Analysis Of Population Dynamics Research Articles

Impact of novel methods and research approaches in plant pathology: Are individual advances sufficient to meet the wider challenges of disease management?

AbstractAdvances continue to be made by plant pathologists on topics in plant health, environmental protection and food security. Many advances have been made for individual crops, pathogens and diseases that in many cases have led to their successful management. A wider impact of research depends on recognition of the multifaceted challenges posed by plant diseases and the need to integrate studies in a systems level approach. The adoption of high‐throughput sequencing for diagnosis and detection is widespread but impact depends upon the agricultural and ecological context combined with improved surveillance. Deployment of host resistance in the field needs to be aligned with a greater appreciation of plant genetic diversity and the complementary contribution made by tolerance of disease. Epidemiological understanding of the spatiotemporal spread of plant diseases has improved through population dynamic and genetic analyses. Research emphasis on the plant microbiome has invigorated soil microbial studies, especially for disease complexes and declines, but the challenge is to move to interventions that benefit plant health. Analysis of the impacts of climate change has been made for single‐crop disease studies, but seldom have these been placed in the context of pathogen adaptation, new crops, wild plants, vectors and soil microbes. Advances in informatic analysis illustrate not only the global impacts of plant disease introductions, but also the challenges inherent in marshalling and integrating information. Advances have been made in applying artificial intelligence technologies across many areas of plant pathology but have yet to be integrated within any coordinated research agenda.

Population Status of the Endangered Semi-Mangrove Dolichandrone spathacea on Hainan Island, China

In China, Dolichandrone spathacea is a rare and endangered semi-mangrove plant species with an extremely small population, naturally distributed only in Zhanjiang City and the east coast of Hainan Island. Despite conservation concerns, the population status of D. spathacea has received little scientific attention. In this study, we evaluated the current status of D. spathacea on Hainan Island, China, in order to propose sustainable conservation strategies for future ecological restoration of its natural population. D. spathacea on Hainan Island can be divided into four populations. All the D. spathacea populations present a state of overall dispersion, local concentration, and occasionally sporadic existence, and they exist in geographical isolation. The young, middle, and old D. spathacea plants account for 20.42%, 66.20%, and 13.38%, respectively, indicating that the D. spathacea population on Hainan Island is declining. Furthermore, instead of temporal structure, we used diameter at breast height (DBH) to establish a static life table, draw a population survival curve, and quantify the future development trend through population dynamic analysis and time-series prediction. These results suggest that the D. spathacea population in the Bamen Gulf (Wenchang) and Qingmei Harbor (Sanya) on Hainan Island is sensitive to external disturbances and possesses two main increases in mortality rate—namely, in its juvenile and mature stages—due to competition and anthropogenic interferences, which might be the most important reasons for its endangered status. Depending on the current conditions of the D. spathacea population, we should conserve and expand mature trees in situ, preserve their germplasm resources, rehabilitate their habitats to promote provenance restoration, and conduct artificial cultivation and spreading planting in order to realize the sustainable conservation and management of D. spathacea.

Triggering Toll-Like Receptor 5 signaling during pneumococcal superinfection prevents the selection of antibiotic resistance.

Toll-like receptor 5 (TLR5) signaling plays a key role in antibacterial defenses. We previously showed that respiratory administration of flagellin, a potent TLR5 agonist, in combination with amoxicillin improves the treatment of primary pneumonia or superinfection caused by amoxicillin-sensitive or -resistant Streptococcus pneumoniae. Here, the impact of adjunct flagellin therapy on antibiotic dose/regimen and the selection of antibiotic-resistant S. pneumoniae was investigated using superinfection with isogenic antibiotic-sensitive and -resistant bacteria and population dynamics analysis. Our findings demonstrate that flagellin allows for a 200-fold reduction in the antibiotic dose, achieving the same therapeutic effect observed with antibiotic alone. Adjunct treatment also reduced the selection of antibiotic-resistant bacteria in contrast to the antibiotic monotherapy. Finally, we developed a mathematical model that captured the population dynamics and estimated a 20-fold enhancement immune-modulatory factor on bacterial clearance. This work paves the way for the development of host-directed therapy and refinement of treatment by modeling.

