Phylogenetic Lineages Research Articles

The divergence of mean phenotypes under persistent directional selection.

Numerous organismal traits, particularly at the cellular level, are likely to be under persistent directional selection across phylogenetic lineages. Unless all mutations affecting such traits have large enough effects to be efficiently selected in all species, gradients in mean phenotypes are expected to arise as a consequence of differences in the power of random genetic drift, which varies by approximately five orders of magnitude across the Tree of Life. Prior theoretical work examining the conditions under which such gradients can arise focused on the simple situation in which all genomic sites affecting the trait have identical and constant mutational effects. Here, we extend this theory to incorporate the more biologically realistic situation in which mutational effects on a trait differ among nucleotide sites. Pursuit of such modifications leads to the development of semi-analytic expressions for the ways in which selective interference arises via linkage effects in single-effects models, which then extend to more complex scenarios. The theory developed clarifies the conditions under which mutations of different selective effects mutually interfere with each others' fixation and shows how variance in effects among sites can substantially modify and extend the expected scaling relationships between mean phenotypes and effective population sizes.

Insights on the Existence of Ancient Glacial Refugee in the Northern Black/Azov Sea Lowland, with the Description of the First Stygobiotic Microcrustacean Species of the Genus Niphargus Schiödte, 1849 from the Mouth of the Don River

A new species of the genus Niphargus Schiödte, 1849 (Crustacea: Amphipoda: Niphargidae), co-existing with other stygobiotic amphipods, Diasynurella kiwi Marin and Palatov, 2023 and Pontonyx donensis (Martynov, 1919) (Crangonyctidae), is described from a small spring on a shore of Kiziterinka River in Rostov-on-Don City in the mouth of the Don River. Two of the three species in the studied spring, D. kiwi and the discovered Niphargus, belong to microcrustaceans not exceeding the total body size of 3 mm. The new species, Niphargus rostovi sp. nov., represents one of the smallest species within the genus and is mostly related to the Greek Niphargus karkabounasi Ntakis, Anastasiadou, Zakšek and Fišer, 2015, which is also not reaching the body size of 3 mm. One more related undescribed species is found on the Crete Island by the molecular genetic data. These species represent a separate phylogenetic lineage within the “carpathicus” species complex, which diverged from the congeners in the Late Miocene for more than 10 Mya. At the same time, the speciation within the ingroup started about 5–6 Mya, obviously correlating with the drainage of the Euxinian basin of the Eastern Paratethys, connecting the lower Don and southern Greece areas. Niphargus potamophilus Birštein, 1954 is also first recorded from the mouth of the Belbek River in the Crimean Peninsula, closing the known area from the Kuban River delta to Rostov-on-Don area and further along the western coast of the Black Sea to Bulgaria. Analysis of the recent records of long-time lineages of endemic/subterranean/stygobiotic animals unable to disperse for long distances assumed that glacial refugium existed at the mouth of the Don River, along with the South Caucasus (Colchis) and the southern Caspian (Hyrcania), where many species have survived several periods of glaciation since the late Miocene.

Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).

Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.

Comparison of the Efficiency of Single-Locus Species Delimitation Methods: A Case Study of a Single Lake Fish Population in Comparison against the Barcodes from International Databases

To date, a rather large set of both mathematical theories for species delimitation, based on single-locus genetic data, and their implementations as software products, has been accumulated. Comparison of the efficiencies of different delineation methods in the task of accumulating and analyzing data with reference to different taxa in different regions, is vital. The aim of this study was to compare the efficiency of fifteen single-locus species delimitation methods using the example of a fish species found in a single lake in European Russia (Lake Plescheyevo) with reference to other sequences of revealed taxa deposited in international databases. We analyzed 186 original COI sequences belonging to 24 haplotypes, and 101 other sequences previously deposited in GenBank and BOLD. Comparison of all 15 alternative taxonomies demonstrated that all methods adequately separate only the genera, while the number of delimited mOTUs differed from 16 (locMin) to 43 (HwM/CoMa). We can assume that the effectiveness of each method is correlated with the number of matches based on Ctax and MatchRatio criteria. The most comparable results were provided by bGMYC, mPTP, STACEY, KoT and ASAP and the most synchronous results were obtained from bGMYC, mPTP, STACEY and ASAP. We believe that these results are maximally realistic in the number of revealed mOTUs. A high genetic diversity, resulting in the existence of several mOTUs and phylogenetic lineages within many species, demonstrates the usefulness of the “polymorphic species” concept, which does not underestimate species richness and does not prevent the rational use and protection of biodiversity.

