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Conservation genetics and demographic history of the endangered Cape Fear shiner (Notropis mekistocholas).

We examined allelic variation at 22 nuclear-encoded markers (21 microsatellites and one anonymous locus) and mitochondrial (mt)DNA in two geographical samples of the endangered cyprinid fish Notropis mekistocholas (Cape Fear shiner). Genetic diversity was relatively high in comparison to other endangered vertebrates, and there was no evidence of small population effects despite the low abundance reported for the species. Significant heterogeneity (following Bonferroni correction) in allele distribution at three microsatellites and in haplotype distribution in mtDNA was detected between the two localities. This heterogeneity may be due to reduced gene flow caused by a dam built in the early 1900 s. Bayesian coalescent analysis of microsatellite variation indicated that effective population size of Cape Fear shiners has declined in recent times (11-25 435 years ago, with highest posterior probabilities between 126 and 2007 years ago) by one-two orders of magnitude, consistent with the observed decline in abundance of the species. A decline in effective size was not indicated by analysis of mtDNA, where sequence polymorphism appeared to carry the signature of an older expansion phase that dated to the Pleistocene ( approximately 12 700 > 1 million years ago). Cape Fear shiners thus appear to have undergone an expansion phase following a glacial cycle but to have declined significantly in more recent times. These results suggest that rapidly evolving markers such as microsatellites may constitute a suitable tool when inferring recent demographic dynamics of populations.

Animals↗

Varying degrees of Apis mellifera ligustica introgression in protected populations of the black honeybee, Apis mellifera mellifera, in northwest Europe.

The natural distribution of honeybee subspecies in Europe has been significantly affected by human activities during the last century. Non-native subspecies of honeybees have been introduced and propagated, so that native black honeybee (Apis mellifera mellifera) populations lost their identity by gene-flow or went extinct. After previous studies investigated the remaining gene-pools of native honeybees in France and Spain, we here assess the genetic composition of eight northwest European populations of the black honeybee, using both mitochondrial (restriction fragment length polymorphisms of the intergenic transfer RNAleu-COII region) and nuclear (11 microsatellite loci) markers. Both data sets show that A. m. mellifera populations still exist in Norway, Sweden, Denmark, England, Scotland and Ireland, but that they are threatened by gene flow from commercial honeybees. Both Bayesian admixture analysis of the microsatellite data and DraI-RFLP (restriction fragment length polymorphism) analysis of the intergenic region indicated that gene-flow had hardly occurred in some populations, whereas almost 10% introgression was observed in other populations. The most introgressed population was found on the Danish Island of Laeso, which is the last remaining native Danish population of A. m. mellifera and the only one of the eight investigated populations that is protected by law. We discuss how individual admixture analysis can be used to monitor the restoration of honeybee populations that suffer from unwanted hybridization with non-native subspecies.

Animals↗

Genetic entities and mating system in hermaphroditic Fucus spiralis and its close dioecious relative F. vesiculosus (Fucaceae, Phaeophyceae).

To date, molecular markers have not settled the question of the specific status of the closely related, but phylogenetically unresolved, brown seaweeds, hermaphroditic Fucus spiralis and dioecious Fucus vesiculosus, nor their propensity for natural hybridization. To test the degree of species integrity and to assess effect of the mating system on the population genetic structure, 288 individuals coming from parapatric (discontinuous) and sympatric (contiguous) spatial configurations at two sites were genotyped with five microsatellite loci. Using a Bayesian admixture analysis, our results show that F. spiralis and F. vesiculosus comprise clearly distinct genetic entities (clusters) generally characterized by cosexual and unisexual individuals, respectively. Genetic diversity within each entity suggests that F. spiralis reproduces primarily through selfing while F. vesiculosus is characterized by an endogamous breeding regime. Nevertheless, aberrant sexual phenotypes were observed in each cluster, no diagnostic alleles were revealed and 10% of study individuals were intermediate between the two genetic entities. This pattern can be explained by recent divergence of two taxa with retention of ancestral polymorphism or asymmetrical, introgressive hybridization. However, given (i) coincident monomorphism at three loci in spiralis clusters and (ii) that significantly more intermediates were observed in sympatric stations than in parapatric stations, we argue that interspecific gene flow has occurred after divergence of the two taxa. Finally, we show that whether recently separated or recently introgressive, the divergent breeding systems probably contribute to species integrity in these two taxa.

Bayes Theorem↗

Dispersal and rapid evolution in brown trout colonizing virgin Subantarctic ecosystems.

