We propose an approach for modeling the pattern of the genetic diversity of microsatellite markers in a population with a mixed breeding strategy. Part of the population is reproduced sexually, and ...part is produced asexually. The method of the proposed simulation is different from others in that it produces a set of microsatellite markers as the outcome of a computer simulation of processes in a fixed-size population. These markers can be utilized with the assistance of available software to calculate various metrics of genetic diversity. Our approach is implemented in Python 3.10 and is accompanied by additional scripts that ensure result compatibility with programs that calculate different population characteristics.
The SARS-CoV-2 is the third coronavirus in addition to SARS-CoV and MERS-CoV that causes severe respiratory syndrome in humans. All of them likely crossed the interspecific barrier between animals ...and humans and are of zoonotic origin, respectively. The origin and evolution of viruses and their phylogenetic relationships are of great importance for study of their pathogenicity and development of antiviral drugs and vaccines. The main objective of the presented study was to compare two methods for identifying relationships between coronavirus genomes: phylogenetic one based on the whole genome alignment followed by molecular phylogenetic tree inference and alignment-free clustering of triplet frequencies, respectively, using 69 coronavirus genomes selected from two public databases. Both approaches resulted in well-resolved robust classifications. In general, the clusters identified by the first approach were in good agreement with the classes identified by the second using K-means and the elastic map method, but not always, which still needs to be explained. Both approaches demonstrated also a significant divergence of genomes on a taxonomic level, but there was less correspondence between genomes regarding the types of diseases they caused, which may be due to the individual characteristics of the host. This research showed that alignment-free methods are efficient in combination with alignment-based methods. They have a significant advantage in computational complexity and provide valuable additional alternative information on the genomes relationships.
Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida ...constitutes one of these novel deep branches that precede the emergence of osmotrophic fungal lifestyle and hold particular significance as the pathogens of algae. Here, we obtain and analyze the genomes of aphelid species Amoeboaphelidium protococcarum and Amoeboaphelidium occidentale. Genomic data unmask the vast divergence between these species, hidden behind their morphological similarity, and reveal hybrid genomes with a complex evolutionary history in two strains of A. protococcarum. We confirm the proposed sister relationship between Aphelida and Fungi using phylogenomic analysis and chart the reduction of characteristic proteins involved in phagocytic activity in the evolution of Holomycota. Annotation of aphelid genomes demonstrates the retention of actin nucleation-promoting complexes associated with phagocytosis and amoeboid motility and also reveals a conspicuous expansion of receptor-like protein kinases, uncharacteristic of fungal lineages. We find that aphelids possess multiple carbohydrate-processing enzymes that are involved in fungal cell wall synthesis but do not display rich complements of algal cell-wall-processing enzymes, suggesting an independent origin of fungal plant-degrading capabilities. Aphelid genomes show that the emergence of Fungi from phagotrophic ancestors relied on a common cell wall synthetic machinery but required a different set of proteins for digestion and interaction with the environment.
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•Strains of A. protococcarum have a complex evolutionary history involving hybridization•Phylogenomic analysis confirms a sister relationship between Aphelida and Fungi•Aphelids demonstrate independent reduction of flagella in two aphelid lineages•Aphelids retain key genes involved in phagocytic activity that were lost in Fungi
Mikhailov et al. report the genomes of Amoeboaphelidium species, revealing vast divergence within the phylum Aphelida and confirming their close phylogenetic relationship to Fungi. Genomic analyses show the conservation of phagocytic proteins, expansions of receptor-like kinases, and evidence for horizontally transferred genes in aphelids.
