Fitness conferred by the same allele may differ between genotypes and environments, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the ...course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that confer different fitness in different groups of species from combined sequence and phylogenetic data. Using the fact that the probability of a substitution to an amino acid depends on its fitness, our method looks for amino acids such that substitutions to them occur more frequently in one group of lineages than in another. We validate our method using simulated evolution of a protein site under different scenarios and show that it has high specificity for a wide range of assumptions regarding the underlying changes in selection, while its sensitivity differs between scenarios. We apply our method to the env gene of two HIV-1 subtypes, A and B, and to the HA gene of two influenza A subtypes, H1 and H3, and show that the inferred fitness changes are consistent with the fitness differences observed in deep mutational scanning experiments. We find that changes in relative fitness of different amino acid variants within a site do not always trigger episodes of positive selection and therefore may not result in an overall increase in the frequency of substitutions, but can still be detected from changes in relative frequencies of different substitutions.
The gradual drying up of saltwater bodies creates habitats that are characterised by changing environmental conditions and might be available only for a subset of plants from the local flora. Using ...two terrestrial areas with different ages on the Caspian Coast as a chronosequence, we investigated factors including microtopography, ground water level and soil salinity that drive plant community succession after the retreat of the sea. Vegetation of the two key sites appearing after the retreat of the Caspian Sea about 365 and 1412 years ago were compared in terms of both evolutionary and ecological traits of plants. Both edaphic conditions and vegetation differed between the two sites with harsher edaphic conditions and more xerophytes on the elder site. Species that grew only in the 'early' site were dispersed across the phylogenetic tree, but their loss on the 'late' site was not random. Species that grew only on the 'late' site were phylogenetically clustered. On the level of microtopography, elevated spots were more densely populated in the 'early' site than lowered spots, but on the 'late' site the situation was opposite. The main edaphic factors that drive the difference in vegetation composition between the two sites are likely salinity and moisture. During environmental changes, different plant traits are important to survive and to appear in the community de novo. Microtopography is important for forming plant communities, and its role changes with time.
Disease caused by mutations of mitochondrial DNA (mtDNA) are highly variable in both presentation and penetrance. Over the last 30 years, clinical recognition of this group of diseases has increased. ...It has been suggested that haplogroup background could influence the penetrance and presentation of disease-causing mutations; however, to date there is only one well-established example of such an effect: the increased penetrance of two Complex I Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducts the most extensive investigation to date into the importance of haplogroup context in the pathogenicity of mtDNA mutations in Complex I. We searched for proven human point mutations across more than 900 metazoans finding human disease-causing mutations and potential masking variants. We found more than a half of human pathogenic variants as compensated pathogenic deviations (CPD) in at least in one animal species from our multiple sequence alignments. Some variants were found in many species, and some were even the most prevalent amino acids across our dataset. Variants were also found in other primates, and in such cases, we looked for non-human amino acids in sites with high probability to interact with the CPD in folded protein. Using this "local interactions" approach allowed us to find potential masking substitutions in other amino acid sites. We suggest that the masking variants might arise in humans, resulting in variability of mutation effect in our species.
In 2021, the COVID-19 pandemic was characterized by global spread of several lineages with evidence for increased transmissibility. Throughout the pandemic, Russia has remained among the countries ...with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern that have spread globally by late 2020, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none have been sampled in Russia before the end of 2020. Instead, between summer 2020 and spring 2021, the epidemic in Russia has been characterized by the spread of two lineages that were rare in most other countries: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). Their frequency has increased concordantly in different parts of Russia. On top of these lineages, in late December 2020, alpha (B.1.1.7) emerged in Russia, reaching a frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, B.1.1.524 and B.1.1.525, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140–142, S:Δ144 or S:Δ136–144), and nsp6:Δ106–108 (also known as ORF1a:Δ3675–3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.524 and B.1.1.525, 15.2% (95% C.I.: 7.6%-28.2%). Although these variants have been displaced by the onset of delta variant in May-June 2021, lineages B.1.1.317, B.1.1.397+, AT.1, B.1.1.524 and B.1.1.525 and the combinations of mutations comprising them that are found in other lineages merit monitoring.
