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PubMed2001

Perception viewed as an inverse problem.

The modern study of perception began when Fechner published his 'Elements of Psychophysics' in 1860. This book has guided most perception research ever since. It has become increasingly clear that there are problems with Fechner's approach, which assumes that the percept is completely determined by the sensory input. Fechner's approach cannot explain the processes that allow our percepts to be veridical. Post-Fechnerian schools (Helmholtzian, Structural, Gestalt and Gibsonian) have tried to deal with this problem, but have not been successful. An alternative to the Fechnerian approach is required. This paper describes an alternative that has been developing over the last 20 years within the computer vision community. It treats perceptual interpretation as a solution of an inverse problem that depends critically on the operation of a priori constraints. Contemporary research, which adopted this approach, has concentrated on verifying the usefulness of Bayesian and standard regularization methods. This paper takes the next step; it discusses theoretical and empirical aspects of studying human perception as an inverse problem. It reviews the literature that illustrates the power of the inverse problem approach. This review leads to the suggestion that progress in the study of perception will benefit if the inverse approach were to be adopted by experimentalists, as well as by the computational modelers, who have been actively exploring its potential to date.

Bayes Theorem↗
PubMed2004

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↗
PubMed1990

Estimating the distribution of times from HIV seroconversion to AIDS using multiple imputation. Multicentre AIDS Cohort Study.

Multiple imputation is a model based technique for handling missing data problems. In this application we use the technique to estimate the distribution of times from HIV seroconversion to AIDS diagnosis with data from a cohort study of 4954 homosexual men with 4 years of follow-up. In this example the missing data are the dates of diagnosis with AIDS. The imputation procedure is performed in two stages. In the first stage, we estimate the residual AIDS-free time distribution as a function of covariates measured on the study participants with data provided by the participants who were seropositive at study entry. Specifically, we assume the residual AIDS-free times follow a log-normal regression model that depends on the covariates measured at enrolment on the seropositive participants. In the second stage we impute the date of AIDS diagnosis for the participants who seroconverted during the course of the study and are AIDS-free with use of the log-normal distribution estimated in the first stage and the covariates from each seroconverter's latest visit. The estimated proportions developing AIDS within 4 and within 7 years of seroconversion are 15 and 36 per cent respectively, with associated 95 per cent confidence intervals of (10, 21) and (26, 47) per cent. We discuss the Bayesian foundations of the multiple imputation technique and the statistical and scientific assumptions.

AIDS Serodiagnosis↗
PubMed2002

BALSA: Bayesian algorithm for local sequence alignment.

The Smith-Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained are dependent upon the lengths of the aligned sequences, requiring a post-analysis conversion. To overcome some of these shortcomings, we developed a Bayesian algorithm for local sequence alignment (BALSA), that takes into account the uncertainty associated with all unknown variables by incorporating in its forward sums a series of scoring matrices, gap parameters and all possible alignments. The algorithm can return both the joint and the marginal optimal alignments, samples of alignments drawn from the posterior distribution and the posterior probabilities of gap penalties and scoring matrices. Furthermore, it automatically adjusts for variations in sequence lengths. BALSA was compared with SSEARCH, to date the best performing dynamic programming algorithm in the detection of structural neighbors. Using the SCOP databases PDB40D-B and PDB90D-B, BALSA detected 19.8 and 41.3% of remote homologs whereas SSEARCH detected 18.4 and 38% at an error rate of 1% errors per query over the databases, respectively.

Algorithms↗
PubMed1987

Clinical pharmacokinetics of factor VIII in patients with classic haemophilia.