Genomic analysis of Brucella melitensis reveals new insights into phylogeny and evolutionary divergence

PurposeBrucellosis is a bacterial zoonotic disease caused by genus Brucella. The disease is often transmitted to humans by direct or indirect contact with infected livestock or from laboratory exposure. In this study two clinical isolates of Brucella melitensis were subjected to whole genome sequencing (WGS) using Ion Torrent PGM and Oxford Nanopore MinIon platform. MethodsThe two hybrid complete genomes were subjected to core gene SNP analysis to identify the relative evolutionary position. To distinguish between the various lineages of B. melitensis, Pangenome analysis was carried out. ResultsPhylogenetic analysis revealed that both the study isolates (ST8) clustered along the other Asian isolates that formed genotype II. Genome wide analyses of 326 B melitensis isolates suggests 2171 gene clusters were shared across all the genomes while 3552 gene clusters were considered as accessory genes. ConclusionHere we attempted to provide the gain and loss of six unique genes that defined the phylogenetic lineages and complex evolutionary process. As the severity and prevalence of human brucellosis is increasing a better understanding of Brucella genomics and transmission dynamics is needed.

Catalogue of specimens of Felidae family (Mammalia, Carnivora) specimens deposited in the State Museum of Natural History NASU, Lviv, Ukraine

Currently, modern cats (Felidae) are divided into 8 lineages (phylogenetic lines), which include 14 genera and approximately 40 modern species (Загороднюк та ін., 2022). The cat collection of the State Museum of Natural History NASU, like all vertebrate collections, has a regional character, therefore it is represented by only two species: European wildcat – Felis silvestris Schreber, 1775 and Eurasian lynx – Lynx lynx (Linnaeus, 1758). The collection has been filled since the foundation of the Didushytskyi Museum, the heir of which is a modern museum, that is, from the middle of the 19th century. According to the method of making, the collection consists of stuffed animals (25), skulls (10) and skins (2). It consists of 37 samples (20 of European wildcat and 17 Eurasian lynx). Earlier in the collection there were 13 more samples, which were lost for various reasons or transferred to other collections (5 stuffed Eurasian lynx and European wildcat, and 3 skulls of Eurasian lynx). In the archive of the Museum preserved acts of transfer of exhibits to the Institute of Zoology NASU and Kyiv zoological museum and Uzhhorod University, where among others there are Felidae, however, we failed to find these samples in the mentioned museums. One Eurasian lynx was transferred to the museum of Grodno city (Belarus) in 1924. The oldest exhibit is Eurasian lynx skull, dated of 1857, the youngest – European wildcat skin dated of 2013. The main number of samples, almost 40%, collected from 1880 to 1889. The largest number of exhibits (4) arrived during 1880. All samples collected in the Carpathians and Ciscarpathians (14 – Lvivska oblast, 11 – Ivano-Frankivska oblast, 1 – Ternopilska oblast of Ukraine and 3 – form South-Eastern Poland) and one Eurasian lynx collected in Polissia region. The main ways of income – gifts to the founder of the museum Volodymyr Didushytskyi from his friends and acquaintances, some samples were purchased. Three samples (stuffed Eurasian lynx, stuffed animal and two skulls of a European wildcat) came from the Natural History Museum (disbanded in 1940) of the Shevchenko Scientific Society in Lviv. Scientific analysis of the State Museum of Natural History NASU cat collection was not carried out, indirectly the collection is mentioned in the guidebooks by the museum (Dzieduszycki, 1895; Guidebook, 1957; State, 1982) and K.A. Tatarynov monograph (Татаринов, 1973).

