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Spatial analysis of bovine spongiform encephalopathy in Galicia, Spain (2000-2005).

In Spain, the first bovine spongiform encephalopathy (BSE) case was detected in 2000 in a cow born in the Galicia region (Northwestern Spain). From then and until October 2005, 590 cases were detected, 223 of them in Galicia. In 1994, meat and bone meal (MBM) was banned on ruminant feed and, in 1996, an EU decision mandating an overall change in MBM processing was implemented. This decision was gradually applied in the territory and not enforced before July 1998. The objective of this study was to explore clustering of BSE cases and estimate the standard incidence ratio (SIR) of BSE in Galicia. Our study was based on the BSE cases detected during the surveillance period 2000-2005 in the Galicia region. These cases were divided, based on birth date, into two periods: animals born from 1994 to July 1998, and those born after July 1998. We tested the role of cross-contamination on the geographical SIR distribution for both periods. Hierarchical Bayesian models were used to model the overdispersion and lack of independence of the SIR estimates. The geographical distribution of the standard incidence ratio of BSE between both periods was different. In the second period, the SIR was reduced in some areas. The reduction in these areas could be attributable to the changes in the processing of MBM. We did not find any statistical link between the poultry population and the standard incidence ratio, but pig population had a positive effect.

Animal Feed↗

Single origin of Malagasy Carnivora from an African ancestor.

The Carnivora are one of only four orders of terrestrial mammals living in Madagascar today. All four (carnivorans, primates, rodents and lipotyphlan insectivores) are placental mammals with limited means for dispersal, yet they occur on a large island that has been surrounded by a formidable oceanic barrier for at least 88 million years, predating the age of origin for any of these groups. Even so, as many as four colonizations of Madagascar have been proposed for the Carnivora alone. The mystery of the island's mammalian origins is confounded by its poor Tertiary fossil record, which leaves us with no direct means for estimating dates of initial diversification. Here we use a multi-gene phylogenetic analysis to show that Malagasy carnivorans are monophyletic and thus the product of a single colonization of Madagascar by an African ancestor. Furthermore, a bayesian analysis of divergence ages for Malagasy carnivorans and lemuriforms indicates that their respective colonizations were temporally separated by tens of millions of years. We therefore conclude that a single event, such as vicariance or common dispersal, cannot explain the presence of both groups in Madagascar.

Africa↗

[Meta-analysis of the Italian studies on short-term effects of air pollution].