Projection of Interspecific Competition (PIC) Matrices: A Conceptual Framework for Inclusion in Population Risk Assessments.

Accounting for intraspecific and interspecific competition when assessing the effects of chemical and nonchemical stressors is an important uncertainty in ecological risk assessments. We developed novel projection of interspecific competition (PIC) matrices that allow for analysis of population dynamics of two or more species exposed to a given stressor(s) that compete for shared resources within a landscape. We demonstrate the application of PIC matrices to investigate the population dynamics of two hypothetical fish species that compete with one another and have differences in net reproductive rate and intrinsic rate of population increase. Population status predictions were made under scenarios that included exposure to a chemical stressor that reduced fecundity for one or both species. The results of our simulations demonstrated that measures obtained from the life table and Leslie matrix of an organism, including net reproductive rate and intrinsic rate of increase, can result in erroneous conclusions of population status and viability in the absence of a consideration of resource limitation and interspecific competition. This modeling approach can be used in conjunction with field monitoring efforts and/or laboratory testing to link effects due to stressors to possible outcomes within an ecosystem. In addition, PIC matrices could be combined with adverse outcome pathways to allow for ecosystem projection based on taxonomic conservation of molecular targets of chemicals to predict the likelihood of relative cross-species susceptibility. Overall, the present study shows how PIC matrices can integrate effects across the life cycles of multiple species, provide a linkage between endpoints observed in individual and population-level responses, and project outcomes at the community level for multiple generations for multiple species that compete for limited resources. Environ Toxicol Chem 2024;43:1406-1422. Published 2024. This article is a U.S. Government work and is in the public domain in the USA.

Genome-Enabled Analysis of Population Dynamics and Virulence-Associated Loci in the Oat Crown Rust Fungus Puccinia coronata f. sp. avenae.

Puccinia coronata f. sp. avenae (Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against Pca is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of Pca using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse Pca collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of Pca involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved Pca reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate Avr effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked Avr effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Co-Packaged PARP inhibitor and photosensitizer for targeted photo-chemotherapy of 3D ovarian cancer spheroids

BackgroundWithin the last decade, poly(ADP-ribose) polymerase inhibitors (PARPi) have emerged in the clinic as an effective treatment for numerous malignancies. Preclinical data have demonstrated powerful combination effects of PARPi paired with photodynamic therapy (PDT), which involves light-activation of specialized dyes (photosensitizers) to stimulate cancer cell death through reactive oxygen species generation.ResultsIn this report, the most potent clinical PARP inhibitor, talazoparib, is loaded into the core of a polymeric nanoparticle (NP-Tal), which is interfaced with antibody-photosensitizer conjugates (photoimmunoconjugates, PICs) to form PIC-NP-Tal. In parallel, a new 3D fluorescent coculture model is developed using the parental OVCAR-8-DsRed2 and the chemo-resistant subline, NCI/ADR-RES-EGFP. This model enables quantification of trends in the evolutionary dynamics of acquired chemoresistance in response to various treatment regimes. Results reveal that at a low dosage (0.01 μM), NP-Tal kills the parental cells while sparing the chemo-resistant subline, thereby driving chemoresistance. Next, PIC-NP-Tal and relevant controls are evaluated in the 3D coculture model at multiple irradiation doses to characterize effects on total spheroid ablation and relative changes in parental and subline cell population dynamics. Total spheroid ablation data shows potent combination effects when PIC and NP-Tal are co-administered, but decreased efficacy with the conjugated formulation (PIC-NP-Tal). Analysis of cell population dynamics reveals that PIC, BPD + NP-Tal, PIC + NP-Tal, and PIC-NP-Tal demonstrate selection pressures towards chemoresistance.ConclusionsThis study provides key insights into manufacturing parameters for PARPi-loaded nanoparticles, as well as the potential role of PDT-based combination therapies in the context of acquired drug resistance.

