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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.
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Epistasis Genética , Evolución Molecular , Proteínas Mitocondriales/genética , Selección Genética , Sustitución de Aminoácidos/genética , Aminoácidos/genética , Animales , Hongos/genética , Genoma Mitocondrial/genética , Mitocondrias/genética , Filogenia , Conformación Proteica , Mapas de Interacción de Proteínas/genéticaRESUMEN
Insertions and deletions of lengths not divisible by 3 in protein-coding sequences cause frameshifts that usually induce premature stop codons and may carry a high fitness cost. However, this cost can be partially offset by a second compensatory indel restoring the reading frame. The role of such pairs of compensatory frameshifting mutations (pCFMs) in evolution has not been studied systematically. Here, we use whole-genome alignments of protein-coding genes of 100 vertebrate species, and of 122 insect species, studying the prevalence of pCFMs in their divergence. We detect a total of 624 candidate pCFM genes; six of them pass stringent quality filtering, including three human genes: RAB36, ARHGAP6, and NCR3LG1. In some instances, amino acid substitutions closely predating or following pCFMs restored the biochemical similarity of the frameshifted segment to the ancestral amino acid sequence, possibly reducing or negating the fitness cost of the pCFM. Typically, however, the biochemical similarity of the frameshifted sequence to the ancestral one was not higher than the similarity of a random sequence of a protein-coding gene to its frameshifted version, indicating that pCFMs can uncover radically novel regions of protein space. In total, pCFMs represent an appreciable and previously overlooked source of novel variation in amino acid sequences.
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Mutación INDEL , Proteínas , Secuencia de Aminoácidos , Humanos , Mutación , Sistemas de Lectura Abierta , Proteínas/genéticaRESUMEN
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.
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Aminoácidos , Gripe Humana , Sustitución de Aminoácidos , Aminoácidos/genética , Evolución Molecular , Humanos , Gripe Humana/genética , Filogenia , Alineación de SecuenciaRESUMEN
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.
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Metales Pesados/metabolismo , Filogenia , Plantas/metabolismo , Hidrocarburos Policíclicos Aromáticos/metabolismo , Contaminantes del Suelo/metabolismo , Monitoreo del Ambiente , SueloRESUMEN
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.
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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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The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021-early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between 16-29 December 2021, which was the earliest known instance of a large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR-positive. Among the 118 residents for whom the variant had been tested by whole-genome sequencing, 111 (94.1%) were found to carry the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported a previous infection of COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sub-lineage of the Omicron variant. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint Petersburg and has spread to other regions of Russia and even to other countries. The rapid spread of the Omicron variant in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/epidemiología , Filogenia , Brotes de Enfermedades , Federación de Rusia/epidemiologíaRESUMEN
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.
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COVID-19 , Esguinces y Distensiones , Humanos , SARS-CoV-2/genética , COVID-19/epidemiología , Genómica , Federación de Rusia/epidemiologíaRESUMEN
Evolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin's lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented the binding of known immunogenic SARS-CoV-2 HLA class I antigens. By experimentally assessing the effect of a subset of the escape mutations, we show that they resulted in a loss of as much as ~1% of effector CD8 T cell response. Our results indicate that CD8 T cell escape represents a major underappreciated contributor to SARS-CoV-2 evolution in humans.