BACKGROUND: In recent years, much attention has been given to review reports on the early effects of air pollution on health, measured through daily series of deaths and/or hospital admissions. A number of large planned meta-analyses (in which methods for data retrieval and processing are commonly planned a priori for all participating centers) are on going both in the US and in Europe. The National Mortality, Morbidity and Air Pollution Study included data from 90 US cities, whereas APHEA (Air Pollution and Health, a European Approach) considers data from about 30 european cities. The present paper summarizes methods and findings of MISA, a meta-analysis of data from 8 Italian cities. It belongs to an ad hoc supplement of Epidemiologia & Prevenzione (Epidemiol Prev 2001; 25 (2) Suppl: 1-72), the official Journal of the Italian Association of Epidemiology, which contains a full description of the study. MISA was launched on March 2000, within the project "Statistics, Environment and Health" (GRASPA), funded by the Italian Ministry of Education. Additional support was given by the Authorities of the 8 participating cities (from North to South: Turin, Milan, Verona, Ravenna, Bologna, Florence, Rome and Palermo). DAILY HEALTH DATA: Deaths certificate and hospital admission data have been collected respectively from the Local Health Authority and regional files. The same programme for retrieval of data on selected hospital admissions for acute conditions was used in the 8 cities. Main data are summarized in Table 1. DAILY CONCENTRATION OF POLLUTANTS: Most data were obtained from Regional Environmental Protection Agencies, which are responsible for environmental monitoring since 1993. Verona, Palermo and Milan (1990-94) data were obtained from local sources. Monitors with more than 25% of missing data were excluded. Meteorological data were collected by the same monitors and completed with data from monitors situated in the suburbs or (in Milan and Bologna) in the airport. The monitors were selected by a group of experts to ensure comparability. For SO2 and NO2 daily averages of hourly measurements were used, whereas concentrations of ozone and CO were estimated as the maximum 8 hours moving average. Total suspended particulate or PM10 were measured as 24 hours deposition. All analyses used the whole range of observed values (Table 2). Daily data were considered as missing when more than 25% of hourly data were not available. Missing data in one monitor were imputed as average of data from the remaining monitors weighted by the ratio between the specific monitor's year average and the general year average of all the selected city monitors. Missing data in one day were imputed as average of four days (preceding and following day, the same day of the previous and following weeks). In the city of Florence and Palermo PM10 concentrations were available. For the other cities we applied a conversion factor from PTS to PM10 (0.6 for Turin and 0.8 for all the others) estimated through validation studies. Ozone concentrations were used only where background monitors were available (Turin, Verona, Bologna and Florence) and limited to the warm season (May through September). METHODS: A common protocol for the city-specific analyses was defined on the basis of a structured exploratory analysis. The adopted basic model was a Generalized Additive Model for Poisson data. Effect estimates were age-adjusted (0-64, 65-74, 75+) and formal tests of interaction pollutant-age were conducted. In the first two age groups, indicator variables for seasonality were specified, and cubic splines with fixed number of degree of freedom were specified for the last age group and for all age groups for the morbidity data. Model adequacy was checked by residual analysis and inspection of the partial autocorrelation function. In a sensitivity analysis non linear pollutant effects were considered and overdispersed [table: see text] transitional models were fitted; the analysis was conducted for all lags 0-3 and some distributed lags (0-1, 1-2, 0-3); no multipollutant models were fitted. The same model was fitted to the city data. No model selection was done: Table 3 describes the steps in model building. In the meta-analysis, for each outcome, the estimates for each pollutant and for each city were combined using fixed and random effects models. Heterogeneity of effects was tested according to DerSimonian and Laird. Results were checked using a hierarchical bayesian model, which was used to investigate heterogeneity across cities in a meta-regression phase. Non informative priors were used. Posterior distributions of parameters of interest have been obtained with WinBUGS. 10,000 iterations (excluding [table: see text] the first 2000) were retained, while for the meta-regression 100,000 iterations (excluding the first 4000) were stored. To approximate the marginal posteriors only one sample out of five were used. Achieved convergence was assessed using the Gelman and Rubin approach. In the meta-regression the models specified were the following: [formula: see text] i denotes city, j calendar period (1990-1994; 1995-1999). The first model includes only period as effect modifier, while the second model other potential variables. The ui terms (which do not vary with j) represent city specific random effects. RESULTS: For each pollutant, the meta-analysis detected a statistically significant association with mortality for natural causes. But for ozone, positive associations were commonly found for death and hospital admissions for both cardiovascular and respiratory diseases. Indeed, the only estimates whose lower 95% confidence limit bore a negative sign regarded the association between PM10 and mortality from respiratory diseases. Ozone in the warm season was positively and significantly associated with daily mortality and mortality for cardiovascular diseases whereas other estimates did not reach statistical significance and some were negative (only lag 0-1 for external comparability are reported in Table 4). Risks were highest (up to 4%) for respiratory conditions (Table 4). They were more pronounced at lag 1-2 for mortality, and at lag 0-3 for hospital admissions. Age was an effect modifier for mortality, the elderly being more susceptible. In the random effect meta-analysis, at lag 1-2, excess risks for unit increase of the pollutants at age 75+ and at age 0-64 were respectively: 4.9% and -0.4% for SO2, 1.7% and 0.6% for NO2; 2.3% and 0.2% for CO. Corresponding figures for PM10 at lag 0-1 were 1.1% and 0.2%. The effect of PM10 on mortality [table: see text] was greater during the warm season (2.8% vs 0.8%). A complete analysis is reported in the Italian text. Here we provide some details on the effects of PM10, about which the residual heterogeneity across cities was highest (Table 4). In addition, the epidemiological evidence on the hazards from this fraction of particulate matter is more controversial. Table 5 reports the excess risk estimated through the meta-analysis in 1995-99 for a 10 micrograms/m3 increase of PM10 for some outcomes. Proper prior distributions (overdispersed normal and inverse gamma) were adopted in the final bayesian analyses. The sensitivity of results to the choice of the priors were investigated (we defined proper and improper uniform, student's t), obtaining comparable results. Total natural mortality was significantly heterogeneous across cities (Q = 18.96, 5 df, p < 0.001). City-specific estimates are represented graphically in Fig. 1. As expected, the confidence (credibility) intervals are widest [table: see text] for bayesian estimates, intermediate for those obtained under a random effects model, and narrowest for those found under a fixed effects model. Nevertheless, differences in point estimates are negligible. A North-South gradient in risk is obvious. Table 6 shows, for the cities for which mortality data were available, the improvement in precision and the shrinkage of effect estimates toward the overall mean introduced by the bayesian modelling. In the meta-regression, total mortality and a deprivation score were associated with greater effects. The excess risks on hospital admission were modified by the deprivation score and by the NO2/PM10 ratio. Overall, the risk estimates were greater in the calendar period 1995-99 and there was a North-South gradient, with larger effects in cities located in Central and Southern Italy (Florence, Rome, Palermo). CONCLUSIONS: The meta-analysis of the Italian studies on short-term effects of air pollution in 8 cities, MISA, exhibits the following features: With the exception of Naples, all greatest Italian cities were included; overall a population of 7 million was enrolled. The study protocol was accurate with regard to the selection of hospital admissions for acute conditions. Monitored data of concentration of pollutant were carefully evaluated before their inclusion in the meta-analysis. City specific analyses were carried out according to a common protocol controlling for seasonality, influenza epidemics, age and meterological variables; [table: see text] the protocol derived from a structured exploratory analysis. The meta-analysis was done using fixed and random effects models; a hierarchical bayesian model was fitted in a sensitivity analysis. The heterogeneity of effects across cities was investigated using a hierarchical bayesian model for meta-regression. While mortality data are of good quality, hospital admission data are more problematic. Since the filing criteria for the latter changed around 1995, comparability of results before and after such date is limited. Moreover, hospital admissions rely on availability of beds, the offer of which may be restricted during the warm season. Comparability of pollutant concentration estimates among cities may have been influenced by differences in monitor characteristics. (ABSTRACT TRUNCATED)

