The role of systematics in biology.
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Biological Evolution↗
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Results for “systematic evolution”
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Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.
BACKGROUND: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution. RESULTS: In this study, we perform a systematic comparative analysis of centromeres in common wheat and its corresponding ancestral species, utilizing the latest comprehensive reference genome assembly available. Our findings reveal that wheat centromeres predominantly consist of five types of centromeric-specific retrotransposon elements (CRWs), with CRW1 and CRW2 being the most prevalent. We identify distinct evolutionary trajectories in the functional centromeres of each subgenome, characterized by variations in copy number, insertion age, and CRW composition. By utilizing CENH3-ChIP data across various ploidy levels, we uncover a series of CRW invasion events that have shaped the evolution of AA subgenome centromeres. Conversely, the evolutionary process of the DD subgenome centromeres involves their expansion from diploid to hexaploid wheat, facilitating adaptation to a larger genomic context. Integration of complete einkorn centromere assemblies and Aegilops tauschii pan-genomes further revealed subgenome-specific centromere evolutionary trajectories. By inclusion of synthetic hexaploid from S2-S3 generations, alongside 2x/6 × natural accessions, we demonstrate that DD subgenome centromere expansion represents a gradual evolutionary process rather than an immediate response to polyploidization. CONCLUSIONS: Our study provides a comprehensive landscape of centromere adaptation, evolution, and maturation, along with insights into how retrotransposon invasions drive centromere evolution in polyploid wheat.
Centromere↗
Evolutionary trends of the histological pattern in the teeth of Edentata (Xenarthra).
In a comparative study of the dental structure of Edentata, the central tissue was identified as a modified orthodentine, except in the Glyptodontidae where an osteodentine was found. Some evolutionary trends of the tissues in these teeth may have been related with the extinction of ground sloths. Comparative studies of the tissues in mammalian teeth seem to be good tests for systematics.
Animals↗
Interactive analysis of phylogeny and character evolution using the computer program MacClade.
Computer programs for phylogenetic analysis have been important tools in systematics and evolutionary biology, but most have been designed primarily for the reconstruction of phylogenetic trees and not the interpretation of patterns of character evolution. Described here is the computer program MacClade, designed for interactive analysis of character evolution and phylogeny. For a given tree and a matrix of character data, MacClade displays its reconstruction of character evolution by shading the branches of the tree to indicate ancestral states. Trees can be manipulated for instance by picking up and moving branches. Assumptions underlying the reconstruction of character evolution can be varied extensively. With these manipulations and MacClade's graphical feedback, one can explore the relationships among phylogenetic trees, character data, assumptions and interpretations of character evolution. MacClade has extensive facilities for editing data, displaying various summaries of character evolution in charts and diagrams, and printing.
Animals↗
SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.
Monitoring and understanding the transmission and evolution of SARS-CoV-2 remains a significant public health priority. Within-host genetic variation provides insight into viral evolution during infection and may help infer transmission events. In this study, we analysed intra-host variation in SARS-CoV-2 genome sequences from Boston University's testing mandate. Focusing on intra-host single nucleotide variants (iSNVs), we inferred transmission events and assessed the selective forces shaping within-host viral evolution. To minimize false-positive iSNVs resulting from systematic biases, we implemented stringent data filtering and developed a heuristic to exclude contamination-derived artefacts arising from batched sequencing. We find that intra-host variation is limited and infrequently transmitted during acute infections, suggesting that shared iSNVs serve as highly specific but insensitive markers of transmission. We also observed incomplete purifying selection shaping within-host diversity, with the loci most affected changing among variants of concern. Finally, we identified a highly recurrent iSNV (G11083T) which may represent a site of positive selection. Our results highlight that within-host variation provides insight into within-host pathogen evolution, in spite of its limited use in genomic epidemiology.
SARS-CoV-2↗
Classical taxonomy of mosquitoes--a memorial to John N. Belkin.
The major contributions of John N. Belkin to the field of mosquito systematics are noted. Hallmarks of his publications are presented and his hypotheses about the evolution, speciation, competition, distribution and classification of mosquitoes are summarized. The current status of the field of mosquito systematics is examined. It is argued that mosquito systematics is still largely at the alpha taxonomy level, that at best only 25-50% of mosquito species are known, and that we have not even begun to develop a natural classification for the Culicidae. It is concluded that there will be little improvement in the status of mosquito taxonomy unless there is increased support for systematics.
Animals↗
Primary pulmonary malignant lymphoma, clinical and pathological findings, immunocytochemical and ultrastructural studies in 15 cases.
Fifteen cases of primary pulmonary malignant lymphoma (M.L.) were studied using strict criteria to distinguish them from secondary pulmonary manifestations. All were M.L.'s of the lymphoid B type. Diagnosis on the basis of non specific clinical, X-ray and endoscopic findings if often difficult but can be facilitated by the systematic use of immunocytochemical and ultrastructural techniques. Their evolution is in good agreement with the prognostic data given by the Kiel-Lennert histopathological classification. 14 of the patients had M.L. of low grade malignancy; the one case of high grade malignancy was quickly fatal. A few cases appeared as a complication of a preexisting dysimmune disease (Pigeon breeder's disease, Gougerot-Sjogren disease, Liebow's lymphomatoid granulomatosis).