Studies of Factor VIII pharmacokinetics in haemophiliacs can be classified into 2 groups depending on whether single-dose or multiple-dose Factor VIII curves are used. This review analyses information published so far in both these areas, with particular emphasis on the choice of appropriate models for pharmacokinetic analysis. Single-dose studies of Factor VIII kinetics have previously used a wide variety of methods for pharmacokinetic analysis (empirical methods of Factor VIII level prediction, graphical techniques for semilog analysis, 1-compartment and 2-compartment models). However, Factor VIII poses unique problems to the pharmacokineticist because decay curves can be either monophasic (monoexponential) or biphasic (biexponential) for unknown reasons, and because Factor VIII concentrations are generally subject to significant assay error. Problems of compartmental analysis that occurred in previous studies are highlighted, and a model-independent non-compartmental approach for analysing Factor VIII curves is proposed. To date, fewer data have been published on multiple-dose kinetics of Factor VIII. From a clinical point of view, repeated-dose regimens are most commonly required in patients undergoing surgery and in patients with severe bleeding. A fairly well defined 'therapeutic window' of optimal Factor VIII plasma concentrations has been identified, particularly in surgical patients. This fact has spurred research aimed at applying to haemophilia patients the pharmacokinetic dosing methods commonly used for therapeutic monitoring of drugs (e.g. Bayesian method for dosage individualization). A few papers have already been published in this field, and this review summarises problems encountered by previous investigators, and evaluates comparatively the pharmacokinetic methods used.

Factor VIII↗
PubMed2003

Performance-based selection of likelihood models for phylogeny estimation.

Phylogenetic estimation has largely come to rely on explicitly model-based methods. This approach requires that a model be chosen and that that choice be justified. To date, justification has largely been accomplished through use of likelihood-ratio tests (LRTs) to assess the relative fit of a nested series of reversible models. While this approach certainly represents an important advance over arbitrary model selection, the best fit of a series of models may not always provide the most reliable phylogenetic estimates for finite real data sets, where all available models are surely incorrect. Here, we develop a novel approach to model selection, which is based on the Bayesian information criterion, but incorporates relative branch-length error as a performance measure in a decision theory (DT) framework. This DT method includes a penalty for overfitting, is applicable prior to running extensive analyses, and simultaneously compares all models being considered and thus does not rely on a series of pairwise comparisons of models to traverse model space. We evaluate this method by examining four real data sets and by using those data sets to define simulation conditions. In the real data sets, the DT method selects the same or simpler models than conventional LRTs. In order to lend generality to the simulations, codon-based models (with parameters estimated from the real data sets) were used to generate simulated data sets, which are therefore more complex than any of the models we evaluate. On average, the DT method selects models that are simpler than those chosen by conventional LRTs. Nevertheless, these simpler models provide estimates of branch lengths that are more accurate both in terms of relative error and absolute error than those derived using the more complex (yet still wrong) models chosen by conventional LRTs. This method is available in a program called DT-ModSel.

Bayes Theorem↗
PubMed2004

Molecular phylogenetics and evolution of maternal care in Membracine treehoppers.

The treehopper subfamily Membracinae (Insecta: Hemiptera: Membracidae) comprises the majority of genera and species diversity in the New World tropics. These treehoppers exhibit a wide range of social behaviors, making them an excellent group for studying patterns of social evolution in insects. However, to date the tribal and generic relationships have remained unclear. We reconstructed the phylogeny of the Membracinae using a combined mitochondrial (COI, COII, tRNA-Leu, and 12S) and nuclear (Wg) gene data set. A total of 2608 aligned nucleotide sites were obtained for 112 species, representing 25 of 38 currently recognized genera and all four tribes. A strict consensus of five equally parsimonious trees recovered the subfamily and three of its four tribes. The majority rule consensus tree derived from the Bayesian analyses based on the GTR+I+G and mixed-models recovered many clades shared with the parsimony trees and is identical to the single best tree inferred from maximum likelihood analysis, aside from the rearrangement of one node. A comparison of mitochondrial and nuclear genes indicated that Wg provided higher consistency index (CI), data decisiveness (DD), partitioned Bremer support (PBS) than any of the mitochondrial genes analyzed. The combined mitochondrial and nuclear DNA provide strong support for the monophyly of the subfamily and three of its four tribes (Aconophorini, Hoplophorionini, and Hypsoprorini). Membracini is paraphyletic with respect to Hoplophorionini and contains two lineages, the Membracini sensu strictu and the newly resurrected tribe Bolbonotini. Our analyses show that there is a strong phylogenetic component to the evolution of maternal care. Given the widespread occurrence of maternal care within the subfamily, this trait is estimated to have < or = 3 origins, two reversals, and one loss. Our results suggest that the evolution of maternal care in insects may not be as evolutionarily labile as previously thought.