Adolescent↗

Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae): tracking Tertiary plant migration.

Data from four DNA regions (rbcL, matK, 26S rDNA, and ITS) as well as extant and fossil morphology were used to reconstruct the phylogeny and biogeographic history of an intercontinentally disjunct plant group, the cornelian cherries of Cornus (dogwoods). The study tests previous hypotheses on the relative roles of two Tertiary land bridges, the North Atlantic land bridge (NALB) and the Bering land bridge (BLB), in plant migration across continents. Three approaches, the Bayesian, nonparametric rate smoothing (NPRS), and penalized likelihood (PL) methods, were employed to estimate the times of geographic isolations of species. Dispersal and vicariance analysis (DIVA) was performed to infer the sequence and directionality of biogeographic pathways. Results of phylogenetic analyses suggest that among the six living species, C. sessilis from western North America represents the oldest lineage, followed by C. volkensii from Africa. The four Eurasian species form a clade consisting of two sister pairs, C. mas-C. officinalis and C. chinensis-C. eydeana. Results of DIVA and data from fossils and molecular dating indicate that the cornelian cherry subgroup arose in Europe as early as the Paleocene. Fossils confirm that the group was present in North America by the late Paleocene, consistent with the DIVA predictions that, by the end of the Eocene, it had diversified into several species and expanded its distribution to North America via the NALB and to Africa via the last direct connection between Eurasia and Africa prior to the Miocene, or via long-distance dispersal. The cornelian cherries in eastern Asia appear to be derived from two independent dispersal events from Europe. These events are inferred to have occurred during the Oligocene and Miocene. This study supports the hypothesis that the NALB served as an important land bridge connecting the North American and European floras, as well as connecting American and African floras via Europe during the early Tertiary.

Base Sequence↗

Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats.