Two brown trout Salmo trutta stocks of different origin (wild Polish, domestic commercial) came into secondary contact after deliberate releases conducted in virgin rivers systems of the Subantarctic Kerguelen Islands (70 degrees E 49 degrees S). Samples obtained in 2001-2003 and a historical sample from 1993 were analysed for genetic variation at seven microsatellite loci and one allozyme locus (LDH-C1*). Bayesian clustering analysis demonstrated that rapid genetic differentiation formed separate genetic units in neighbouring rivers in less than 20 years. These genetic units were characterized by a large proportion of Polish genotypes mixed with some genomes of domestic origin (up to 30%). A different colonization strategy of the naturalized stocks, likely related with differential performance, was identified as a cause of rapid population differentiation in this area.

Animals↗

Chronology for the Aegean Late Bronze Age 1700-1400 B.C.

Radiocarbon (carbon-14) data from the Aegean Bronze Age 1700-1400 B.C. show that the Santorini (Thera) eruption must have occurred in the late 17th century B.C. By using carbon-14 dates from the surrounding region, cultural phases, and Bayesian statistical analysis, we established a chronology for the initial Aegean Late Bronze Age cultural phases (Late Minoan IA, IB, and II). This chronology contrasts with conventional archaeological dates and cultural synthesis: stretching out the Late Minoan IA, IB, and II phases by approximately 100 years and requiring reassessment of standard interpretations of associations between the Egyptian and Near Eastern historical dates and phases and those in the Aegean and Cyprus in the mid-second millennium B.C.

Archaeology↗

Population pharmacokinetics of cefepime in the neonate.

Newborn infants cared for in neonatal intensive care units may develop nosocomial infections. Cefepime, a "fourth-generation" cephalosporin (i.e., with activity against virtually all of the chromosomal-beta-lactamase-producing and many extended-spectrum-beta-lactamase-producing organisms), provides excellent activity against many gram-negative pathogens resistant to expanded-spectrum cephalosporins currently used to treat neonatal infections. The purpose of this study was to determine the pharmacokinetics of cefepime in this population to optimize dosing and minimize potential adverse events. Premature and term infants <4 months of age hospitalized in two neonatal intensive care units were studied. Limited pharmacokinetic (PK) sampling occurred following a dose of cefepime at 50 mg/kg of body weight infused over 30 min. Population pharmacokinetic parameters were determined using the program NONMEM. Fifty-five infants were enrolled. Their average (+/- standard deviation) gestational age at birth was 30.5 +/- 5.3 weeks, and their average postnatal age at PK evaluation was 14.5 +/- 14.7 days. In the final PK model, cefepime clearance (CL) was strongly associated with serum creatinine (SCr) (CL [ml/min/kg] = 0.26 + 0.59/SCr). The volume of distribution for infants with a postconceptional age of <30 weeks was larger than that for infants with a postconceptional age of >30 weeks (0.51 versus 0.39 liter/kg, respectively). The Bayesian analysis-predicted cefepime trough concentration at a dose of 50 mg/kg every 12 h for infants < or = 14 days of age was 29.9 +/- 16.6 microg/ml. Cefepime, dosed at 30 mg/kg/dose every 12 h for infants less than 14 days of age, regardless of gestational age, should provide antibiotic exposure equivalent to or greater than 50 mg/kg every 8 h in older infants and children.

Anti-Bacterial Agents↗

Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023.

Recombination plays a crucial role in the evolution of SARS-CoV-2. The Omicron XBB* recombinant lineages are a noteworthy example, as they have been the dominant SARS-CoV-2 variant worldwide in the first half of 2023. Since November 2023, a new recombinant lineage between Omicron subvariants XBB and BA.2.86, designated XDR, has been detected mainly in Brazil. In this study, we reconstructed the spatiotemporal dynamics and estimated the absolute and relative transmissibility of the XDR lineage. The XDR lineage displayed a recombination breakpoint in the ORF1a-coding region, and the most closely related sequences to the 5' and 3' ends of the recombinant correspond to JD.1.1 and JN.1.1 lineages, respectively. The first XDR sequences were detected in November 2023 in the Northeastern Brazilian region, and their prevalence rapidly surged from <1% to 25% by February 2024. The Bayesian phylogeographic analysis supports that the XDR lineage likely emerged in the Northeastern Brazilian region around late October 2023 and rapidly disseminated within and outside Brazilian borders from mid-November onward. The median effective reproductive number of the XDR lineage in Brazil during the initial expansion phase was estimated to be around 1.5, and the average relative instantaneous reproduction numbers of XDR and JN* lineages were estimated to be 1.37 and 1.29 higher than that of co-circulating XBB* lineages. In summary, these findings support that the recombinant lineage XDR arose in the Northeastern Brazilian region in October 2023, shortly after the first detection of JN.1 sequences in the country. In Brazil, the XDR lineage exhibited a higher transmissibility level than its parental XBB.* lineages and is spreading at a rate similar to or slightly faster than the JN.1* lineages.IMPORTANCEThis study highlights the emergence and rapid dissemination of the recombinant SARS-CoV-2 XDR lineage, derived from the Omicron lineages JD.1.1 and JN.1.1. The XDR lineage exhibited equivalent transmissibility to its JN.1* parental lineages and quickly spread across Brazil in late 2023. The findings underscore the critical role of real-time genomic surveillance in detecting novel variants with higher transmission potential. By utilizing phylogenetic and epidemiological methods, this research provides important insights into the molecular dynamics of XDR, which could inform public health responses and vaccine composition updates. The study's significance lies in its ability to document the impact of recombination on viral evolution, offering valuable information to the field of virology and pandemic preparedness.