Mumps resurgence in a highly vaccinated population: Insights gained from surveillance in Canada, 2002–2020

Although mumps vaccination has been routine in Canada for decades, mumps cases and outbreaks continue to occur periodically. Mumps surveillance, including monitoring of the mumps virus genotype associated with disease activity, is important to document baseline activity and to advance further research into vaccine effectiveness. Here we describe a detailed analysis of mumps cases that have been detected in Canada from 2002 to 2020, with a focus on the mumps molecular epidemiology. In total, 7395 cases of mumps were reported to the surveillance system, with outbreaks occurring in the years 2007, 2010 and 2016 to 2018. Adolescents and young adults aged 15 to 29 years had the highest risk of being a case (rate ratios ranging from 1.50 to 2.29), compared to adults aged 30 to 39. Genotypes of mumps viruses were determined in 3225 specimens. Genotype G was predominantly detected (96% of genotyped specimens) and was first reported in 2005. Other genotypes were more likely to be detected in cases that also reported travel (or were linked to imported cases) than the cases with genotype G detected (p < 0.0001). The genotype G viruses had little sequence diversity in the 316 nucleotide window used for genotyping (the small hydrophobic protein gene) and mainly belonged to a single phylogenetic lineage that included the MuVi/Sheffield.GBR/1.05 reference sequence. The analysis of over ten years of data has demonstrated that mumps genotype G, specifically belonging to a single lineage, the Sheffield lineage, is the endemically circulating virus in Canada. This lineage is seen also in other countries using the genotype A vaccine. Mumps remains endemic despite high MMR vaccination coverage which has been sufficient to eliminate circulation of measles and rubella in Canada, raising the hypothesis of the evolution towards a vaccine escape mumps virus.

High Diversity of Bradyrhizobial Species Fix Nitrogen with Woody Legume Spartocytisus supranubius in a High Mountain Ecosystem.

The symbiosis between rhizobia and legumes is of pivotal importance in nitrogen-poor ecosystems. Furthermore, as it is a specific process (most legumes only establish a symbiosis with certain rhizobia), it is of great interest to know which rhizobia are able to nodulate key legumes in a specific habitat. This study describes the diversity of the rhizobia that are able to nodulate the shrub legume Spartocytisus supranubius in the harsh environmental conditions of the high mountain ecosystem of Teide National Park (Tenerife). The diversity of microsymbionts nodulating S. supranubius was estimated from a phylogenetic analysis of root nodule bacteria isolated from soils at three selected locations in the park. The results showed that a high diversity of species of Bradyrhizobium and two symbiovars can nodulate this legume. Phylogenies of ribosomal and housekeeping genes showed these strains distributed into three main clusters and a few isolates on separate branches. These clusters consist of strains representing three new phylogenetic lineages of the genus Bradyrhizobium. Two of these lineages belong to the B. japonicum superclade, which we refer to as B. canariense-like and B. hipponense-like, as the type strains of these species are the closest species to our isolates. The third main group was clustered within the B. elkanii superclade and is referred to as B. algeriense-like as B. algeriense is its closest species. This is the first time that bradyrhizobia of the B. elkanii superclade have been reported for the canarian genista. Furthermore, our results suggest that these three main groups might belong to potential new species of the genus Bradyrhizobium. Analysis of the soil physicochemical properties of the three study sites showed some significant differences in several parameters, which, however, did not have a major influence on the distribution of bradyrhizobial genotypes at the different locations. The B. algeriense-like group had a more restrictive distribution pattern, while the other two lineages were detected in all of the soils. This suggests that the microsymbionts are well adapted to the harsh environmental conditions of Teide National Park.

Difficult-to-Treat Pathogens: A Review on the Management of Multidrug-Resistant Staphylococcus epidermidis.