Molecular and morphological hypotheses disagree on the phylogenetic position of New Zealand's short-tailed bat Mystacina tuberculata. Most morphological analyses place Mystacina in the superfamily Vespertilionoidea, whereas molecular studies unite Mystacina with the Neotropical noctilionoids and imply a shared Gondwanan history. To date, competing hypotheses for the placement of Mystacina have not been addressed with a large concatenation of nuclear protein sequences. We investigated this problem using 7.1kb of nuclear sequence data that included segments from five nuclear protein-coding genes for representatives of 14 bat families and six laurasiatherian outgroups. We employed the Thorne/Kishino method of molecular dating, allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution on different branches on the phylogenetic tree, to estimate basal divergence times within key chiropteran clades. Maximum likelihood, minimum evolution, maximum parsimony, and Bayesian posterior probabilities all provide robust support for the association of Mystacina with the South American noctilionoids. The basal divergence within Chiroptera was estimated at 67mya and the mystacinid/noctilionoid split was calculated at 47mya. Although the mystacinid lineage is too young to have originated in New Zealand before it split from the other Gondwanan landmasses (80mya), the exact geographic origin of these lineages is still uncertain and will not be answered until more fossils are found. It is most probable that Mystacina dispersed from Australia to New Zealand while other noctilionoid bats either remained in or dispersed to South America.

Animals↗

Genetic basis of climatic adaptation in scots pine by bayesian quantitative trait locus analysis.

We examined the genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine. As a mapping population, we considered an "open-pollinated backcross" progeny by collecting seeds of a single F(1) tree (cross between trees from southern and northern Finland) growing in southern Finland. Due to the special features of the design (no marker information available on grandparents or the father), we applied a Bayesian quantitative trait locus (QTL) mapping method developed previously for outcrossed offspring. We found four potential QTL for timing of bud set and seven for frost hardiness. Bayesian analyses detected more QTL than ANOVA for frost hardiness, but the opposite was true for bud set. These QTL included alleles with rather large effects, and additionally smaller QTL were supported. The largest QTL for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in selection of at least some alleles of rather large effect.

Acclimatization↗

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.

Animals↗

Placing confidence limits on the molecular age of the human-chimpanzee divergence.

Molecular clocks have been used to date the divergence of humans and chimpanzees for nearly four decades. Nonetheless, this date and its confidence interval remain to be firmly established. In an effort to generate a genomic view of the human-chimpanzee divergence, we have analyzed 167 nuclear protein-coding genes and built a reliable confidence interval around the calculated time by applying a multifactor bootstrap-resampling approach. Bayesian and maximum likelihood analyses of neutral DNA substitutions show that the human-chimpanzee divergence is close to 20% of the ape-Old World monkey (OWM) divergence. Therefore, the generally accepted range of 23.8-35 millions of years ago for the ape-OWM divergence yields a range of 4.98-7.02 millions of years ago for human-chimpanzee divergence. Thus, the older time estimates for the human-chimpanzee divergence, from molecular and paleontological studies, are unlikely to be correct. For a given the ape-OWM divergence time, the 95% confidence interval of the human-chimpanzee divergence ranges from -12% to 19% of the estimated time. Computer simulations suggest that the 95% confidence intervals obtained by using a multifactor bootstrap-resampling approach contain the true value with >95% probability, whether deviations from the molecular clock are random or correlated among lineages. Analyses revealed that the use of amino acid sequence differences is not optimal for dating human-chimpanzee divergence and that the inclusion of additional genes is unlikely to narrow the confidence interval significantly. We conclude that tests of hypotheses about the timing of human-chimpanzee divergence demand more precise fossil-based calibrations.

Animals↗

Monitoring and analysis of bovine spongiform encephalopathy (BSE) testing in Denmark using statistical models.

The evolution of monitoring and surveillance for bovine spongiform encephalopathy (BSE) from the phase of passive surveillance that began in the United Kingdom in 1988 until the present is described. Currently, surveillance for BSE in Europe consists of mass testing of cattle slaughtered for human consumption and cattle from certain groups considered to be at higher risk of having clinical or detectable BSE. The results of the ongoing BSE testing in Denmark have been analyzed using two statistical approaches: the "classical" frequentist and the Bayesian that is widely used in quantitative risk analysis. The analyses were intended to provide information for decision-makers, the media and the public as well as to provide inputs for future BSE surveillance models. The results to date suggest that the total number of BSE cases that will be found in Denmark in 2001 will not exceed 16.

Age Distribution↗

Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population.

The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

Animal Migration↗

Pretest probability estimates: a pitfall to the clinical utility of evidence-based medicine?

