Psoriasis vulgaris (PV) is a chronic, recurrent inflammatory dermatosis mediated by aberrantly activated immune cells. The role of the innate-like T cells, particularly gammadelta T (γδT) cells and MR1-restricted T lymphocytes, is incompletely explored, mainly through animal models, or by use of surrogate lineage markers, respectively. Here, we used case-control settings, multiparameter flow cytometry, 5-OP-RU-loaded MR1-tetramers, Luminex technology and targeted qRT-PCR to dissect the cellular and transcriptional landscape of γδ and MR1-restricted blood T cells in untreated PV cases (n=21, 22 matched controls). High interpersonal differences in cell composition were observed, fueling transcriptional variability at healthy baseline. A minor subset of canonical CD4+CD8+MR1-tet+TCRVα7.2+ and CD4+CD8-MR1-tet+TCRVα7.2+ T cells was the most significantly underrepresented community in male PV individuals, whereas Vδ2+ γδ T cells expressing high levels of TCR and Vδ1-δ2- γδ T cells expressing intermediate levels of TCR were selectively enriched in affected males, partly reflecting disease severity. Our findings highlight a formerly unappreciated skewing of human circulating MAIT and γδ cytomes during PV, and reveal their compositional changes in relation to sex, CMV exposure, serum cytokine content, BMI, and inflammatory burden. Complementing numerical alterations, we finally show that flow-sorted, MAIT and γδ populations exhibit divergent transcriptional changes in mild type I psoriasis, consisting of differential bulk expression for signatures of cytotoxicity/type-1 immunity (EOMES, RUNX3, IL18R), type-3 immunity (RORC, CCR6), and T cell innateness (ZBTB16).
- MeSH
- Cell Differentiation MeSH
- Cytotoxicity, Immunologic MeSH
- Adult MeSH
- Blood Circulation MeSH
- Middle Aged MeSH
- Humans MeSH
- Mucosal-Associated Invariant T Cells immunology MeSH
- Histocompatibility Antigens Class I metabolism MeSH
- Young Adult MeSH
- Immunity, Innate MeSH
- Promyelocytic Leukemia Zinc Finger Protein genetics metabolism MeSH
- Psoriasis immunology MeSH
- Receptors, Antigen, T-Cell, gamma-delta metabolism MeSH
- T-Lymphocytes immunology MeSH
- Th1 Cells immunology MeSH
- Minor Histocompatibility Antigens metabolism MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Young Adult MeSH
- Male MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
- MeSH
- Bayes Theorem MeSH
- Ciliophora classification genetics MeSH
- Species Specificity MeSH
- Phylogeny * MeSH
- Macronucleus genetics MeSH
- DNA, Ribosomal analysis MeSH
- RNA, Protozoan analysis MeSH
- RNA, Ribosomal, 18S analysis MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Background and Aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean. Methods: A combined approach involving sequencing of two plastid regions ( trnL-trnF and rpl32-trnL ), nrDNA ITS, rDNA FISH analyses, climatic niche characterization and spatio-temporal modelling was used. Key Results: Among the examined diploid species, only two well-differentiated evolutionary lineages were recognized: Anthoxanthum gracile and A. alpinum . The other taxa - A. aristatum, A. ovatum, A. maderense and the 'Mediterranean diploid' - form a rather intermixed group based on the examined molecular data. In situ rDNA localization enabled identification of the ancestral Anthoxanthum karyotype, shared by A. gracile and two taxa from the crown group. For the studied taxa, ancestral location probabilities for six discrete geographical regions in the Mediterranean were proposed and likely scenarios of gradual expansion from them were suggested. Modelling past and present distributions shows that the 'Mediterranean diploid' has already been occurring in the same localities for 120 000 years. Conclusions: Highly congruent results were obtained and dated the origin and first diversification of Anthoxanthum to the Miocene. The later divergence probably took place in the Pleistocene and started polyploid evolution within the genus. The most recent diversification event is still occurring, and incomplete lineage sorting prevents full diversification of taxa at the molecular level, despite clear separation based on climatic niches. The 'Mediterranean diploid' is hypothesized to be a possible relic of the most recent common ancestor of Anthoxanthum due to their sharing of ancestral features.