Systematic Genomic Surveillance of SARS-CoV-2 at Xiamen International Airport and the Port of Xiamen Reveals the Importance of Incoming Travelers in Lineage Diversity.

Sever Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still a threat to human health globally despite the World Health Organization (WHO) announcing the end of the COVID-19 pandemic. Continued surveillance of SARS-CoV-2 at national borders would be helpful in understanding the epidemics of novel imported variants and updating local strategies for disease prevention and treatment. This study focuses on the surveillance of imported SARS-CoV-2 variants among travelers entering Xiamen International Airport and the Port of Xiamen from February to August 2023. A total of 97 imported SARS-CoV-2 sequences among travelers from 223 cases collected from 12 different countries and regions were identified by real-time RT-PCR. Next-generation sequencing was used to generate high-quality complete sequences for phylogenetic and population dynamic analysis. The study revealed a dominant shift in variant distribution, in which the XBB subvariant (XBB.1.5, XBB.1.16, XBB.1.9, XBB.2.3, and EG.5.1) accounted for approximately 88.8% of the sequenced samples. In detail, clades 23D and 23E accounted for 26.2% and 21.4% of the sequenced samples, respectively, while clades 23B (13.6%) and 23F (10.7%) took the third and fourth spots in the order of imported sequences, respectively. Additionally, the XBB.2.3 variants were first identified in imported cases from the mainland of Xiamen, China on 27 February 2023. The spatiotemporal analyses of recent viral genome sequences from a limited number of travelers into Xiamen provide valuable insights into the situation surrounding SARS-CoV-2 and highlight the importance of sentinel surveillance of SARS-CoV-2 variants in the national border screening of incoming travelers, which serves as an early warning system for the presence of highly transmissible circulating SARS-CoV-2 lineages.

Insights into the genetic variability and evolutionary dynamics of tomato spotted wilt orthotospovirus in China

BackgroundViral diseases are posing threat to annual production and quality of tobacco in China. Recently, tomato spotted wilt orthotospovirus (TSWV) has been reported to infect three major crops including tobacco. Current study was aimed to investigate the population dynamics and molecular diversity of the TSWV. In the current study, to assess and identify the prevalence and evolutionary history of TSWV in tobacco crops in China, full-length genome sequences of TSWV isolates from tobacco, were identified and analyzed.MethodsAfter trimming and validation, sequences of new isolates were submitted to GenBank. We identified the full-length genomes of ten TSWV isolates, infecting tobacco plants from various regions of China. Besides these, six isolates were partially sequenced. Phylogenetic analysis was performed to assess the relativeness of newly identified sequences and corresponding sequences from GenBank. Recombination and population dynamics analysis was performed using RDP4, RAT, and statistical estimation. Reassortment analysis was performed using MegaX software.ResultsPhylogenetic analysis of 41 newly identified sequences, depicted that the majority of the Chinese isolates have separate placement in the tree. RDP4 software predicted that RNA M of newly reported isolate YNKM-2 had a recombinant region spanning from 3111 to 3811 bp. The indication of parental sequences (YNKMXD and YNHHKY) from newly identified isolates, revealed the conservation of local TSWV population. Genetic diversity and population dynamics analysis also support the same trend. RNA M was highlighted to be more capable of mutating or evolving as revealed by data obtained from RDP4, RAT, population dynamics, and phylogenetic analyses. Reassortment analysis revealed that it might have happened in L segment of TSWV isolate YNKMXD (reported herein).ConclusionTaken together, this is the first detailed study revealing the pattern of TWSV genetic diversity, and population dynamics helping to better understand the ability of this pathogen to drastically reduce the tobacco production in China. Also, this is a valuable addition to the existing worldwide profile of TSWV, especially in China, where a few studies related to TSWV have been reported including only one complete genome of this virus isolated from tobacco plants.