Brazil↗

Geochemistry of ground water and the incidence of acute myocardial infarction in Finland.

STUDY OBJECTIVE: To examine the association of spatial variation in acute myocardial infarction (AMI) incidence and its putative environmental determinants in ground water such as total water hardness, the concentration of calcium, magnesium, fluoride, iron, copper, zinc, nitrate, and aluminium. DESIGN: Small area study using Bayesian modelling and the geo-referenced data aggregated into 10 km x 10 km cells. SETTING: The population data were obtained from Statistics Finland, AMI case data from the National Death Register and the Hospital Discharge Register, and the geochemical data from hydrogeochemical database of Geological Survey of Finland. PARTICIPANTS: A total of 18 946 men aged 35-74 years with the first AMI attack in the years 1983, 1988, and 1993. MAIN RESULTS: One unit (in German degree degrees dH) increment in water hardness decreased the risk of AMI by 1%. Geochemical elements in ground water included in this study did not show a statistically significant effect on the incidence and spatial variation of AMI, even though suggestive findings were detected for fluoride (protective), iron and copper (increasing). CONCLUSIONS: The results of this study with more specific Bayesian statistical analysis confirm findings from earlier observations of the inverse relation between water hardness and coronary heart disease. The role of environmental geochemistry in the geographical variation of the AMI incidence should be studied further in more detail incorporating the individual intake of both food borne and water borne nutrients. Geochemical-spatial analysis provides a basis for the selection of areas suitable for such research.

Adult↗

Application of probability techniques to the objective interpretation of veterinary clinical biochemistry data.

Methods for the interpretation of veterinary clinical biochemistry have not developed as rapidly as biochemical technology. However, the results of clinical biochemistry tests are only of value when they are interpreted appropriately. A retrospective study was undertaken to investigate the equine biochemistry data which had been stored in a veterinary hospital database. By applying percentile analysis and Bayesian probability methods to the clinical biochemistry and corresponding diagnosis data, a novel method for the interpretation of clinical biochemistry data has been developed. The method allows clinicians to determine whether a biochemistry value is abnormal, its degree of abnormality, and the most likely associated diagnoses. The method could be used to investigate a practice-based population and may have significant implications for the interpretation of clinical biochemistry data in veterinary medicine in the future.

Animals↗

Identification of a novel HIV-1 circulating recombinant form (CRF209_cpx) and its descendant unique recombinant form (URF) CRF209_cpx/B among MSM in Guangdong, southern China.

BACKGROUND: The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07_BC, CRF01_AE, CRF55_01B, and subtype B. This study characterizes a novel CRF209_cpx and its descendant recombinant CRF209_cpx/B among men who have sex with men (MSM) in Guangdong, southern China. METHODS: Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2.5 and the HIVcoPRED tool. RESULTS: Four NFLG sequences were obtained and identified as a novel CRF209_cpx, generated by recombination among CRF01_AE, CRF07_BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209_cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209_cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209_cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. CONCLUSIONS: The emergence of the complex CRF209_cpx and novel URF of CRF209_cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

HIV-1↗

Diversity of model approaches for breast cancer screening: a review of model assumptions by the Cancer Intervention and Surveillance Network (CISNET) Breast Cancer Groups.