- MeSH
- Biological Evolution * MeSH
- Diploidy * MeSH
- DNA, Chloroplast genetics MeSH
- Phylogeny * MeSH
- Poaceae classification MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Mediterranean Region MeSH
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese.
- MeSH
- Cyprinidae genetics MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- Genome, Mitochondrial MeSH
- Hybridization, Genetic MeSH
- DNA, Mitochondrial genetics MeSH
- Mitochondria genetics MeSH
- Evolution, Molecular * MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
BACKGROUND: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. RESULTS: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. CONCLUSIONS: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
- MeSH
- Arabidopsis classification cytology genetics MeSH
- Biological Evolution MeSH
- Chloroplasts genetics MeSH
- Ecotype MeSH
- Phylogeography MeSH
- Genetic Variation MeSH
- Genome, Chloroplast MeSH
- Gene Pool MeSH
- Microsatellite Repeats MeSH
- Gene Flow MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
A South African endemic antelope, the Grey Rhebok (Pelea capreolus), has long been an evolutionary enigma in bovid systematics-its phylogenetic intractability attributed to its curious combination of derived and primitive morphological attributes and the consequences of a rapid radiation. By using a combination of DNA sequences, chromosomal characteristics and quantitative and qualitative morphological features we show that the species is a sister taxon to a clade that comprises the waterbuck, reedbuck and allies. Our finding of few unambiguous synapomorphies reinforces suggestions of a rapid radiation and highlights the effects of incomplete lineage sorting, including the hemiplasic nature of several chromosomal rearrangements. We investigate these data to address the general question of what may have led to Pelea being both genetically and ecologically distinct from the Reduncini. We argue that its adaptation to exposed habitats, free of standing water, arose by vicariance prompted by increasing aridity of the extreme south/southwestern region of the African continent in the Miocene. Ancestral lineages leading to the extant Redunca and Kobus, on the other hand, retreated to water-abundant refugia in the north during these mostly globally cool phases. The mosaic of water-rich environments provided by the Okavango and the drainage systems in the southwestern extension of the East African Rift system are considered to have facilitated speciation and chromosomal evolution within these antelope.
- MeSH
- Antelopes genetics MeSH
- Biological Evolution MeSH
- Y Chromosome MeSH
- Ecosystem MeSH
- Phylogeny * MeSH
- In Situ Hybridization, Fluorescence MeSH
- Chromosome Painting MeSH
- DNA, Mitochondrial MeSH
- Molecular Sequence Data MeSH
- Cattle MeSH
- Genetic Speciation * MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Cattle MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
We investigated genetic variation and evolutionary history of closely related taxa of Picris subsect. Hieracioides with major focus on the widely distributed P. hieracioides and its closely related congeners, P. hispidissima, P. japonica, P. olympica, and P. nuristanica. Accessions from 140 sample sites of the investigated Picris taxa were analyzed on the infra- and the inter-specific level using nuclear (ITS1-5.8S-ITS2 region) and chloroplast (rpl32-trnL(UAG) region) DNA sequences. Genetic patterns of P. hieracioides, P. hispidissima, and P. olympica were shown to be incongruent and, in several cases, both plastid and nuclear alleles transcended borders of the taxa and genetic lineages. The widespread P. hieracioides was genetically highly variable and non-monophyletic across both markers, with allele groups having particular geographic distributions. Generally, all gene trees and networks displayed only a limited and statistically rather unsupported resolution among ingroup taxa causing their phylogenetic relationships to remain rather unresolved. More light on these intricate evolutionary relationships was cast by the Bayesian coalescent-based analysis, although some relationships were still left unresolved. A combination of suite of phylogenetic analyses revealed the ingroup taxa to represent a complex of genetically closely related and morphologically similar entities that have undergone a highly dynamic and recent evolution. This has been especially affected by the extensive and recurrent gene flow among and within the studied taxa and/or by the maintenance of ancestral variation. Paucity of phylogenetically informative signal further hampers the reconstruction of relationships on the infra- as well as on the inter-specific level. In the present study, we have demonstrated that a combination of various phylogenetic analyses of datasets with extremely complex and incongruent phylogenetic signal may shed more light on the interrelationships and evolutionary history of analysed species groups.