Adult↗
[The cardiovascular manifestations of Paget's disease].
After reviewing the old ideas (peripheral syndrome and cardiac insufficiency at high outputs) and more recent ideas (arterial and intracardiac vascular calcification), the authors report their experiences based on the study of the histories of 150 patients suffering from Paget's disease followed for several years. First they emphasize the frequent latency of cardiac manifestations looked for systematically by means of the electrocardiogram particularly during evolutive stages of the disease. Electrocardiographic disturbances were observed 91 times and included 43 cases of conduction disorders and 48 of repolarization disorders; their distribution was studied as a function of various inherent parameters, of the patient (age and sex) and of the disease (its evolutive character and its degree of diffusion). On the basis of the anti-arythmic power of calcitonin found during experiments and obtained excellent results three times. Finally the place of cardiovascular manifestations in the pathogenic hypotheses and nosology of Paget's disease is discussed.
Adult↗
[A developmental anomaly of Meckel's cartilage].
An atypical evolution of the mandibular cartilage was recorded in systematic dissections of the neck in the Anatomy Laboratory. This anomaly led to the formation of a supernumerary bony fragment in the concavity of the lower edge of the mandibular arch, with a slight adhesion thereto. This observation is reported by the authors after a recapitulation of the embryology.
Aged↗
The bearing of East Rudolf fossils on early hominid systematics.
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Anthropology, Physical↗
[Psychology of relationships as a theoretical concept in medical psychology and psychotherapy].
The theoretical concept called "psychology of relations" (A. F. Lazursky, V. N. Myasishchev) is offered as the basis for a study of a patient's personality and psychotherapy. The author stresses ideological relationship of psychology of relations with phylosophy of dialectical materialism and I. P. Pavlov's studies about conditioned reflexes, its relationship with clinical psychoneurology, its direction to a study of the personality and adherence to primacy of consciousness over unconciousness. The perspectiveness of the evolutionally ontogenetic approach to the analysis of the system of relations and necessity to elaborate working systematizations determined by the research purpose, is stated.
Biological Evolution↗
Unraveling evolutionary relationships in the Sida generic alliance (Malvaceae, Malvoideae): a phylogenetic and cytotaxonomic overview.
Sida (Malvaceae), the largest Malveae-Abutilinae member, has poorly defined morphological limits which overlaps with 11 phylogenetically closely related genera that comprises the "Sida generic alliance". The 12 genera are distributed in the tropics especially in Brazil where one third of its species diversity is found. Evolutionary relationships within Sida generic alliance remain unresolved due to morphological convergence, limited taxon sampling, and lack of integrative approaches including cytogenetic data. We reconstructed the phylogeny of Sida and allied genera using a multilocus dataset (nuclear ITS and seven plastid loci) including 193 species classified in 19 genera and analyzed chromosome evolution using cytogenetic data (chromosome number) for 79 species of the 19 genera. The phylogeny recovered seven clades-Abutilon, Bakeridesia, Callianthe, Gaya, and three Sida clades (I-III)-and confirmed the polyphyly of Sida, the largest genera. We detected reticulate evolution, with incongruence between nuclear and plastid topologies. Chromosome number ranged from 2n = 12 to 60 and represented synapomorphies for most clades. Ancestral character reconstruction indicated that ascending dysploidy and polyploidy predominated in karyotype evolution of Sida and allied genera. Our results reveal taxonomic incongruence in current classifications probably related to reticulate evolution. A generic-level taxonomic revision is necessary and should rely on integrated phylogenetic and karyotypic evidence. This study provides a framework for phylogenetic systematics and emphasizes the role of Brazil as a hotspot for plant genomic research.
Phylogeny↗
Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus.
The length of the small subunit ribosomal DNA (SSU rDNA) differs significantly among individuals from natural populations of the ascomycetous lichen complex Cladonia chlorophaea. The sequence of the 3' region of the SSU rDNA from two individuals, chosen to represent the shortest and longest sequences, revealed multiple insertions within a region that otherwise aligned with a 520-nucleotide sequence of the SSU rDNA in Saccharomyces cerevisiae. The high degree of variability in SSU rDNA size can be accounted for by different numbers of insertions; one individual had two group I introns and the second had five introns, two of which were clearly related to introns at identical positions in the other individual. Yet, introns in different positions, whether within an individual or between individuals, were not similar in sequence. The distribution of introns at three of the positions is consistent with either intron loss or acquisition, and clearly indicates the dynamic variability in this region of the nuclear genome. All seven insertions, which ranged in size from 210 to 228 nucleotides, had the conserved sequence and secondary structural elements of group I introns. The variation in distribution and sequence of group I introns within a short highly conserved region of rDNA presents a unique opportunity for examining the molecular evolution and mobility of group I introns within a systematics framework.
Ascomycota↗
Genomic characterization of aggressiveness in pituitary neuroendocrine tumors.