Latent neural population dynamics underlying breathing, opioid-induced respiratory depression and gasping

Breathing is vital and must be concurrently robust and flexible. This rhythmic behavior is generated and maintained within a rostrocaudally aligned set of medullary nuclei called the ventral respiratory column (VRC). The rhythmic properties of individual VRC nuclei are well known, yet technical challenges have limited the interrogation of the entire VRC population simultaneously. Here we characterize over 15,000 medullary units using high-density electrophysiology, opto-tagging and histological reconstruction. Population dynamics analysis reveals consistent rotational trajectories through a low-dimensional neural manifold. These rotations are robust and maintained even during opioid-induced respiratory depression. During severe hypoxia-induced gasping, the low-dimensional dynamics of the VRC reconfigure from rotational to all-or-none, ballistic efforts. Thus, latent dynamics provide a unifying lens onto the activities of large, heterogeneous populations of neurons involved in the simple, yet vital, behavior of breathing, and well describe how these populations respond to a variety of perturbations.

ENVIRONMENTAL FACTORS’ INFLUENCE ON THE DIAMONDBACK MOTH (PLUTELLA XYLOSTELLA L.) POPULATION DYNAMICS ON CRUCIFEROUS CROPS

The diamondback moth (Plutella xylostella L.) (Lepidoptera: Plutellidae) is one of the most severe pests for cruciferous crops. Its widespread distribution and the ability to submissive migration led to an unexpected enhancement in its population, thereby obscuring the control measures aimed at this phytophagous. The presented study sought to determine the expansion of diamondback moth in cruciferous crops (rapeseed, mustard) in two agroclimatic zones of Northern Kazakhstan (Zone I: moderately humid and warm; Zone II: slightly humid and moderately warm). Analysis of population dynamics ran for the long-term during 2012–2022 based on bioecological patterns of the diamondback moth and factors affecting them. Numerical variables of population density and abundance indices served as diagnostic predictors for characterizing the phase state of the pest in a given period and, therefore, recognizing the population dynamics pattern of the diamondback moth. Based on the results, the biological regularity of the stage inception of the phytophagous abundance dynamics does not always persevere, and variations occur with the sway of environmental factors. Hence, the abundance dynamics of diamondback moth depend upon the weather conditions of the previous and current year, as well as, on the accomplishment of the extent of chemical treatment and its regulations. The obtained data can be criteria for predicting the phase state of diamondback moth populations in the agroclimatic zones of northern Kazakhstan to justify and plan protective measures, as well as, to improve phytosanitary control.

Evolutionary Analysis of a Parrot Bornavirus 2 Detected in a Sulphur-Crested Cockatoo (Cacatua galerita) Suggests a South American Ancestor.

Parrot bornavirus (PaBV) is an RNA virus that causes Proventricular Dilatation Disease (PDD), neurological disorders, and death in Psittaciformes. Its diversity in South America is poorly known. We examined a Cacatua galerita presenting neuropathies, PDD, and oculopathies as the main signs. We detected PaBV through reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of the nucleoprotein (N) and matrix (M) genes. Maximum likelihood and Bayesian phylogenetic inferences classified it as PaBV-2. The nucleotide identity of the sequenced strain ranged from 88.3% to 90.3% against genotype PaBV-2 and from 80.2% to 84.4% against other genotypes. Selective pressure analysis detected signs of episodic diversifying selection in both the N and M genes. No recombination events were detected. Phylodynamic analysis estimated the time to the most recent common ancestor (TMRCA) as the year 1758 for genotype PaBV-2 and the year 1049 for the Orthobornavirus alphapsittaciforme species. Substitution rates were estimated at 2.73 × 10-4 and 4.08 × 10-4 substitutions per year per site for N and M, respectively. The analysis of population dynamics showed a progressive decline in the effective population size during the last century. Timescale phylogeographic analysis revealed a potential South American ancestor as the origin of genotypes 1, 2, and 8. These results contribute to our knowledge of the evolutionary origin, diversity, and dynamics of PaBVs in South America and the world. Additionally, it highlights the importance of further studies in captive Psittaciformes and the potential impact on endangered wild birds.