OBJECTIVES: The Bayesian application of likelihood ratios has become incorporated into evidence-based medicine (EBM). This approach uses clinicians' pretest estimates of disease along with the results of diagnostic tests to generate individualized posttest disease probabilities for a given patient. To date, there is minimum scientific validation for the clinical application of this approach. This study is designed to evaluate variability in the initial step of this process, clinicians' estimates of pretest probability of disease, to assess whether this approach can be expected to yield consistent posttest disease estimates. METHODS: This cross-sectional cohort study was conducted at an urban county teaching hospital by using a sample of emergency and internal medicine residents and faculty, as well as emergency department (ED) midlevel practitioners. Participants read clinical vignettes designed to raise consideration for common ED disorders and were asked to estimate the likelihood of the suggested diagnosis based on the history and physical examination findings alone. No information about laboratory results or imaging studies was provided. RESULTS: Mean pretest probability estimates of disease ranged from 42% (95% confidence interval [95% CI] = 36.6% to 47.4%) to 77% (95% CI = 72.9% to 81.1%). The smallest difference in pretest probability magnitude for a single vignette was 70% (range 30-100%; interquartile range [IQR] 64-80%), whereas the largest was 95% (range 3-98%; IQR 30-60%). CONCLUSIONS: Wide variability in clinicians' pretest probability estimates of disease may present a possible concern about decision-making models based on Bayes' theorem, because it may ultimately yield inconsistent posttest disease estimates.

Bayes Theorem↗

Evolutionary relationships of "Candidatus Riesia spp.," endosymbiotic enterobacteriaceae living within hematophagous primate lice.

The primary endosymbiotic bacteria from three species of parasitic primate lice were characterized molecularly. We have confirmed the characterization of the primary endosymbiont (P-endosymbiont) of the human head/body louse Pediculus humanus and provide new characterizations of the P-endosymbionts from Pediculus schaeffi from chimpanzees and Pthirus pubis, the pubic louse of humans. The endosymbionts show an average percent sequence divergence of 11 to 15% from the most closely related known bacterium "Candidatus Arsenophonus insecticola." We propose that two additional species be added to the genus "Candidatus Riesia." The new species proposed within "Candidatus Riesia" have sequence divergences of 3.4% and 10 to 12% based on uncorrected pairwise differences. Our Bayesian analysis shows that the branching pattern for the primary endosymbionts was the same as that for their louse hosts, suggesting a long coevolutionary history between primate lice and their primary endosymbionts. We used a calibration of 5.6 million years to date the divergence between endosymbionts from human and chimpanzee lice and estimated an evolutionary rate of nucleotide substitution of 0.67% per million years, which is 15 to 30 times faster than previous estimates calculated for Buchnera, the primary endosymbiont in aphids. Given the evidence for cospeciation with primate lice and the evidence for fast evolutionary rates, this lineage of endosymbiotic bacteria can be evaluated as a fast-evolving marker of both louse and primate evolutionary histories.

Animals↗

Plastome evolution and phylogenomic relationships in Ajuga (Lamiaceae, Ajugoideae).

BACKGROUND: Ajuga is currently known to include approximately 69 species, with a combined distribution extending throughout Eurasia, Africa, and Australia. Its popularity and significance are largely based on an extensive history of medicinal and horticultural use. It is divided into two sections based on morphological characters, and this sectional classification is also reflected in pronounced geographic patterns. Although previous studies have largely focused on Ajuga sect. Ajuga in East Asia, A. sect. Chamaepithys, which ranges from the Mediterranean to Central Asia, remains insufficiently sampled, thereby limiting a comprehensive understanding of infrageneric sectional relationships within the genus. Here, we generated complete plastid genomes for 12 species representing both sections of the genus and used these data to characterize plastome structure and infer evolutionary relationships. RESULTS: In this study, 21 Ajuga plastomes were analyzed, including 12 newly sequenced plastomes and 9 previously published plastomes representing 19 species. Comparative analyses showed that all plastomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 149,963 to 150,740&#xa0;bp and GC contents varying from 38.2% to 38.3%. Each plastome contained 133 genes, including 88 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The boundaries between the inverted repeat (IR) and single-copy (SC) regions were also highly conserved across species. In addition, 796 simple sequence repeats (SSRs), 874 long repeat sequences (LRSs), and 12 highly variable regions (ccsA-ndhD, ndhF-rpl32, petA-psbJ, rpl32-trnL-UAG, rps2-rpoC2, trnH-GUG-psbA, trnK-UUU-rps16, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, ycf15-trnL-CAA, ndhF, and ycf1) were identified among the 21 plastomes. Phylogenetic analyses based on four datasets and conducted using Maximum Likelihood and Bayesian Inference recovered two major clades corresponding to the traditionally recognized sectional classification, with one distributed from the Mediterranean to Central Asia and the other in East Asia. CONCLUSION: This study represents the most comprehensive plastome-based sampling of Ajuga to date, including representative species from the Mediterranean, Central Asia, and East Asia. Our results have significantly enhanced our understanding of its infrageneric relationships. The plastome resources generated in this study provide a valuable foundation for future research on species delimitation, phylogeny, and the evolutionary history of Ajuga.