BACKGROUND: Aggressive evolution of PitNETs is rare; metastatic spread is even more. Defining aggressiveness and malignancy is challenging, subsequently hard to predict, and to understand. The aim was to provide a molecular definition of aggressiveness using genomic approaches. METHODS: PitNETs from 206 patients were included. Associations between 9 clinicopathological features of aggressiveness and PitNETs' omics were explored. Omics included transcriptome, DNA methylation, chromosomal alterations, and mutations. Clonal tumor evolution was monitored in 7 patients. RESULTS: Among the 9 clinicopathological features of aggressiveness, only rapid progression, progression after radiotherapy, Ki67/MIB1 proliferation index ≥10%, temozolomide treatment, metastases, and specific death were associated with specific omics signatures, while tumour maximal diameter ≥40 mm, cavernous, and sphenoid invasion were not. The omic signatures associated with these features of aggressiveness overlapped but remained distinct between corticotroph and mammo-somato-thyrotroph lineages. For each lineage, a common signature of aggressiveness was identified, associating a proliferative transcriptome signature and DNA hypermethylation. Alterations in specific genes were associated with aggressive features, including a novel PitNET gene, LRP1B, and known cancer genes (TP53, CDKN2A), while USP8 and GNAS alterations were not. Integration of gene alterations with methylome and transcriptome signatures isolated a subset of molecularly aggressive PitNETs. Molecular signatures were stable during the course of the disease, despite evolution toward aggressiveness and potential clonal divergence. CONCLUSION: This systematic analysis of clinicopathological features of aggressiveness using an integrated multiomic approach establishes a histomolecular definition of aggressiveness in PitNETs. Prospective cohort studies are needed to validate these molecular signatures and establish their prognostic value.
Humans↗
Bacterial evolution.
The deliberate application of the methodology of contemporary molecular genetics to problems in bacterial systematics has led to a broad new understanding of the evolutionary history of both prokaryotes and eukaryotes. In this review, I discuss some of the major conclusions of this endeavour and try to predict future directions.
Animals↗
[Congenital paravertebral arteriovenous fistulae in children and adolescents].
These arteriovenous fistulae (AVF) situated in the paravertebral area present as a murmur which explains their cardiological orientation. They are characterised by the presence of one or more afferent paravertebral arteries giving rise to collateral vessels irrigating the bone marrow. The aim of this study of 13 cases was to study the diagnostic and therapeutic problems, and the evolution of this particular localisation of AVF. Two groups of paravertebral AVF were individualised: - Cervical AVF in which the vertebral artery was always involved (7 cases). Four were simple (only one fistula) and three were complex, having several afferent arteries. Two presented as a rapidly growing vascular tumour. Two caused an asymptomatic angiographic vertebral steal syndrome. Two simple forms were obturated by a detachable balloon and one by surgical excision. Two complex forms were treated by embolisation and surgery. Total closure of the AVF was obtained in all cases without complications. - Dorso-lumbar AVF (6 cases). The afferent vessels are the intercostal (D6 to D8) or lumbar (L2 to L4) arteries. Anatomically, these are extra-medullary fistulae with an extra or intra-vertebral venous drainage. Enlargement in an adjacent conjugating foramen forms a tumour which may narrow the spinal canal (1 case diagnosed by CAT) or erode the vertebral body, so compromising the spinal support. Spontaneous closure of the AVF was observed in 1 case. Three cases were treated surgically with good results; two patients are waiting for embolisation. A review of the literature provides complementary information on the long-term evolution of these AVF and confirms the need for systematic therapy as demonstrated in our study.(ABSTRACT TRUNCATED AT 250 WORDS)
Adolescent↗
The evolution strategy--a search strategy used in individual optimization of electrical parameters for therapeutic carotid sinus nerve stimulation.
Optimization problems, arising in the search for parameters and/or techniques of functional electrostimulation (FES), disproportionally increase when multiple electrodes, electrode configurations, electrical parameters, and stimulation modes may be applied. When computational or investigational effort precludes systematic studies in FES, we propose to apply and evaluate Rechenberg's evolution strategy, which in technical use and numerical optimization has been valid in comparison to more traditional methods. This strategy implements mutation and selection processes in analogy to biological evolution. The effect of combined multiple input variables on a quality function (Q) is experimentally evaluated. The actual computed value of Q serves as a selection criterion for those input variable combinations which lead Q to approach a target value (maximization), similar to a hill-climbing procedure. In radiofrequency controlled, therapeutic electrical carotid sinus nerve stimulation (CSNS), we varied (mutated) combinations of pulse frequency and pulse amplitude parameters, according to the evolution strategy, in individual patients. CSNS lowers blood pressure and decreases heart rate. Q was computed from blood pressure and heart rate responses to CSNS. The strategy individually optimized electrical parameters to achieve large depressor responses upon CSNS. Although, in contrast to technical usage, only two input variables were investigated, and biomedical experience with the evolution strategy is limited so far, its potential use in other fields of FES, especially when more input variables are to be optimized, is discussed and encouraged.
Algorithms↗