The maternal phylogenetic insights of Yunnan Miao group revealed by complete mitogenomes

The Miao group is one of the representative Hmong-Mien-speaking populations and primarily scattered in southern China and Southeast Asia, which has experienced massive migrations in history and thus forms distinctive evolutionary genetics. Yet, the genetic explorations of Miao group are relatively limited based on complete mitochondrial genome (mitogenome), especially for the Miao group from Yunnan Province (YNM). Here, we sequenced complete mitogenomes of 132 Miao individuals from Yunnan Province using massively parallel sequencing method. Total 132 Miao individuals could be allocated to 119 various haplotypes, which were mainly dominated by haplogroups prevalent in southern East Asia (B, F, M7 and R9), and rarely occupied by northern lineages (A, D, G and M8). In order to dissect the genetic background of YNM more comprehensively, we introduced 99 published population data with 7135 complete mitochondrial sequences for population genetic comparisons. YNM exhibited closer genetic relationships with Hmong-Mien, Tai-Kadai, Sino-Tibetan and Austroasiatic populations, especially for Hmong-Mien populations; we further speculated that Miao group might have certain direct or indirect gene exchanges with ancient Baiyue groups. Several maternal lineages, such as B5a1c1a, F1g1, B4a5 and D4e1a3, were found to be specifically shared by YNM and other Hmong-Mien populations, and these matrilineal expansions occurred roughly during the Neolithic period. Eventually, according to the population dynamic analyses of YNM, the population size began to emerge recovery ∼1–0.5 kya after a long-term population reduction ∼1–5 kya, during which the B5a1c1a haplogroup manifested relatively apparent lineage expansion.

Analysis and Forecast of Contemporary Chinese Population

The analysis and projection of current Chinese population dynamics is the main emphasis of this study. This topic is extremely important in terms of demography, economics, sociology, and international relations. With approximately 1.43 billion people, China is the most populous country in the world and a worldwide giant in both economic and geopolitical terms. This study looks at historical, cultural, economic, and policy-related issues in an effort to understand the intricacies that have led China to this demographic prominence. China's population increase may be traced back to its ancient civilization, which cultivated cultural customs and conventions that still have an impact on demographic patterns now. The demographic dividend, a population surge in the middle of the 20th century, signaled a turning point, and the one-child policy that followed, implemented in 1979, produced distinctive demographic contours and long-term repercussions. Fertility rates and generational dynamics have been influenced by the government's evolution of family planning programs, which have ranged from strict measures to more relaxed methods. Understanding and predicting China's population changes is urgent because of the societal and worldwide repercussions of this country's changing demographics. This study sets out on an exploratory trip to understand the complex causes and possible future trends in light of previous studies. This paper wants to contribute to a thorough knowledge of China's demographic evolution and its effects on global society by shedding light on these factors.

Single-cell RNA sequencing analysis of immune cell population dynamics from peripheral blood in pig-to-non-human primate islet xenotransplantation treated with clinically applicable immunosuppressants

Single-cell RNA sequencing analysis of immune cell population dynamics from peripheral blood in pig-to-non-human primate islet xenotransplantation treated with clinically applicable immunosuppressants

Enhancing Anaerobic Digestion with an UASB Reactor of the Winery Wastewater for Producing Volatile Fatty Acid Effluent Enriched in Caproic Acid

