An ecological perspective on microbial genes of unknown function in soil

Genes that remain hypothetical, uncharacterized, and unannotated comprise a substantial portion of metagenomic datasets and are likely to be particularly prevalent in soils where poorly characterized taxa predominate. Documenting the prevalence, distribution, and potential roles of these genes of unknown function is an important first step to understanding their functional contributions in soil communities. We identified genes of unknown function from 50 soil metagenomes and analyzed their environmental distributions and ecological associations. We found that genes of unknown function are prevalent in soils, particularly fine-textured, higher pH soils that harbor greater abundances of Crenarchaeota, Gemmatimonadota, Nitrospirota, and Methylomirabilota. We identified 43 dominant (abundant and ubiquitous) gene clusters of unknown function and determined their associations with soil microbial phyla and other “known” genes. We found that these dominant unknown genes were commonly associated with microbial phyla that are relatively uncharacterized, with the majority of these dominant unknown genes associated with mobile genetic elements. This work demonstrates a strategy for investigating genes of unknown function in soils, emphasizes the biological insights that can be learned by adopting this strategy, and highlights specific hypotheses that warrant further investigation regarding the functional roles of abundant and ubiquitous genes of unknown function in soil metagenomes.

Examining the Association between the COVID-19 Pandemic and Self-Harm Death Counts in Four Canadian Provinces

Governments implemented lockdowns and other physical distancing measures to stop the spread of SARS-CoV-2 (COVID-19). Resulting unemployment, income loss, poverty, and social isolation, coupled with daily reports of dire news about the COVID-19 pandemic, could serve as catalysts for increased self-harm deaths (SHD). This ecological study examined whether observed SHD counts were higher than predicted SHD counts during the pandemic period in the Canadian provinces of Alberta, British Columbia, Ontario, and Quebec. The study also explored whether SHD counts during the pandemic were affected by lockdown severity (measured using the lockdown stringency index [LSI]) and COVID-19 case numbers. We utilized publicly available SHD data from January 2018 through November 2020, and employed AutoRegressive Integrated Moving Average (ARIMA) modelling, to predict SHD during the COVID-19 period (March 21 to November 28, 2020). We used Poisson and negative binomial regression to assess ecological associations between the LSI and COVID-19 case numbers, controlling for seasonality, and SHD counts during the COVID-19 period. On average, observed SHD counts were lower than predicted counts during this period (p < 0.05 [except Alberta]). Additionally, LSI and COVID-19 case numbers were not statistically significantly associated with SHD counts.

The first molecular insight into the genus Turanium Baeckmann, 1922 (Coleoptera: Cerambycidae: Callidiini) with a description of a new species from Middle Asia

This paper sheds the first light on the phylogeny of the Central Asian genus Turanium Baeckmann, 1922. By applying an integrative taxonomy approach, we revealed and described a new species from Kyrgyzstan—Turanium losi Karpiński, Plewa &amp; Hilszczański sp. nov. Distinguishing characters from closely related Turanium pilosum (Reitter, 1891) are presented and their ecological associations are discussed. The key characters, including the male terminalia, were examined by means of scanning electron microscopy. High-quality stacked photographs of the habitus of the specimens are presented for both species and their geographical distributions are mapped. While the new species shows stable morphological characters that allow its differentiation from T. pilosum and the COI genetic distance between them is approx. 3%, the different species delimitation methods gave discordant results. Although the new species remained unrecognized for so long, it seems that these cerambycids are common in the region and both can be considered potentially invasive as they are apparently highly polyphagous. It has also been documented that they occur sympatrically in Kyrgyzstan. Both the Bayesian and maximum likelihood analyses of COI sequences confirmed the monophyly of the genus Turanium with strong support (PP 1 and BS 90, respectively). Moreover, the recently revealed polyphyly of the tribe Callidiini was supported by our analyses and, consequently, the discussion on the establishment of a new tribe Ropalopini is raised. This study further corroborates the effectiveness of DNA barcoding as a tool in detecting new species and provides some of the first sequences for Central Asian cerambycids, which remain almost completely unknown in terms of molecular studies.

Predictions of primate–parasite coextinction

Future biodiversity loss threatens the integrity of complex ecological associations, including among hosts and parasites. Almost half of primate species are threatened with extinction, and the loss of threatened hosts could negatively impact parasite associations and ecosystem functions. If endangered hosts are highly connected in host–parasite networks, then future host extinctions will also drive parasite extinctions, destabilizing ecological networks. If threatened hosts are not highly connected, however, then network structure should not be greatly affected by the loss of threatened hosts. Networks with high connectance, modularity, nestedness and robustness are more resilient to perturbations such as the loss of interactions than sparse, nonmodular and non-nested networks. We analysed the interaction network involving 213 primates and 763 parasites and removed threatened primates (114 species) to simulate the effects of extinction. Our analyses revealed that connections to 23% of primate parasites (176 species) may be lost if threatened primates go extinct. In addition, measures of network structure were affected, but in varying ways because threatened hosts have fewer parasite interactions than non-threatened hosts. These results reveal that host extinctions will perturb the host–parasite network and potentially lead to secondary extinctions of parasites. The ecological consequences of these extinctions remain unclear. This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.

Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages

Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual’s genetic makeup influences its tolerance of karyotypic imbalance. Here we investigated within-species variation in aneuploidy prevalence and tolerance, using Saccharomyces cerevisiae as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The relationships between lineages with high aneuploidy frequencies suggest that increased aneuploidy prevalence emerged multiple times in S. cerevisiae evolution. Separate from aneuploidy prevalence, analyzing growth phenotypes revealed that some genetic backgrounds—such as the European Wine lineage—show fitness costs in aneuploids compared to euploids, whereas other clades with high aneuploidy frequencies show little evidence of major deleterious effects. Our analysis confirms that chromosome gain can produce phenotypic benefits, which could influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.

Genetic variation in aneuploidy prevalence and tolerance across the Saccharomyces cerevisiae phylogeny

Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual's genetic makeup influences its tolerance of karyotypic imbalance. Here we took a population genetics perspective to investigate the selective forces influencing aneuploidy prevalence in Saccharomyces cerevisiae populations as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The phylogenetic context of lineages showing high aneuploidy rates suggests that increased aneuploidy frequency arose multiple times in S. cerevisiae evolution. Separate from aneuploidy frequency, analyzing growth phenotypes reveals that some backgrounds – such as European Wine strains – show fitness costs upon chromosome duplication, whereas other clades with high aneuploidy rates show little evidence of major deleterious effects. Our analysis confirms that chromosome amplification can produce phenotypic benefits that can influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.

Deep Roots and Splendid Boughs of the Global Plant Virome

Land plants host a vast and diverse virome that is dominated by RNA viruses, with major additional contributions from reverse-transcribing and single-stranded (ss) DNA viruses. Here, we introduce the recently adopted comprehensive taxonomy of viruses based on phylogenomic analyses, as applied to the plant virome. We further trace the evolutionary ancestry of distinct plant virus lineages to primordial genetic mobile elements. We discuss the growing evidence of the pivotal role of horizontal virus transfer from invertebrates to plants during the terrestrialization of these organisms, which was enabled by the evolution of close ecological associations between these diverse organisms. It is our hope that the emerging big picture of the formation and global architecture of the plant virome will be of broad interest to plant biologists and virologists alike and will stimulate ever deeper inquiry into the fascinating field of virus–plant coevolution.