Phylogeny↗

Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae).

Molecular clock methods allow biologists to estimate divergence times, which in turn play an important role in comparative studies of many evolutionary processes. It is well known that molecular age estimates can be biased by heterogeneity in rates of molecular evolution, but less attention has been paid to the issue of potentially erroneous fossil calibrations. In this study we estimate the timing of diversification in Centrarchidae, an endemic major lineage of the diverse North American freshwater fish fauna, through a new approach to fossil calibration and molecular evolutionary model selection. Given a completely resolved multi-gene molecular phylogeny and a set of multiple fossil-inferred age estimates, we tested for potentially erroneous fossil calibrations using a recently developed fossil cross-validation. We also used fossil information to guide the selection of the optimal molecular evolutionary model with a new fossil jackknife method in a fossil-based model cross-validation. The centrarchid phylogeny resulted from a mixed-model Bayesian strategy that included 14 separate data partitions sampled from three mtDNA and four nuclear genes. Ten of the 31 interspecific nodes in the centrarchid phylogeny were assigned a minimal age estimate from the centrarchid fossil record. Our analyses identified four fossil dates that were inconsistent with the other fossils, and we removed them from the molecular dating analysis. Using fossil-based model cross-validation to determine the optimal smoothing value in penalized likelihood analysis, and six mutually consistent fossil calibrations, the age of the most recent common ancestor of Centrarchidae was 33.59 million years ago (mya). Penalized likelihood analyses of individual data partitions all converged on a very similar age estimate for this node, indicating that rate heterogeneity among data partitions is not confounding our analyses. These results place the origin of the centrarchid radiation at a time of major faunal turnover as the fossil record indicates that the most diverse lineages of the North American freshwater fish fauna originated at the Eocene-Oligocene boundary, approximately 34 mya. This time coincided with major global climate change from warm to cool temperatures and a signature of elevated lineage extinction and origination in the fossil record across the tree of life. Our analyses demonstrate the utility of fossil cross-validation to critically assess individual fossil calibration points, providing the ability to discriminate between consistent and inconsistent fossil age estimates that are used for calibrating molecular phylogenies.

Animals↗

A model selection-based interval-mapping method for autopolyploids.

While extensive progress has been made in quantitative trait locus (QTL) mapping for diploid species, similar progress in QTL mapping for polyploids has been limited due to the complex genetic architecture of polyploids. To date, QTL mapping in polyploids has focused mainly on tetraploids with dominant and/or codominant markers. Here, we extend this view to include any even ploidy level under a dominant marker system. Our approach first selects the most likely chromosomal marker configurations using a Bayesian selection criterion and then fits an interval-mapping model to each candidate. Profiles of the likelihood-ratio test statistic and the maximum-likelihood estimates (MLEs) of parameters including QTL effects are obtained via the EM algorithm. Putative QTL are then detected using a resampling-based significance threshold, and the corresponding parental configuration is identified to be the underlying parental configuration from which the data are observed. Although presented via pseudo-doubled backcross experiments, this approach can be readily extended to other breeding systems. Our method is applied to single-dose restriction fragment autotetraploid alfalfa data, and the performance is investigated through simulation studies.

Algorithms↗

Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling.