The production of Volatile Fatty Acids (VFAs) from wastewater holds significant importance in the context of biorefinery concepts due to their potential as valuable precursors for various bio-based processes. Therefore, the primary objective of this research is to investigate the fermentation of Winery Wastewater (WW) in an Upflow Anaerobic Sludge Blanket (UASB) reactor to generate VFAs, with particular emphasis on Caproic Acid (HCa) production and the dynamics of the microbiota, under varying Hydraulic Retention Time (HRT) periods (8, 5, and 2.5 h). The change from an 8 h to a 5 h HRT period resulted in an approximately 20% increase in total VFA production. However, when the HRT was further reduced to 2.5 h, total VFA production decreased by approximately 50%. Concerning the specific production of HCa, expressed in grams of Chemical Oxygen Demand (gCOD), the maximum yield was observed at around 0.9 gCOD/L for a 5-h HRT. Microbial population analysis revealed that Eubacteria outnumbered Archaea across all HRTs. Population dynamics analysis indicated that the Firmicutes Phylum was predominant in all cases. Within this phylum, bacteria such as Clostridium kluyveri and Clostridium sp., known for their ability to produce HCa, were identified. Based on the results obtained, the application of the UASB reactor for WW treatment, within the biorefinery framework, has the potential to provide a practical alternative for HCa production when operated with a 5 h HRT.

Estimation of the Population Dynamics of Taxus cuspidata by Using a Static Life Table for Its Conservation

Taxus cuspidata is a rare and endangered plant species with an extremely small population which is endemic to China. This study focused on the natural T. cuspidata population in Jilin Province in China. Conventional population ecology survey methods were used to describe its population structure characteristics. Then, we chose diameter structure instead of temporal structure to establish a static population life table, draw a population survival curve, and quantify the future development trend by using population dynamic analysis and time sequence prediction. The results showed that: (1) the static life table suggested that the population of T. cuspidata was stable overall. The population survival curve tended to be Deevey Ⅱ, with a high early seedling mortality, and the later population growth tended to be stable; (2) the survival curve suggested that the population initially experienced higher mortality rates in the early stage. However, as time progressed and the population aged, the mortality rates decreased, resulting in a more stable population in the middle and late stages; (3) The diameter class structure of T. cuspidata was stable overall, and the dynamic indices showed that the population was fluctuating. The population was influenced by external disturbances and showed some resistance to human disturbance; (4) time sequence prediction analysis showed that the mortality rate of young individuals was high, natural renewal could be maintained, and the population size would remain at a certain amount in the future. The result shows that the Jilin region is a highly suitable area for the growth of Taxus cuspidata’s population in Northeast China. We recommend in situ conservation of remaining wild populations, relocation of germplasm resources, and reduction of human activities; these actions will be beneficial to Taxus cuspidata’s long-term survival.

Luring Triatomines (Hemiptera: Reduviidae) into a Trap: Aliphatic and Aromatic Aldehydes as Attractants of Triatoma infestans.

To assess the attracting capacity of aliphatic and aromatic aldehydes to Triatoma infestans, the Chagas disease vector, laboratory tests were conducted using individual compounds and mixtures to evaluate their potential use in baited traps for intradomicile population dynamics analysis. Commercial samples of hexanal, nonanal, and benzaldehyde were used at 95% purity. The experiments were performed at 25°C and 65% relative humidity using two procedures: a glass arena with filter papers impregnated with 1, 5, and 10 μL of the tested compounds and a double-choice olfactometer. Attraction was scored positively if the insect remained more than 30 seconds on one of the surfaces. The results of the study showed that hexanal was attractive to females at higher concentrations (5-10 μL; P < 0.0001), and IV instar nymphs were only attracted at the highest concentration (10 μL; P < 0.01). Nonanal was attractive to IV instar nymphs at 1 and 5 μL (P < 0.0001), whereas males and females were more attracted at 1 μL (P < 0.01 and P < 0.05, respectively). Benzaldehyde showed significant differences with respect to controls, attracting females at low concentrations (1 μL; P < 0.0001) and IV instar nymphs at 5 and 10 μL (P < 0.0001 and P < 0.001, respectively). In the olfactometer, the 60:40 hexanal/nonanal mixture was the most effective. In conclusion, this study demonstrated that the aliphatic and aromatic aldehydes studied here, both individually and in mixtures, could be used as effective attractants for T. infestans in intradomicile-baited traps. These results suggest that mixtures of these compounds could be implemented in field trials for Chagas disease surveillance.