The taxonomic position and phylogenetic affinities of the endemic North Asian genus Kolhymamnicola Starobogatov and Budnikova, 1976 (Gastropoda: Amnicolidae) remain unknown. To resolve this, we ...studied key morpho-anatomical characteristics of Kolhymamnicola snails and performed a molecular phylogenetic analysis based on sequences of COI mtDNA, 16S rRNA, and 18S rRNA genes. In terms of protoconch microsculpture, operculum, radular teeth, and gill complex morphology, Kolhymamnicola snails do not differ significantly from the North American genera Amnicola Gould and Haldeman, 1840 and Taylorconcha Hershler et al., 1994, and the European genus Marstoniopsis van Regteren Altena 1936. The bifid penis found in Kolhymamnicola is similar to that in the genus Marstoniopsis. The female reproductive anatomy has some features shared by Kolhymamnicola and Taylorconcha (absence of bursa copulatrix, single seminal receptacle in rs2′ position, and ventral channel). The molecular analysis has revealed Taylorconcha as the closest relative to Kolhymamnicola; the COI-based genetic distance between them amounted to 0.113. We discuss the possible time of divergence of these two genera, as well as of European Marstoniopsis and the Baikal Lake endemic family Baicaliidae. The last common ancestor of these groups was widely distributed in Miocene–Pliocene in the Holarctic waterbodies. Recent Kolhymamnicola snails are distributed in Northern Asia, including lakes of the Baikal rift zone. We rank the Baicaliidae as a family rather than a subfamily of Amnicolidae based on their distinct, unique morpho-anatomical characteristics and highly supported separate position on the molecular tree. The tribe Erhaiini Davis and Kuo, 1985 is elevated to the rank of the family, with 3–4 recent genera included. The family Palaeobaicaliidae Sitnikova et Vinarski fam. nov. is established to embrace the Cretaceous North Asian gastropods conchologically similar to the recent Baicaliidae and Pyrgulidae.
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for ...studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species
The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of
has a unique gene order within amphipods, duplications of the four tRNA genes and
, and a long non-coding region, that makes up about two thirds of the genome's size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.
The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical ...differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.
We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.
Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.
In this paper, molecular analyses of Baikal hydras from the '
group', based on COI and ITS1-5.8S-ITS2, and morphological analysis of their holotrichous isorhizas, were performed. Low genetic ...diversity and shared haplotypes were found between
Pallas, 1766 and
Swarczewsky, 1923 specimens, which is evidence of the mixing of these lineages. Genetic distances among all Baikal hydras (0.006) were less than the interspecific distances of other hydras. The size of hydras and proportions of their holotrichous isorhizas varied depending on microhabitat and environmental conditions. Our combined molecular and morphological approach proves that
is synonymous with
.
While the impact of climate fluctuations on the demographic histories of species caused by changes in habitat availability is well studied, populations of species from systems without geographic ...isolation have received comparatively little attention. Using CO1 mitochondrial sequences, we analysed phylogeographic patterns and demographic histories of populations of five species (four gastropod and one amphipod species) co-occurring in the southwestern shore of Lake Baikal, an area where environmental oscillations have not resulted in geographical isolation of habitats.
Species with stronger habitat preferences (gastropods B. turriformis, B. carinata and B. carinatocostata) exhibit rather stable population sizes through their evolutionary history, and their phylogeographic pattern indicates moderate habitat fragmentation. Conversely, species without strong habitat preference (gastropod M. herderiana and amphipod G. fasciatus) exhibit haplotype networks with a very abundant and widespread central haplotype and a big number of singleton haplotypes, while their reconstructed demographic histories show a population expansion starting about 25-50 thousand years ago, a period marked by climate warming and increase in diatom abundance as inferred from bottom-lake sedimentary cores.
In agreement with previous studies, we found that species reacted differently to the same environmental changes. Our results highlight the important role of dispersal ability and degree of ecological specialization in defining a species' response to environmental changes.
The data presented here are related to the research article entitled “Hidden cases of tRNA genes duplication and remolding in mitochondrial genomes of amphipods” (Romanova et al., 2020) 1. Correct ...tRNA gene sequence annotation in mitochondrial (mt) and nuclear genomes sometimes can be a challenging task because of the differential performances of tRNA annotation/prediction programmes. These programmes may cause false positive or false negative predictions. Moreover, additional difficulties with annotation may be caused by the presence of duplicated tRNA genes and those coding tRNAs with altered identities occurring as due to a mutation in their anticodon sequence (tRNA gene remolding/recruitment).
We developed an R script automating the diagnosis of ancestor tRNA gene coding specificity regardless of anticodon sequence based on genetic distance comparison. Some of the predicted tRNA genes from the mt genomes of amphipods are presented. We also developed an R script for estimation of the best mode of sequence alignment, which was applied to determine the best alignment of tRNA genes in 1, but is also suitable for testing of any nucleotide alignment sets used in phylogenetic inferences.
...every transformative technology so far invented to improve human medicine or other areas of applied science was immediately embraced by traditional biologists and contributed to the extraction of ...evolutionary insights. The second one was the introduction of the molecular analysis (see 4) that approximately coincided with the establishment of the synthetic theory of evolution. Since that, the methods of the analysis of molecular traits kept progressing.
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