The National Cancer Institute-sponsored Cancer Intervention and Surveillance Network program on breast cancer is composed of seven research groups working largely independently to model the impact of screening and adjuvant therapy on breast cancer mortality trends in the US from 1975 to 2000. Each of the groups has chosen a different modeling methodology without purposeful attempt to be in contrast with each other. The seven groups have met biannually since November 2000 to discuss their methodology and results. This article investigates the differences in methodology. To facilitate this comparison, each of the groups submitted a description of their model into a uniformly structured web based 'model profiler'. Six of the seven models simulate a preclinical natural history that cannot be observed directly with parameters estimated from published evidence concerning screening and therapy effects. The remaining model regards published evidence on intervention effects as prior information and updates that with information from the US population in a Bayesian type analysis. In general, the differences between the models appear to be small, particularly among the models driven by natural history assumptions. However, we demonstrate that such apparently small differences can have a large impact on surveillance of population trends. We describe a systematic approach to evaluating differences in model assumptions and results, as well as differences in modeling culture underlying the differences in model structure and parameters.

Breast Neoplasms↗

A bayesian hierarchical model for the analysis of Affymetrix arrays.

An area of active research in DNA microarray analysis focuses on identifying differentially expressed genes between normal and malignant tissues. The analysis is complicated by the presence of several unreliable expression readings. Here, we illustrate a methodology where the expression estimates are modeled as censored data and discriminating genes are selected using ANOVA-based criteria.

Analysis of Variance↗

Successful implementation of the randomized discontinuation trial design: an application to the study of the putative antiangiogenic agent carboxyaminoimidazole in renal cell carcinoma--CALGB 69901.

PURPOSE: To assess the disease-stabilizing activity of carboxyaminoimidazole (CAI) in patients with metastatic renal cell cancer (RCC) using a randomized discontinuation trial (RDT) design. PATIENTS AND METHODS: Recruited patients had a performance status of 0 to 2, minimal neuropathy or cerebellar dysfunction, measurable disease, and normal organ function. Treatment with 250 mg/d CAI was initiated in all patients and continued until disease progression in those with an objective response. Protocol treatment was discontinued for unacceptable toxicity or progressive disease; patients with stable disease at the 16-week evaluation point were randomly assigned in a double-blind manner to continued CAI or placebo. The primary end point was the stable disease rate in the randomized groups. RESULTS: A total of 368 patients were accrued and received therapy. Ninety percent had a performance status of 0 or 1, 80% underwent a prior nephrectomy, and 41% had received no prior systemic therapy. Serious or life-threatening toxicity was experienced by 34%, with asthenia (15%) and neuropsychiatric difficulties (7%) being most common. At the randomization point, 51% of patients had progressed, 30% withdrew, 1% experienced a partial response, and 17% had stable disease and were randomly assigned. A Bayesian futility analysis utilizing the first 49 randomly assigned patients suggested that the probability of demonstrating a higher stable disease rate in the experimental group was less than 9% even under the most optimistic a priori assumptions, and further trial accrual was halted. CONCLUSION: CAI is inactive in RCC. The RDT design should be further explored for evaluating activity of putative disease stabilizing agents.

Adult↗

Calcium:magnesium ratio in local groundwater and incidence of acute myocardial infarction among males in rural Finland.

Several epidemiologic studies have shown an association between calcium and magnesium and coronary heart disease mortality and morbidity. In this small-area study, we examined the relationship between acute myocardial infarction (AMI) risk and content of Ca, Mg, and chromium in local groundwater in Finnish rural areas using Bayesian modeling and geospatial data aggregated into 10 km times symbol 10 km grid cells. Data on 14,495 men 35-74 years of age with their first AMI in the years 1983, 1988, or 1993 were pooled. Geochemical data consisted of 4,300 measurements of each element in local groundwater. The median concentrations of Mg, Ca, and Cr and the Ca:Mg ratio in well water were 2.61 mg/L, 12.23 mg/L, 0.27 microg/L, and 5.39, respectively. Each 1 mg/L increment in Mg level decreased the AMI risk by 4.9%, whereas a one unit increment in the Ca:Mg ratio increased the risk by 3.1%. Ca and Cr did not show any statistically significant effect on the incidence and spatial variation of AMI. Results of this study with specific Bayesian statistical analysis support earlier findings of a protective role of Mg and low Ca:Mg ratio against coronary heart disease but do not support the earlier hypothesis of a protective role of Ca.

Adult↗

Assessing the emergence time of SARS-CoV-2 zoonotic spillover.