Multidrug-resistant Staphylococcus epidermidis (MDRSE) is responsible for difficult-to-treat infections in humans and hospital-acquired-infections. This review discusses the epidemiology, microbiology, diagnosis, and treatment of MDRSE infection and identifies knowledge gaps. By using the search term "pan resistant Staphylococcus epidermidis" OR "multi-drug resistant Staphylococcus epidermidis" OR "multidrug-resistant lineages of Staphylococcus epidermidis", a total of 64 records have been identified from various previously published studies. The proportion of methicillin resistance in S. epidermidis has been reported to be as high as 92%. Several studies across the world have aimed to detect the main phylogenetic lineages and antibiotically resistant genes through culture, mass spectrometry, and genomic analysis. Molecular biology tools are now available for the identification of S. epidermidis and its drug resistance mechanisms, especially in blood cultures. However, understanding the distinction between a simple colonization and a bloodstream infection (BSI) caused by S. epidermidis is still a challenge for clinicians. Some important parameters to keep in mind are the number of positive samples, the symptoms and signs of the patient, the comorbidities of the patient, the presence of central venous catheter (CVC) or other medical device, and the resistance phenotype of the organism. The agent of choice for empiric parenteral therapy is vancomycin. Other treatment options, depending on different clinical settings, may include teicoplanin, daptomycin, oxazolidinones, long-acting lipoglycopeptides, and ceftaroline. For patients with S. epidermidis infections associated with the presence of an indwelling device, assessment regarding whether the device warrants removal is an important component of management. This study provides an overview of the MDRSE infection. Further studies are needed to explore and establish the most correct form of management of this infection.

Development of an Integrated System for Molecular-Genetic Identification of &lt;i&gt;Yersinia pestis&lt;/i&gt; Strains

The paper describes a developed comprehensive system for molecular-genetic identification of Yersinia pestis strains according to their appurtenance to certain subspecies, biovars, phylo-geographic populations, using realtime PCR (RT-PCR), allele-specific RT-PCR, and multiplex PCR with hybridization fluorescent registration of results on a solid substrate. Application of this system makes it possible to establish the appurtenance of Y. pestis strains to the following phylogenetic branches: 0.ANT1, 0.ANT2, 0.ANT3, 0.ANT5, 3.ANT, 4.ANT of antique biovar of the main subspecies; 2.MED0, 2.MED1, 2.MED2, 2.MED3, 2.MED4 of medieval biovar of the main subspecies; 1.IN1, 1.IN2, 1.IN3 of intermedium biovar of the main subspecies; 1.ORI1, 1.ORI2, 1.ORI3 of oriental biovar of the main subspecies; 0.PE3 (angolica subspecies), 0.PE7 (tibetica subspecies) and 0.PE10 (qinghaica subspecies). The first stage of the studies within the frames of the developed system is indication of plague agent using registered diagnostic drugs. The second stage is the determination of belonging to individual subspecies through RT-PCR or by the method of multiplex PCR system with hybridization-fluorescent registration of results on a solid substrate, which also allows for establishing to which biovars of the main subspecies and the main phylogenetic lines of the ancient biovar the strains belong. The third stage is the identification of strain appurtenance to phylogenetic branches by the AS-RT-PCR method. The designed complex system for molecular-genetic identification of Y. pestis strains can be applied at the regional and federal levels of the laboratory network of the Russian Federation for diagnostics of infectious diseases. Its use will considerably facilitate and increase the efficiency of intraspecific differentiation of Y. pestis strains within the framework of the epidemiological investigation of outbreaks or importation of strains of plague pathogen into the territory of the Russian Federation or during the certification of strains in collection activities.

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring.

A novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is validated by sequencing and comparing the results with QIAGEN spin-column DNA extractions using BLAST analyses. Two sets of DNA extractions were conducted on 13 species spanning various leaf anatomies and phylogenetic lineages: (i) fresh leaves were punched with custom polymeric microneedle patches to recover genomic DNA, or (ii) QIAGEN DNA extractions. Three plastid (matK, rbcL, and trnH-psbA) and one nuclear ribosomal (ITS) DNA regions were amplified and sequenced using Sanger or nanopore technology. The proposed method reduced the extraction time to 1 min and yielded the same DNA sequences as the QIAGEN extractions. Our drastically faster and simpler method is compatible with nanopore sequencing and is suitable for multiple applications, including high-throughput DNA-based species identifications and monitoring.