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COVID-19 , Linfocitos T Citotóxicos , Humanos , SARS-CoV-2 , Linfocitos T CD8-positivos , Anticuerpos Neutralizantes , Anticuerpos Antivirales , Glicoproteína de la Espiga del CoronavirusRESUMEN
In rural areas, research on the environment in native (untaught) soils is important to understand the rate of pedogenesis and to prevent the problems associated with hidden huger. In this article, original data on vegetation, chemical properties and elemental and mineralogical composition of Kastanozems (Protosalic, Siltic) and Hypersalic Solonetz (Siltic) of the small gully catchment (2 ha in total) located at the NE Ergeni Upland (Western Kalmykia, Russia) were presented. Vegetation was described and cut off (to characterize an aboveground biomass) at 13 key plots of 1 × 1 m. The list of species of the small gully catchment area amounts to 23 species (predominantly, perennial herbs) belonging to 13 families and 11 orders. The main dominants are Artemisia lerchiana, A. austriaca, Festuca valesiaca and Poa bulbosa. Soils were described and sampled in 11 cross-sections and two key plots (0 - 10 cm topsoil sampling). In soil water extracts (79 samples in total), electrical conductivity (EC) and pH were measured. In soil samples, particle size distribution, soil organic carbon and CaCO3 contents, total concentration of all the macro elements, some trace (Cl, Nb, Rb, Th, Y, Zr) and potentially toxic elements (As, Co, Cr, Cu, Ni, Pb, Sr, V, and Zn) were described. Moreover, the concentration of three mobile fractions of elements (Li, Be, B, Na, Mg, Al, Si, P, S, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Sr, Ba, Cd, Pb) measured using Inductively Coupled Plasma Atomic Emission Spectrometry (AES-ICP) was presented. Geochemical indexes of weathering (R - Silica/Alumina, CIW - Chemical Index of Weathering, CIA - Chemical Index of Alteration, WIP - Weathering Index of Parker, PWI -Product of Weathering Index, Vogt Ratio, PIA - Plagioclase Index of Alteration, STI - Silica-Titanium Index, B/A - Bases/Alumina, B/R - Bases/R2O3, Si/R - Silica/R2O3, Weathering indexes WI-1 and WI-2, Si/Ses - Silica/Sesquioxides, Si/Fe - Silica/Iron, a - Potassium/Sodium, ba-1 - (Potassium-Sodium)/Alumina, ba-2 - (Calcium-Magnesium)/Alumina, Ba - (Potassium-Sodium-Calcium)/Alumina) were calculated. In 12 bulk soil samples from Kastanozems and Solonetz, mineralogy (X-Ray diffractometry, the Rietveld full-pattern fitting method for quantitative analysis) was described. Data obtained can be used for more confident identification of pollution sources and pollutants' migration routes, as well as for more effective land-use management, calculating the required doses of nutrients and for adaptation of land use.
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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.
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Salinidad , Suelo , Filogenia , Mar Caspio , Plantas , EcosistemaRESUMEN
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.
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COVID-19 , SARS-CoV-2 , COVID-19/epidemiología , Humanos , Mutación , Pandemias , Federación de Rusia/epidemiología , SARS-CoV-2/genética , Glicoproteína de la Espiga del CoronavirusRESUMEN
The article highlights the course of long-term SARS-CoV-2 infection in a patient with a secondary immunodeficiency developed with B-cell-depleting therapy of the underlying disease. Analysis of the intrapatient virus evolution revealed an inpatient S:G75A mutation that alters the 72GTNGTKR78 motif of the S-protein, with a possible role in binding to alternative cellular receptors. Therapy with a ready-made COVID-19-globulin preparation (native human immunoglobulin G (IgG) derived from the plasma of convalescent COVID-19-patients) resulted in rapid improvement of the patient's condition, fast, and stable elimination of the virus, and passive immunization of the patient for at least 30 days. The results suggest the use of products containing neutralizing antibodies opens new prospects for treatment algorithms for patients with persistent coronavirus infection, as well as for passive immunization schemes for patients with a presumably reduced specific response to vaccination.
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , Anticuerpos Antivirales , Inmunización Pasiva/métodos , Anticuerpos NeutralizantesRESUMEN
Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to the emergence of multiple sublineages, most of which are well-mixed between countries. By contrast, here we show that nearly the entire Delta epidemic in Russia has probably descended from a single import event, or from multiple closely timed imports from a single poorly sampled geographic location. Indeed, over 90 per cent of Delta samples in Russia are characterized by the nsp2:K81N + ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect rather than a transmission advantage. The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.
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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.
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Complejo I de Transporte de Electrón/genética , Predisposición Genética a la Enfermedad , Genómica , Mitocondrias/genética , Mutación , Alelos , Sustitución de Aminoácidos , Complejo I de Transporte de Electrón/metabolismo , Estudio de Asociación del Genoma Completo , Genómica/métodos , Humanos , Mitocondrias/metabolismo , Filogenia , Selección GenéticaRESUMEN
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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Queroseno , Taiga , Asia Oriental , Humanos , Filogenia , Federación de Rusia , SueloRESUMEN
BACKGROUND: Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to emergence of multiple sublineages, many of which are well-mixed between countries. AIM: Here, we aim to study the emergence and spread of the Delta lineage in Russia. METHODS: We use a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread. RESULTS: We show that nearly the entire Delta epidemic in Russia has probably descended from a single import event despite genetic evidence of multiple Delta imports. Indeed, over 90% of Delta samples in Russia are characterized by the nsp2:K81N+ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect. CONCLUSION: The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.