Understanding the evolution of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) and its relationship to other coronaviruses in the wild is crucial for preventing future virus outbreaks. While the origin of the SARS-CoV-2 pandemic remains uncertain, mounting evidence suggests the direct involvement of the bat and pangolin coronaviruses in the evolution of the SARS-CoV-2 genome. To unravel the early days of a probable zoonotic spillover event, we analyzed genomic data from various coronavirus strains from both human and wild hosts. Bayesian phylogenetic analysis was performed using multiple datasets, using strict and relaxed clock evolutionary models to estimate the occurrence times of key speciation, gene transfer, and recombination events affecting the evolution of SARS-CoV-2 and its closest relatives. We found strong evidence supporting the presence of temporal structure in datasets containing SARS-CoV-2 variants, enabling us to estimate the time of SARS-CoV-2 zoonotic spillover between August and early October 2019. In contrast, datasets without SARS-CoV-2 variants provided mixed results in terms of temporal structure. However, they allowed us to establish that the presence of a statistically robust clade in the phylogenies of gene S and its receptor-binding (RBD) domain, including two bat (BANAL) and two Guangdong pangolin coronaviruses (CoVs), is due to the horizontal gene transfer of this gene from the bat CoV to the pangolin CoV that occurred in the middle of 2018. Importantly, this clade is closely located to SARS-CoV-2 in both phylogenies. This phylogenetic proximity had been explained by an RBD gene transfer from the Guangdong pangolin CoV to a very recent ancestor of SARS-CoV-2 in some earlier works in the field before the BANAL coronaviruses were discovered. Overall, our study provides valuable insights into the timeline and evolutionary dynamics of the SARS-CoV-2 pandemic.

Animals↗

The population structure of African cultivated rice oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation.

Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was due not to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, subspecies indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits-possibly reflecting ecological adaptation to different growing environments.

Acclimatization↗

Diversification of the forest beetle genus Tarphius on the Canary Islands, and the evolutionary origins of island endemics.

The flightless beetle genus Tarphius Erichson (Coleoptera: Colydiidae) is a distinctive element of the beetle fauna of the Canary Islands with 29 species distributed across the five western islands. The majority of Tarphius species are rare and intimately associated with the monteverde forest and only two species occur on more than one island. In this study we investigate the phylogeography of the Canary Island Tarphius, and their relationship to Tarphius from the more northerly archipelagos of Madeira and the Azores using maximum parsimony and Bayesian inference analysis of mitochondrial cytochrome oxidase I and II sequence data. We use geological datings for the Canary Islands, Azores, and Madeira to calibrate specific nodes of the tree for the estimation of divergence times using a penalized likelihood method. Data suggest that the Canary Island species assemblage is of some antiquity, however, much of this species diversity is relatively recent in origin. The phylogenetic relationships of species inhabiting the younger islands of El Hierro and La Palma indicate that colonization events between islands have probably been a significant factor in the evolutionary history of the Canary Island species assemblage. A comparison of molecular phylogenetic studies of arthropods on the Canary Islands suggests that, in the evolution of the arthropod species community of an island, the origin of endemic species is initially the result of colonizing lineages differentiating from their source populations. However, as an island matures a greater proportion of endemic species originate from intra-island speciation.

Animals↗

Random regression models for male and female fertility evaluation using longitudinal binary data.

A longitudinal Bayesian threshold analysis of insemination outcomes was carried out using 2 random regression models with 3 (Model 1) and 5 (Model 2) parameters to model the additive genetic values at the liability scale. All insemination events of first-parity Holstein cows were used. The outcome of an insemination event was treated as a binary response of either a success (1) or a failure (0). Thus, all breeding information for a cow, including all service sires, was included, thereby allowing for a joint evaluation of male and female fertility. An edited data set of 369,353 insemination records from 210,373 first-lactation cows was used. On the liability scale, both models included the systematic effects of herd-year, month of insemination, technician, and regressions on age of service sire and milk yield during the first 100 d of lactation. The random effects in the model were the 3 or 5 random regression coefficients specific to each cow, the permanent effect of the cow, and the service sire effect. Using Model 1, the estimated heritability of an insemination outcome decreased from 0.035 at d 50 to 0.032 at d 140 and then increased continuously with DIM. The genetic correlations for insemination success at different time points ranged from 0.83 to 0.99, and their magnitude decreased with an increase in the interval between inseminations. A similar trend was observed for heritability and genetic correlations using Model 2. However, the average estimate of heritability was much higher (0.058) than those obtained using Model 1 or a repeatability model. In addition, the estimated genetic correlations followed the same trend as Model 1, but were lower and with a higher rate of decrease when the interval between inseminations increased. The posterior mean of service sire variance was 0.01 for both models, and permanent environmental variance was 0.05 and 0.02 for Models 1 and 2, respectively. Model comparison based on the Bayes factor indicated that Model 1 was more plausible, given the data.

Animals↗