Why phylogenetic signal of traits is important in ecosystems: uniformity of a plant trait increases soil fauna, but only in a phylogenetically uniform vegetation

Phylogenetically closely related plant species often share similar trait states (phylogenetic signal), but local assembly may favor dissimilar relatives and thereby decouple the diversity of a trait from the diversity of phylogenetic lineages. Associated fauna might either benefit from plant trait diversity, because it provides them complementary resources, or suffer from it due to dilution of preferred resources. We hence hypothesize that decoupling of trait and phylogenetic diversity weakens the relationship between the plant-trait diversity and the abundance and diversity of associated fauna. Studying permanent meadows, we tested for combined effects of plant phylogenetic diversity and diversity of two functional traits (specific leaf area, leaf dry matter content) on major groups of soil fauna (earthworms, mites, springtails, nematodes). We found that only in phylogenetically uniform plant communities, was uniformity in the functional traits associated with (i) high abundance in springtails, and (ii) high abundance of the sub-group that feeds more directly on plant material (in springtails and mites) or those that are more prone to disturbance (in nematodes), and (iii) high diversity in all three groups tested (springtails, earthworms, nematodes). Our results suggest that soil fauna profits from the resource concentration in local plant communities that are uniform in both functional traits and phylogenetic lineages. Soil fauna would hence benefit from co-occurrence of closely related plants that have conserved the same trait values, rather than of distantly related plants that have converged in traits. This might result in faster decomposition and a positive feedback between trait conservatism and ecosystem functioning.

Phylogeography of Oaks in the Crimea Reveals Pleistocene Refugia and Migration Routes

Chloroplast DNA variability was examined in 872 trees of pedunculate oak (Q. robur L.), sessile oak (Q. petraea (Matt.) Liebl.) and downy oak (Q. pubescens Willd.) on the Crimean Peninsula, in the Western Caucasus and in the Balkan region in order to study phylogeography and interaction of these species in the Black Sea region. Sequencing of five fragments with a total length of more than 10,000 base pairs revealed 12 haplotypes of chloroplast DNA. For the haplotype typing in the studied populations, chloroplast microsatellites (cpSSR), sequencing, and restriction analysis were used. Haplotypes detected belong to several divergent phylogenetic lineages. The studied species almost do not differ from each other in the composition of haplotypes and the geographical structure of variability, which demonstrates a certain level of gene flow between them in mixed populations. The haplotypes of the Balkan region are closely related to the haplotypes of previously studied populations from Eastern Europe and the western part of the Russian Plain, and are not found in the Crimea and the Caucasus. On the Crimean Peninsula, two geographical groups of populations are distinguished, which differ sharply in the composition of haplotypes. The difference between the western part of the peninsula and the eastern part is shown, which suggests a multiple origin of oak populations in the Crimea as a result of migrations from two sources, which could be facilitated by fluctuations in the Black Sea level and its desalination, which repeatedly occurred in the Pleistocene and Holocene. The predominance of two divergent haplotypes in the western part of the peninsula, similar to the haplotypes of Asia Minor, indicates the penetration of oak from this region and the presence of an isolated refugium in the mountainous forest regions of Crimea during the last glacial maximum. At the same time, haplotypes common with the Western Caucasus are spread in the east of the mountain-forest part of the Eastern Crimea. The sharp boundary between the areas of distribution of “western” and “eastern” haplotypes in the Eastern Crimea indicates a relatively recent time of the formation of a secondary contact zone between local and Caucasian oak populations as a result of postglacial colonization.

Tahibacter soli sp. nov., isolated from soil and Tahibacter amnicola sp. nov., isolated from freshwater.