The present study is the field experiment on kerosene pollution impact on southern taiga plant communities. Experimental sites were located in a mixed forest, a deciduous forest, a sedge fen and a ...wet meadow within the Amur Region of the Russian Far East. Kerosene loads from 1 to 500 g/kg of soil were applied to 50 × 50 cm plots in three replications and their effects on number of species and projective cover of ground vegetation were analysed in 1.5 months and 1 year after exposure. Statistical analyses of data included Student's t-test, Friedman ANOVA and correlation coefficient (r). Phylogenetic analysis was carried out for herbaceous plants on experimental plots. The highest susceptibility to kerosene pollution was found in the mixed forest, where the edificator species (Pteridium aquilinum subsp. pinetorum) was significantly suppressed by the kerosene load of only 1 g/kg of soil. Wetland communities regenerated faster than ground vegetation of forests, especially, in tests with high (>25 g/kg) kerosene loads. The wet meadow community was the most resistant to kerosene pollution, i.e., despite significant decreases in projective cover and number of species after exposure to kerosene loads of 5 and 25 g/kg in the first season, it had the highest regeneration success in the next season. In our study, the kerosene load of 25 g/kg of soil was the threshold level of pollution, above which there were significant structural changes in the studied plant communities. Depending on their abilities to resist kerosene pollution and to regenerate in the next year, dominant species of the studied plant communities were arranged in the following ascending order: Pteridium aquilinum ssp. pinetorum, Convallaria keiskei < Carex cespitosa, Calamagrostis purpurea < Lespedeza bicolor < Vaccinium uliginosum.
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•We discovered the impact of kerosene pollution on southern taiga phytocenoses.•Kerosene load of 25 g/kg of soil causes significant changes in vegetation structure.•The most vulnerable species to kerosene is Pteridium aquilinum subsp. pinetorum.•The most resistant species to kerosene is Vaccinium uliginosum.•Wetland communities demonstrate lower damage and higher recovery rate than forests.
Increasing concentration of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) in the soil may impose a serious threat to living organisms due to their toxicity and the ability to ...accumulate in plant tissues. The present review focuses on the phylogenetic relationships, sources, biotransformation and accumulation potential of hyperaccumulators for the priority HMs and PAHs. This review provides an opportunity to reveal the role of hyperaccumulators in removal of HMs and PAHs from soils, to understand the relationships between pollutants and their influence on the environment and to find potential plant species for soil remediation. The phylogenetic analysis results showed that the hyperaccumulators of some chemicals (Co, Cu, Mn, Ni, Zn, Cd) are clustered on the evolutionary tree and that the ability to hyperaccumulate different pollutants can be correlated either positively (Cd–Zn, Pb–Zn, Co–Cu, Cd–Pb) or negatively (Cu–PAHs, Co–Cd, Co–PAHs, Ni–PAHs, Cu–Ni, Mn–PAHs). Further research needs to be extended on the focus of commercializing the techniques including the native hyperaccumulators to remediate the highly contaminated soils.
The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for ...distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them.
In 2020, SARS-CoV-2 has spread rapidly across the globe, with most nations failing to prevent or substantially delay its introduction. While many countries have imposed some limitations on ...trans-border passenger traffic, the effect of these measures on the global spread of COVID-19 strains remains unclear. Here, we report an analysis of 3206 whole-genome sequences of SARS-CoV-2 samples from 78 regions of Russia covering the period before the spread of variants of concern (between March and November 2020). We describe recurring imports of multiple COVID-19 strains into Russia throughout this period, giving rise to 457 uniquely Russian transmission lineages, as well as repeated cross-border transmissions of local circulating variants out of Russia. While the phylogenetically inferred rate of cross-border transmissions was somewhat reduced during the period of the most stringent border closure, it still remained high, with multiple inferred imports that each led to detectable spread within the country. These results indicate that partial border closure has had little effect on trans-border transmission of variants, which helps explain the rapid global spread of newly arising SARS-CoV-2 variants throughout the pandemic.
Amino acid preferences at a protein site depend on the role of this site in protein function and structure as well as on external constraints. All these factors can change in the course of evolution, ...making amino acid propensities of a site time-dependent. When viral subtypes divergently evolve in different host subpopulations, such changes may depend on genetic, medical, and sociocultural differences between these subpopulations. Here, using our previously developed phylogenetic approach, we describe sixty-nine amino acid sites of the Gag protein of human immunodeficiency virus type 1 (HIV-1) where amino acids have different impact on viral fitness in six major subtypes of the type M. These changes in preferences trigger adaptive evolution; indeed, 32 (46 per cent) of these sites experienced strong positive selection at least in one of the subtypes. At some of the sites, changes in amino acid preferences may be associated with differences in immune escape between subtypes. The prevalence of an amino acid in a protein site within a subtype is only a poor predictor for whether this amino acid is preferred in this subtype according to the phylogenetic analysis. Therefore, attempts to identify the factors of viral evolution from comparative genomics data should integrate across multiple sources of information.
Abstract
The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is ...associated with emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process is protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, another closely related midge was discovered, Polypedilum pembai, which is able not only to tolerate desiccation but also to survive multiple desiccation–rehydration cycles. To investigate the evolution of anhydrobiosis in these species, we sequenced and assembled the genome of P. pembai and compared it with P. vanderplanki and also performed a population genomics analysis of several populations of P. vanderplanki and one population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including its amplification in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with postduplication adaptation in the former. Overall, our results suggest an extensive relatively recent and likely ongoing adaptation of the mechanisms of anhydrobiosis.
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