Молекулярная филогенетика двухвойных сосен Украины: уточнение таксономического статуса на основе анализа аллозимной изменчивости

На підставі аналізу мінливості 18 алозимних локусів у популяційних вибірках шести автохтонних двохвойних сосен України визначено їх генетичну схожість та уточнено таксономічний статус. Встановлено, що як самостійні види можна розглядати лише чотири з них: P. sylvestris L., P. pallasiana D. Don, P. mugo Turra та P. stankewiczii (Sukacz.) Fomin, а P. cretacea Kalenicz. та P. kochiana Klotzsch ex Koch. — як грунтовий екотип та географічну форму P. sylvestris.Based on the analysis of variability of 18 allozyme loci in population samples of six autochthonous two-needle pines of Ukraine, their genetic similarity is determined, and the taxonomic status is corrected. It is found that the species P. sylvestris L., P. pallasiana D. Don, P. mugo Turra, and P. stankewiczii (Sukacz.) Fomin could be seen as the separate species, whereas P. cretacea Kalenicz. and P. kochiana Klotzsch ex Koch. — as the soil ecotypes and geographical forms of P. sylvestris

Phylogenetics of the paleartic model grass "brachypodium sylvaticum" uncovers two divergent oriental and occidental micro-taxa lineages

Brachypodium sylvaticum has been selected as a model for perennial grasses, and considerable genomic resources have been generated and a reference genome and several resequenced pangenome accessions are available for this species. Despite these genomic advances, the evolution and systematics of diploid B. sylvaticum s. l. is almost unknown. The B. sylvaticum complex is formed by up to seven taxonomically close micro-taxa which differentiate from typical B. sylvaticum s. s. based on a few morphological features. Moreover, some of them show some largely disjunct geographic distributions on both sides of their native Palearctic region. In this study, we used a phylogenomic approach including representative populations from the oriental and occidental distribution range of B. sylvaticum micro-taxa to elucidate their evolutionary relationships and assess the systematic value of the morphological features that separate them. A combined plastome and nuclear phylogenetic tree supports an early split and high divergence of the oriental lineage, showing the close relationship of the Himalayan B. sylvaticum var. breviglume lineages to the Pacific B. miserum / B. kurilense clade, and the contrasting large homogeneity and low divergence of the occidental European, N African and SW and C Asian lineage, with several B. sylvaticum s. s., B. spryginii, and B. glaucovirens samples showing identical or similar sequences. Divergence time estimate analysis suggests that the oriental lineage diverged from the common ancestor in the early Pleistocene (2.0 Ma), followed by subsequent colonization and isolations in the Himalayas (2.0 – 1.7 Ma) and the Far East (0.36 Ma) in more recent times, while the occidental lineage split in the Mid-Late Pleistocene (0.97 Ma), followed by rapid radiation and postglacial spread in the western Paleartic during the last thousand years

The use of statistical phylogenetics in virology

Molecular phylogenetics, particularly statistical phylogenetics, is widely used to solve the fundamental and applied problems in virology. Bayesian, or statistical, phylogenetic methods, which came into practice 10—15 years ago, markedly expanded the range of questions that can be answered based on analyzing nucleotide and amino acid sequences. An opportunity of using various evolution models allows inferring the chronology, geography and dynamics of the infection spreading. For example, analysis of globally distributed HIV group M by Bayesian methods demonstrated with a probability of 99% that the most recent common ancestor of these viruses existed in the surroundings of the city of Kinshasa (Democratic Republic of the Congo) in the early 1920s. Another study showed that H9N2 influenza virus most likely passed on to humans from wild ducks in Hong Kong in the late 1960s. In addition, using of the Bayesian analysis allows to evaluating the effect of measures taken on the development of the epidemic process. For example, it was shown retrospectively that the rate of hepatitis C virus infection cases in Egypt increased by several orders of magnitude in the mid-20th century. A sharp rise in new case rate is associated with the treatment for schistosomiasis by using non-sterile repeatedly used syringes. A set of Bayesian analysis methods has been applied in tens of thousands of researches describing various aspects of the occurrence and spread of infectious diseases in humans and animals. This was facilitated by the development and accessibility of software that implements these methods. The complexity of Bayesian phylogenetic methods imposes strict requirements on the data being analyzed. The correctness of the phylogenetic analysis data depends on various factors. For example, it is necessary to choose an evolutionary model that most adequately describes the studied objects. A mandatory step in formulating the results is the justification of the selected model. For viruses, the acquisition of genetic elements from other organisms is typical, therefore, the genomes even from closely related viruses may have non-homologous regions unsuitable for phylogenetic analysis. Another aspect is the creation of a representative dataset. Sometimes, all stages of the analysis are not indicated in publications, so that the data obtained can be interpreted ambiguously. The correct use of statistical phylogenetics methods in virology is possible only upon understanding their principles, proper methods of data preparation and evolutionary model selection criteria

Программа и контрольные задания по ботанике с основами фитоценологии

Методическое пособие для обучающихся по направлениям: 35.03.01 – «Лесное дело», 35.03.06 – «Экология и природопользование». Заочная форма обучения

Combining and congruence evaluation of phylogenetic signals from different genes based on geometric approach

A new Euclidean distance based algorithm is used for analysis of congruence and combining molecular genetic data. This approach is called geometric, since Euclidean distance satisfies all metric axioms and the points representing the sequences can be placed in a geometric space without distorting the mutual distances and can be endowed with the coordinates in this space. Geometricness of Euclidean distances allows to apply to molecular data methods of multivariate analysis, which are relevant for intra- and interspecies variability investigating, visualization of possible directions of evolution, combining data and evaluation of the congruence of phylogenetic signals. The algorithm is used for the analysis of more than 1500 nucleotide sequences of two nuclear (apoB, brca1) and two mitochondrial (co1, cytb) genes of 15 Palaearctic and Nearctic shrews species of genus Sorex (Soricidae, Eulipotyphla). All sequences of each gene are represented as a set of points in Euclidean space. Centroids of a set of points belonging to the same species are calculated. The matrix of Euclidean distances between the species centroids is calculated for each gene. Mantel test is applied to estimate pairwise similarity (congruence) of interspecies distances matrices relating to different genes. nDNA genes congruence is equal 0.961, mtDNA – 0.748. All matrices of the interspecies distances are combined into a joint matrix by weighing. Joint genetic space for all species is built by principal coordinate method from the joint matrix. Several variability directions reflecting evolutionary events of different scale are visualized in a joint genetic space. In addition, the joint matrix of interspecies distances is used for building a phylogenetic tree which is consistent with the zoological systematics accepted for today. This confirms the efficiency of our proposed method

Рабочая тетрадь по зоологии

учебно-методическое пособие, рабочая тетрадь, зоологи