Two Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, and non-motile rod bacteria, strains BLT and W38T, that were isolated from soil and freshwater, respectively, were taxonomically characterized. Both strains optimally grew at 30 °C and pH 7.0 in Reasoner's 2A medium and contained ubiquinone-8 as the sole respiratory quinone. As major fatty acids (>10 %), strain BLT contained iso-C15 : 0 and summed features 3 and 9 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c and iso-C17 : 1 ω9c and/or C16 : 0 10-methyl, respectively), whereas strain W38T contained iso-C15 : 0, iso-C16 : 0 and summed feature 9. Diphosphatidylglycerol and phosphatidylmonomethylethanolamine as major polar lipids and phosphatidylethanolamine and phosphatidylglycerol as minor polar lipids were detected in both strains. The DNA G+C contents of strains BLT and W38T were 68.3 and 65.3 %, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strains BLT and W38T formed a tight phylogenetic lineage with Tahibacter species, and they shared 98.8 % 16S rRNA gene sequence similarity and 75.5 % average nucleotide identity (ANI) and 16.6 % digital DNA-DNA hybridization (dDDH) values, indicating that they are different species. Strains BLT and W38T were most closely related to Tahibacter caeni BUT-6T and Tahibacter aquaticus PYM5-11T with 97.7 and 98.0 % 16S rRNA gene sequence similarities, respectively. ANI and dDDH values between strain BLT and T. caeni BUT-6T and between strain W38T and T. aquaticus DSM 21667T were 78.5 and 21.6% and 75.3 and 21.0 %, respectively. Based on their phenotypic, chemotaxonomic and genomic properties, strains BLT and W38T represent two different novel species of the genus Tahibacter, for which the names Tahibacter soli sp. nov. and Tahibacter amnicola sp. nov. are proposed. The type strains of T. soli and T. amnicola are BLT (=KACC 22831T=JCM 35402T) and W38T (=KACC 22832T=JCM 35749T), respectively.

Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil.

A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10-37 °C (optimum, 25-30 °C) and pH 6.0-9.0 (optimum, pH 8.0), and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). Strain U1T contained iso-C15 : 0, C16 : 0, C16 : 1 ω5c and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus Dyadobacter. Strain U1T has the highest 16S rRNA sequence similarity to Dyadobacter bucti QTA69T (97.9 %). Average nucleotide identity and digital DNA-DNA hybridization values between strain U1T and D. bucti QTA69T were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).

Simultaneous competition and environmental filtering in woody communities of the understory of Eucalyptus plantations in the Cerrado

Dense and species-rich understory communities have been commonly found in old or abandoned stands of Eucalyptus plantations in the Cerrado domain presenting plant species and ecological niches that suggest a repository of the original biodiversity. This repository depends on the largely unknown effect of Eucalyptus plantations on their understories. We addressed this issue by testing if the effect of Eucalyptus trees on the assembly of Cerrado communities causes environmental filtering or competitive exclusion. For the test, 40 plots (20 inside stands and 20 outside) were allocated and all woody plants with a circumference at the ground level equal to or greater than 10 cm were sampled. Species richness, diversity indexes and species turnover were determined. The phylogenetic structure was evaluated at different scales using the values of Mean Pairwise Distance (MPD), the Mean Nearest Taxon Distance (MNTD), the Net Relatedness Index (NRI) and the Nearest Taxon Index (NTI), as well as phylobetadiversity indices. The metrics of alpha and beta phylogenetic diversity (NTI, MNTD, NRI and MPD, betaMPD and betaMNTD) fell within the random expectation in each plant community, suggesting a phylogenetic uniformity, but fewer plants of the Fabaceae family than expected by chance were detected outside Eucalyptus stands suggesting that this family is filtered in inside Eucalyptus stands. Species richness is lower inside than outside Eucalyptus stands. The pattern is congruent with simultaneous environmental filtering and competitive exclusion in a context of niche conservatism which means that functional traits are conserved within phylogenetic lineages.

Carnivores from Draby 3 (central Poland): The latest record of Lycaon lycaonoides (Kretzoi, 1938) and the final accord in the long history of ancient faunas