We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally linked to Mediterranean-type climatic shifts of the mid-Miocene and whether climate preferences are conservative over phylogenetic timescales. Phyloclimatic modeling combines environmental niche (bioclimatic) modeling with phylogenetics in order to study evolutionary patterns in relation to climate change. We present the largest and most complete such example to date using Drosera. The bioclimatic models of extant species demonstrate clear phylogenetic patterns; this is particularly evident for the tuberous sundews from southwestern Australia (subgenus Ergaleium). We employ a method for establishing confidence intervals of node ages on a phylogeny using replicates from a Bayesian phylogenetic analysis. This chronogram shows that many clades, including subgenus Ergaleium and section Bryastrum, diversified during the establishment of the Mediterranean-type climate. Ancestral reconstructions of bioclimatic models demonstrate a pattern of preference for this climate type within these groups. Ancestral bioclimatic models are projected into palaeo-climate reconstructions for the time periods indicated by the chronogram. We present two such examples that each generate plausible estimates of ancestral lineage distribution, which are similar to their current distributions. This is the first study to attempt bioclimatic projections on evolutionary time scales. The sundews appear to have diversified in response to local climate development. Some groups are specialized for Mediterranean climates, others show wide-ranging generalism. This demonstrates that Phyloclimatic modeling could be repeated for other plant groups and is fundamental to the understanding of evolutionary responses to climate change.

Acclimatization↗

Efficacy of prophylactic antibiotic therapy in spinal surgery: a meta-analysis.

OBJECTIVE: There is considerable variation in practice regarding the use of prophylactic antibiotic therapy in spinal operations. To date, individual studies have not demonstrated a significant benefit for prophylactic antibiotic therapy in spinal operations. METHODS: Systematic database searches for randomized prospective trials of prophylactic antibiotic therapy in spinal surgery, general neurosurgery, and orthopedic surgery were performed. Random-effects meta-analysis and Bayesian meta-regressions of treatment benefits versus baseline infection rates and other trial characteristics were performed. RESULTS: Six prospective randomized trials or trial subgroups, enrolling 843 patients, were identified, i.e., one spinal surgery trial, four general neurosurgery trials, and one general orthopedic surgery trial. No individual trial demonstrated a statistically significant effect of prophylactic antibiotic therapy for spinal surgery patients. Raw pooled infection rates were 2.2% (10 of 451 patients) with antibiotics and 5.9% (23 of 392 patients) without antibiotics. Individual trial infection rates ranged from 1.2 to 8.5%. The pooled odds ratio was 0.37 (95% confidence interval, 0.17-0.78), favoring antibiotic treatment (P < 0.01). There was no significant heterogeneity in treatment efficacy among the trials. Bayesian meta-regression was used to test whether antibiotics were less effective in trials with low baseline infection rates and whether an optimal antibiotic regimen could be identified. There was no significant difference in antibiotic treatment effects in trials with lower baseline infection rates, in trials using antibiotics with gram-negative coverage in addition to gram-positive coverage, or in trials using multiple-dose versus single-dose regimens. Nonrandomized studies of antibiotic therapy in spinal surgery yielded greater treatment effect estimates than did randomized trials, but not significantly so. CONCLUSION: Prophylactic antibiotic therapy is beneficial for spinal surgery, even when expected infection rates without antibiotic treatment are low.

Antibiotic Prophylaxis↗

Genome scan for quantitative trait loci influencing HDL levels: evidence for multilocus inheritance in familial combined hyperlipidemia.

Several genome scans in search of high-density lipoprotein (HDL) quantitative trait loci (QTLs) have been performed. However, to date the actual identification of genes implicated in the regulation of common forms of HDL abnormalities remains unsuccessful. This may be due, in part, to the oligogenic and multivariate nature of HDL regulation, and potentially, pleiotropy affecting HDL and other lipid-related traits. Using a Bayesian Markov Chain Monte Carlo (MCMC) approach, we recently provided evidence of linkage of HDL level variation to the APOA1-C3-A4-A5 gene complex, in familial combined hyperlipidemia pedigrees, with an estimated number of two to three large QTLs remaining to be identified. We also presented results consistent with pleiotropy affecting HDL and triglycerides at the APOA1-C3-A4-A5 gene complex. Here we use the same MCMC analytic strategy, which allows for oligogenic trait models, as well as simultaneous incorporation of covariates, in the context of multipoint analysis. We now present results from a genome scan in search for the additional HDL QTLs in these pedigrees. We provide evidence of linkage for additional HDL QTLs on chromosomes 3p14 and 13q32, with results on chromosome 3 further supported by maximum parametric and variance component LOD scores of 3.0 and 2.6, respectively. Weaker evidence of linkage was also obtained for 7q32, 12q12, 14q31-32 and 16q23-24.

Adolescent↗