- MeSH
- Amplified Fragment Length Polymorphism Analysis MeSH
- Asteraceae classification genetics MeSH
- Biodiversity MeSH
- Datasets as Topic MeSH
- DNA, Plant MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- Genetic Linkage * MeSH
- Genetic Markers MeSH
- Hybridization, Genetic * MeSH
- DNA, Intergenic MeSH
- Evolution, Molecular * MeSH
- Molecular Sequence Data MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.
A course and a site of B cell development in swine are not firmly known. In this study, we show that B cell lymphogenesis is located in the bone marrow (BM). According to expression of MHC class II (MHC-II), CD2, CD21, CD25, CD45RC, CD172a, swine workshop cluster (identification number) (SWC) 7, and μHC, porcine BM cells were resolved into seven subsets representing sequential stages of development. Profile of rearrangement-specific products and transcripts from sorted BM cells confirmed the proposed developmental pathway. The same developmental pathway was further proven by analysis of selection for productive rearrangements in Ig H chains and also by cultivation studies. Cultivation also showed that earliest precursors with incomplete DJ rearrangements can still revert their B cell differentiation and develop along myeloid lineage, whereas this is impossible for later developmental stages. Proliferation and the apoptotic potential of individual developmental stages as well as critical checkpoints were also identified. Colocalization experiments showed early colocalization of MHC-II/CD2/CD172a is replaced by colocalization of MHC-II/CD2/CD21/SWC7/IgM in immature cells, whereas CD25 and CD45RC did not colocalize with any other studied molecules. In this study, we also finally prove that the BM in pigs is fully functional in adult animals and that B lymphogenesis occurs there throughout life. To our knowledge, this is the first study showing a course and a direct site of B cell lymphogenesis in swine.
- MeSH
- Cell Differentiation MeSH
- Bone Marrow Cells cytology immunology MeSH
- Antigens, CD genetics immunology MeSH
- Germ-Free Life MeSH
- Hysterectomy MeSH
- Immunophenotyping MeSH
- Histocompatibility Antigens Class II genetics immunology MeSH
- Animals, Newborn MeSH
- B-Lymphocyte Subsets cytology immunology MeSH
- Swine immunology MeSH
- Primary Cell Culture MeSH
- Immunoglobulin Heavy Chains genetics immunology MeSH
- Gene Expression Regulation, Developmental immunology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Phylogeny reconstruction based on multiple unlinked markers is often hampered by incongruent gene trees, especially in closely related species complexes with high degrees of hybridization and polyploidy. To investigate the particular strengths and limitations of chloroplast DNA (cpDNA), low-copy nuclear and multicopy nuclear markers for elucidating the evolutionary history of such groups, we focus on Hieracium s.str., a predominantly apomictic genus combining the above-mentioned features. Sequences of the trnV-ndhC and trnT-trnL intergenic spacers were combined for phylogenetic analyses of cpDNA. Part of the highly variable gene for squalene synthase (sqs) was applied as a low-copy nuclear marker. Both gene trees were compared with previous results based on the multicopy external transcribed spacer (ETS) of the nuclear ribosomal DNA. The power of the different markers to detect hybridization varied, but they largely agreed on particular hybrid and allopolyploid origins. The same crown groups of species were recognizable in each dataset, but basal relationships were strongly incongruent among cpDNA, sqs and ETS trees. The ETS tree was considered as the best approximation of the species tree. Both cpDNA and sqs trees showed basal polytomies as well as merging or splitting of species groups of non-hybrid taxa. These patterns can be best explained by a rapid diversification of the genus with ancestral polymorphism and incomplete lineage sorting. A hypothetical scenario of Hieracium speciation based on all available (including non-molecular) evidence is depicted. Incorporation of seemingly contradictory information helped to better understand species origins and evolutionary patterns in this notoriously difficult agamic complex.
- MeSH
- Asteraceae genetics MeSH
- DNA, Chloroplast genetics MeSH
- Farnesyl-Diphosphate Farnesyltransferase genetics MeSH
- Phylogeny * MeSH
- Genetic Markers MeSH
- Crosses, Genetic MeSH
- DNA, Ribosomal Spacer genetics MeSH
- Models, Genetic MeSH
- Molecular Sequence Data MeSH
- Plant Proteins genetics MeSH
- Sequence Analysis, DNA MeSH
- Genetic Speciation * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