The occurrence of the phylogenetic lineage of the genus Lycaon covers the entire Pleistocene. A younger form, Lycaon lycaonoides, was recorded from 68 African, Eurasian and North American localities, ranged between 1.8 and 0.4 myr. Among them, six localities are in the territory of Poland, with especially important the youngest record from Draby 3, dated at MIS 11. It seems to be the latest occurrence of this species elsewhere. Draby 3 documented the last, relict occurrence of Lycaon lycaonoides after the most extreme glaciation of MIS 12, which was crucial for a significant decrease in numbers and density, or the complete disappearance of many ancient carnivores. Lycaon lycaonoides was ecologically flexible species able to hunt in a wide prey spectrum; its size, comparable with that of the largest extant Canis lupus, high intelligence, social lifestyle and pack hunting guaranteed the leading position among other ancient large carnivores. This species was a member of a stable by 1.5 myr carnivore paleoguild, one of the top carnivores and the dominant canid. It was also well adapted to changing environmental conditions initiated by glacial-interglacial cycles. It seems that climatic changes have not affected Lycaon lycaonoides as much as previously considered. The main factor responsible for the lycaon decline, alongside with climatic changes, would be the arrival of newcomers of African origin like Panthera spelaea fossilis and Crocuta crocuta spelaea. Lycaon lycaonoides was able to survive longer than other ancient carnivores. It disappeared first in southern Europe (Iberian and Italian Peninsulas), in areas where lion and hyena appeared for the first time. Gradually as the density and abundance of both social and highly intelligent species increased, a compact and wide geographic range of this species started to shrink up to isolated areas located far away one from another. The final collapse of the lycaon population and its disappearance took place during MIS 12. The balance between canids has been broken and a critical point in the lycaon-wolf relationship was passed at that time. During MIS 11, the lycaon was already too rare to be a real competitor and a limiting factor for the wolf. It was also the time when the lycaon completely disappeared. As soon as the lycaon disappeared in Eurasia, a slowly increase in the size of the wolf has been observed.

Phylogeny of the Dipus sagitta Species Complex by Nuclear Gene Sequences.

The northern three-toed jerboa Dipus sagitta had long been considered to be a single polytypic species. High genetic diversity of D. sagitta was earlier revealed on the basis of several mitochondrial and nuclear genes, and several separate species were hypothesized to occur within the taxon. However, the relationships between phylogenetic lineages have not been established because of the small sample size of nuclear genes. In the present work, a far larger set of nuclear DNA loci was used, and thus, a higher resolution of the phylogenetic tree was achieved for ten D. sagitta forms. The structure revealed for the species mainly confirmed the topology and relationships of the mtDNA lineages. Yet the mitochondrial and nuclear phylogenies were not completely consistent. Some of the D. sagitta genetic lineages were therefore assumed to be a product of reticular evolutionary processes. The taxon was concluded to be the diverse species complex D. sagitta sensu lato, in which long-diverged lineages are not always reproductively isolated.

Cutibacterium acnes.

Cutibacterium acnes is a Gram-positive bacterium that colonizes human skin. The lipophilic anaerobic bacterium resides mainly in the sebum-rich pilosebaceaous units, but is also detected in nonsebaceous areas. The species is polyphyletic and includes three different subspecies. Multiple phylogenetic lineages usually coexist on an individual’s skin; however, each pilosebaceous unit is predominately colonized by a single lineage. The bacterium is thought to contribute to skin homeostasis through colonization resistance, antioxidant activity, and immunomodulatory properties.

Longitudinal antigenic and seroepidemiological analyses of parechovirus A1 in Yamagata, Japan.

To investigate the antigenic changes in parechovirus 1 (PeVA1), seroepidemiological analyses were performed against the Harris strain (Harris), isolated in 1956, and PeVA1/Yamagata.JPN/2021-4785, isolated in 2021, using immune sera and 207 and 237 human serum specimens collected in 2021 and 1976, respectively. Although rabbit immune sera showed the highest neutralization antibody (NT-Ab) titers against the immunized viruses at 1:12 800-1:102 400, they were cross-reactive at 1:400-1:800. All 62 Yamagata isolates obtained between 2001 and 2021 (Yamagata strains), belonging to phylogenetic lineage 1B, reacted more strongly (mostly 4-64 times) to antiserum against PeVA1/Yamagata.JPN/2021-4785 than to antiserum against Harris, belonging to phylogenetic lineage 1 A. Human serum specimens obtained in 2021 showed higher NT-Ab titers against PeVA1/Yamagata.JPN/2021-4785, whereas those obtained in 1976 had similar NT-Ab titers against both strains. These findings suggested that Yamagata strains and Harris were antigenically cross-reactive, although there were differences. There are still high NT-Abs titers present against Harris in 2021 in particular, indicating that PeVA1 has been in circulation with high immunity in the population. In conclusion, this study suggested that PeVA1 has been endemically perpetuated with only minor antigenic changes as well as with high immunity over several decades in the community.