The heat tolerance of corals is largely determined by their microbial photosymbionts (Symbiodiniaceae, colloquially known as zooxanthellae). Therefore, manipulating symbiont communities may enhance the ability of corals to survive summer heatwaves. Although heat-tolerant and -sensitive symbiont species occur in nature, even corals that harbour naturally tolerant symbionts have been observed to bleach during summer heatwaves. Experimental evolution (i.e., laboratory selection) of Symbiodiniaceae cultures under elevated temperatures has been successfully used to enhance their upper thermal tolerance, both in vitro and, in some instances, following their reintroduction into corals. In this review, we present the state of this intervention and its potential role within coral reef restoration, and discuss the next critical steps required to bridge the gap to implementation.

BACKGROUND: The emergence of SARS-CoV-2 variants with mutations associated with increased transmissibility and virulence is a public health concern in Ontario, Canada. Characterizing how the mutational patterns of the SARS-CoV-2 genome have changed over time can shed light on the driving factors, including selection for increased fitness and host immune response, that may contribute to the emergence of novel variants. Moreover, the study of SARS-CoV-2 in the microcosm of Ontario, Canada can reveal how different province-specific public health policies over time may be associated with observed mutational patterns as a model system.
OBJECTIVE: This study aimed to perform a comprehensive analysis of single base substitution (SBS) types, counts, and genomic locations observed in SARS-CoV-2 genomic sequences sampled in Ontario, Canada. Comparisons of mutational patterns were conducted between sequences sampled during 4 different epochs delimited by major public health events to track the evolution of the SARS-CoV-2 mutational landscape over 2 years.
METHODS: In total, 24,244 SARS-CoV-2 genomic sequences and associated metadata sampled in Ontario, Canada from January 1, 2020, to December 31, 2021, were retrieved from the Global Initiative on Sharing All Influenza Data database. Sequences were assigned to 4 epochs delimited by major public health events based on the sampling date. SBSs from each SARS-CoV-2 sequence were identified relative to the MN996528.1 reference genome. Catalogues of SBS types and counts were generated to estimate the impact of selection in each open reading frame, and identify mutation clusters. The estimation of mutational fitness over time was performed using the Augur pipeline.
RESULTS: The biases in SBS types and proportions observed support previous reports of host antiviral defense activity involving the SARS-CoV-2 genome. There was an increase in U>C substitutions associated with adenosine deaminase acting on RNA (ADAR) activity uniquely observed during Epoch 4. The burden of novel SBSs observed in SARS-CoV-2 genomic sequences was the greatest in Epoch 2 (median 5), followed by Epoch 3 (median 4). Clusters of SBSs were observed in the spike protein open reading frame, ORF1a, and ORF3a. The high proportion of nonsynonymous SBSs and increasing dN/dS metric (ratio of nonsynonymous to synonymous mutations in a given open reading frame) to above 1 in Epoch 4 indicate positive selection of the spike protein open reading frame.
CONCLUSIONS: Quantitative analysis of the mutational patterns of the SARS-CoV-2 genome in the microcosm of Ontario, Canada within early consecutive epochs of the pandemic tracked the mutational dynamics in the context of public health events that instigate significant shifts in selection and mutagenesis. Continued genomic surveillance of emergent variants will be useful for the design of public health policies in response to the evolving COVID-19 pandemic.

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotic have been proposed, however the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation have been described but more in-depth characterisations are needed, using methodologies that confirm functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

BACKGROUND: Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures.
RESULTS: Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection.
CONCLUSIONS: Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.

Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed \'conserved editing with non-conserved recoding\' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.

Vertebrates exhibit sexual dimorphism in response to infectious diseases and in morbidity and mortality rates to various pathogens. Females are generally more immunocompetent than males, despite their increased reproductive burden and the immunosuppressive effects of gestation. In addition, females generally have lower incidences of cancer compared to males; however, they have higher rates of autoimmune disorders. These sex differences may be a result of life history differences, sexual selection, genetics, and/or the physiological effects of hormones. As highly social mammals with complex life histories, primates offer a unique opportunity to investigate the evolution of enhanced female immunocompetence. This review aims to examine the evidence of this immunity gap, understand current hypotheses for its evolution, and explore the potential role of X chromosome specific genes and heterozygosity within this framework.

AbstractDuring periods of torpor, hibernators can reduce metabolic rate (MR) and body temperature (Tb) substantially. However, to avoid physiological dysfunction at low temperatures, they defend Tb at a critical minimum, often between ~0°C and 10°C via an increase in MR. Because thermoregulation during torpor requires extra energy, individuals with lower Tb\'s and thus minimal MR during torpor should be selected in colder climates. Such inter- and intraspecific variations occur in some placental mammals, but for the evolutionary separate marsupials, available information is scarce. Marsupial eastern pygmy possums (Cercartetus nanus; ~22 g body mass), widely distributed along the Australian southeastern coast including subtropical to alpine areas, were used to test the hypothesis that the defended Tb of torpid individuals is related to the climate of their habitat. Possums were captured from five regions, 1,515 km apart, with midwinter (July) minimum environmental temperatures (min Tenv\'s) ranging from -3.9°C to 6.6°C. Captive possums in deep torpor were slowly cooled with ambient temperature (Ta), while their MR was measured to determine the minimum torpor metabolic rate (TMR), the Ta at which their MR increased for thermoregulation (min Ta), and the corresponding minimum Tb (min Tb). Partial least squares regression analysis revealed that Ta and Tenv were the strongest explanatory variables for the min Tb. The min Tb and Ta were also correlated with latitude but not elevation of the capture sites. However, the best correlations were observed between the min Tenv and the min Tb and Ta for individuals experiencing min Tenv>0°C; these individuals thermoconformed to min Ta\'s between -0.8°C and 3.7°C, and their min Tb ranged from 0.5°C to 6.0°C and was 0.5°C-2.6°C below the min Tenv at the capture site. In contrast, individuals experiencing a min Tenv of -3.9°C regulated Tb at 0.6°C±0.2°C or 4.5°C above the Tenv. The minimum TMR of all possums did not differ with Ta and thus did not differ among populations and was 2.6% of the basal MR. These data provide new evidence that thermal variables of marsupials are subject to regional intraspecific variation. It suggests that min Tb is a function of the min Tenv but only above 0°C, perhaps because the Tb-Ta differential for torpid possums in the wild, at a min Tenv of -3.9°C, remains small enough to be compensated by a small increase in MR and does not require the physiological capability for a reduction of Tb below 0°C.

Genetic changes arising in human pluripotent stem cells (hPSC) upon culture may bestow unwanted or detrimental phenotypes to cells, thus potentially impacting on the applications of hPSCs for clinical use and basic research. In the 20 years since the first report of culture-acquired genetic aberrations in hPSCs, a characteristic spectrum of recurrent aberrations has emerged. The preponderance of such aberrations implies that they provide a selective growth advantage to hPSCs upon expansion. However, understanding the consequences of culture-acquired variants for specific applications in cell therapy or research has been more elusive. The rapid progress of hPSC-based therapies to clinics is galvanizing the field to address this uncertainty and provide definitive ways both for risk assessment of variants and reducing their prevalence in culture. Here, we aim to provide a timely update on almost 20 years of research on this fascinating, but a still unresolved and concerning, phenomenon.