal changes in that environment could place contrasting selection pressures on memory within a single species.