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Research on the environment in recent soils is important to understand geochemical processes in coastal landscapes and the rate of pedogenesis. In this article, we present original data on Gleyic Solonchaks (Loamic) and vegetation described at the eastern part of the Terek-Kuma lowland (Northern Dagestan, Russia). At the key site of 45â¯×â¯30â¯m released from water 293±13 years calBP, we described vegetation at 345 plots of 2â¯×â¯2â¯m (4 m2) and soil properties in 58 auger holes and 2 pedons, the latter characterizing a typical microhigh with Tamarix and a microlow with saltworts. The flora of the sites amounts to 32 species (predominantly, halophytes) belonging to 11 families. Shrubs represented by tamarixes are the dominant. Under their crowns, dense herb and grass microcommunities with a predominance of tall Puccinellia gigantea occur. Sparse stunted halophytic plants (Petrosimonia, Frankenia, Puccinellia) occupy open habitats between shrubs. In soil water extracts from auger holes (696 samples in total), we measured electrical conductivity (EC) and pH. In 49 soil samples from pedons, we described particle size distribution, total concentration of macro elements (Al, Ca, Fe, K, as well as Mg, Mn, P, Ti, and Si) and trace elements (As, Co, Cr, Cu, Ni, Pb, Sr, and Zn), EC, pH, basicity (HCO3 - and CO3 2-) as well as the content of cations (Ca2+, Mg2+, Na+, and K +) and anions (SO4 2- and Cl-) in soil water extracts. Gleyic Solonchaks (Loamic) with bulk density of 1.35±0.12â¯g/cm3 (mean and standard deviation) contain SiO2 69±8%> Al2O3 11.8⯱â¯3.5 and CaO 7.5⯱â¯2.5%, Fe2O3 3.6⯱â¯1.4%, K2O 2.0⯱â¯0.3 and MgO 1.9⯱â¯0.4%> TiO2 0.62±0.25%> P2O5 0.14±0.06% and MnO 713±268â¯mg/kg> Sr 481±262â¯mg/kg > Cr 79±9â¯mg/kg > V 76±36, Zn 68±31, Cu 62±10, and Ni 50±17â¯mg/kg, Co 32±6â¯mg/kg> Pb 11±6â¯mg/kg> As 5.6⯱â¯1.4â¯mg/kg. The particle-size distribution is (WRB system,%): clay 13±5, fine silt 34±12, coarse silt 30±18, as well as very fine sand 11±10, fine sand 7.3⯱â¯10.5, medium sand 3.5⯱â¯5.8, coarse sand 0.9⯱â¯3.2, and very coarse sand 0.08±0.31 (nâ¯=â¯38). Soil water extract has EC 9.4⯱â¯4.1 dSm/m (soils: water ratio of 1:2.5, nâ¯=â¯713), contains Na+ 15.9⯱â¯7.0 > Ca2+7.3⯱â¯5.0 and Mg2+ 7.3⯱â¯3.1 > Kâ¯+â¯0.30±0.20 cmol(eq)/kg, as well as Cl- 15.7⯱â¯7.3 and SO4 2- 14.6⯱â¯7.9 > HCO3 - 0.55±0.15 > CO3 2 -< 0.01 cmol(eq)/kg, and has pH 7.9⯱â¯0.3 (soils: water ratio of 1:5, nâ¯=â¯21). In soil paste, pH is 8.3⯱â¯0.2 (nâ¯=â¯461). Data obtained can be used for more confident identification of pollution sources and pollutants' migration routes and more effective conservation and remediation of human-affected soils at the Caspian Sea coast.
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Research on migration of chemical elements (ChEs) in soils is important for the understanding of geochemical processes in polluted and undisturbed landscapes. In this article, we report original data on Anthric Chernozems and Anthric Planosols within a small gully's catchment area in the Trans Urals (Russia). Mean total concentrations of 24 ChEs and content of mobile fractions (F1 - exchangeable, F2 - bound within organo-mineral complexes and F3 - bound with Fe and Mn hydroxides) of 61 ChEs including macro elements (Al, Ca, Fe, K, Mg, Mn, Na, P, Ti, S, Si), heavy metals (Ba, Co, Cr, Cu, Ni, Pb, Rb, Sr, Th, U, V, Zn), trace elements (Ag, As, B, Be, Bi, Br, Cd, Cs, Ge, Hf, Li, Mo, Nb, Pd, Sb, Sc, Se, Sn, Ta, Te, Tl, W, Zr) and rare earth elements (Ce, Er, Eu, Gd, La, Lu, Nd, Pr, Sm, Tb, Tm, Dy, Ho, Y, Yb) are determined from in a total of 60 samples from topsoil and subsoil of Anthric Chernozems and Anthric Planosols. The data obtained also include pH-value, total organic carbon content (TOC), seven particle-size classes (<2, 2-6.3, 6.3-20, 20-63, 63-200, 200-630 and 630-2000 µm), electrical conductivity and chemical composition (cations and anions) of water extracts as well as soil mineralogical composition.
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Amino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is â¼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared with a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.