Potato Wart Isolates from Europe and North America Form Distinct Clusters of Genetic Variation.

We have extended previously published sets of simple sequence repeat markers for Synchytrium endobioticum, selected to be polymorphic for the German-standard isolates of pathotypes P1, P2, P6, P8, and P18. These markers also complement the extensive published information on DNA polymorphisms for the mitogenomes of Synchytrium endobioticum. This extended set of 35 markers representing 73 alleles differentiated 51 isolates from Europe and North America into three large, well-separated clusters and subclusters using dendrogram analysis, principal coordinates analysis (PCoA), and population substructure analysis using STRUCTURE 2.3.4 software. This suggests a limited number of introgressions of the wart disease pathogen into current potato growing areas, followed by recombination and admixture of populations through human activities. The new markers extend the published marker sets and are useful tools for future analyses of population structure and dynamics in Synchytrium endobioticum, which are necessary to understand the biology of the interaction between the pathogen and its potato host and to develop future control strategies.

Contributions to Dynamic Analysis of Differential Evolution Algorithms.

The Differential Evolution (DE) algorithm is one of the most successful evolutionary computation techniques. However, its structure is not trivially translatable in terms of mathematical transformations that describe its population dynamics. In this work, analytical expressions are developed for the probability of enhancement of individuals after each application of a mutation operator followed by a crossover operation, assuming a population distributed radially around the optimum for the sphere objective function, considering the DE/rand/1/bin and the DE/rand/1/exp algorithm versions. These expressions are validated by numerical experiments. Considering quadratic functions given by f(x)=xTDTDx and populations distributed according to the linear transformation D-1 of a radially distributed population, it is also shown that the expressions still hold in the cases when f(x) is separable (D is diagonal) and when D is any nonsingular matrix and the crossover rate is Cr=1.0. The expressions are employed for the analysis of DE population dynamics. The analysis is extended to more complex situations, reaching rather precise predictions of the effect of problem dimension and of the choice of algorithm parameters.

Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia.

Respiratory syncytial virus (RSV), or human orthopneumovirus, is a major cause of acute lower respiratory infection (ALRI), particularly in young children, causing significant morbidity and mortality. We used pathogen genomics to characterize the population structure and genetic signatures of RSV isolates circulating in children in New South Wales between 2016 and 2018 and to understand the evolutionary dynamics of these strains in the context of publicly available RSV genomes from the region and globally. Whole-genome phylogenetic analysis demonstrated the co-circulation of a few major RSV clades in the paediatric population from Sydney. The whole-genome-based genotypes A23 (RSV-A ON1-like genotype) and B6 (RSV-B BA9-like genotype) were the predominant RSV-A and RSV-B genotypes circulating during the study period, respectively. These genotypes were characterized with high levels of diversity of predicted N- and O-linked glycosylation patterns in both the G and F glycoproteins. Interestingly, a novel 72-nucleotide triplication in the sequence that corresponds to the C-terminal region of the G gene was identified in four of the A23 genotype sequenced in this study. Consistently, the population dynamics analysis demonstrated a continuous increase in the effective population size of A23 and B6 genotypes globally. Further investigations including functional mapping of mutations and identifying the impact of sequence changes on virus fitness are highly required. This study highlights the potential impact of an integrated approach that uses WG-based phylogeny and studying selective pressure events in understanding the emergence and dissemination of RSV genotypes.