Animals↗
PubMed2006

Carryover aquatic effects on survival of metamorphic frogs during pond emigration.

In organisms with complex life cycles, physiological stressors during early life stages may have fitness-level impacts that are delayed into later stages or habitats. We tested the hypothesis that body size and date of metamorphosis, which are highly responsive to aquatic stressors, influence post-metamorphic survival and movement patterns in the terrestrial phase of an ephemeral pond-breeding frog by examining these traits in two populations of northern red-legged frogs (Rana aurora aurora). To increase variation of body size at metamorphosis, we manipulated food availability for 314 of 1045 uniquely marked tadpoles and estimated the probability that frogs survived and emigrated using concentric rings of drift fencing surrounding ponds and Bayesian capture-recapture modeling. The odds of surviving and emigrating from the ponds to the innermost drift fences, approximately 12 m, increased by factors of 2.20 (95% credibility intervals 1.39-4.23) and 2.54 (0.94-4.91) with each millimeter increase in snout-vent length and decreased by factors of 0.91 (0.85-0.96) and 0.89 (0.80-1.00) with each day's delay in metamorphosis for the two ponds. The odds of surviving and moving to the next ring of fencing, 12 m to approximately 40 m from the ponds, increased by a factor of 1.20 (0.45-4.06) with each millimeter increase in size. Our results demonstrated that body size and timing of metamorphosis relate strongly to the performance of newly metamorphosed frogs during their initial transition into terrestrial habitat. Carryover effects of aquatic stressors that reduce size and delay metamorphosis may have population-level impacts that are not expressed until terrestrial stages. Since changes in both aquatic and terrestrial systems are implicated in many amphibian declines, quantifying both immediate and delayed effects of stressors on demographic rates is critical to sound management.

Age Factors↗
PubMed2005

Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic.

For over a century the relationships between the four major groups of the phylum Arthropoda (Chelicerata, Crustacea, Hexapoda and Myriapoda) have been debated. Recent molecular evidence has confirmed a close relationship between the Crustacea and the Hexapoda, and has included the suggestion of a paraphyletic Hexapoda. To test this hypothesis we have sequenced the complete or near-complete mitochondrial genomes of three crustaceans (Parhyale hawaiensis, Squilla mantis and Triops longicaudatus), two collembolans (Onychiurus orientalis and Podura aquatica) and the insect Thermobia domestica. We observed rearrangement of transfer RNA genes only in O. orientalis, P. aquatica and P. hawaiensis. Of these, only the rearrangement in O. orientalis, an apparent autapomorphy for the collembolan family Onychiuridae, was phylogenetically informative.We aligned the nuclear and amino acid sequences from the mitochondrial protein-encoding genes of these taxa with their homologues from other arthropod taxa for phylogenetic analysis. Our dataset contains many more Crustacea than previous molecular phylogenetic analyses of the arthropods. Neighbour-joining, maximum-likelihood and Bayesian posterior probabilities all suggest that crustaceans and hexapods are mutually paraphyletic. A crustacean clade of Malacostraca and Branchiopoda emerges as sister to the Insecta sensu stricto and the Collembola group with the maxillopod crustaceans. Some, but not all, analyses strongly support this mutual paraphyly but statistical tests do not reject the null hypotheses of a monophyletic Hexapoda or a monophyletic Crustacea. The dual monophyly of the Hexapoda and Crustacea has rarely been questioned in recent years but the idea of both groups' paraphyly dates back to the nineteenth century. We suggest that the mutual paraphyly of both groups should seriously be considered.

Animals↗
PubMed2005

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Animals↗
PubMed2025

Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data.

People living with HIV can acquire secondary infections through a process called superinfection, giving rise to simultaneous infection with genetically distinct variants (multiple infection). Multiple infection provides the necessary conditions for the generation of novel recombinant forms of HIV and may worsen clinical outcomes and increase the rate of transmission to HIV seronegative sexual partners. To date, studies of HIV multiple infection have relied on insensitive bulk-sequencing, labor intensive single genome amplification protocols, or deep-sequencing of short genome regions. Here, we identified multiple infections in whole-genome or near whole-genome HIV RNA deep-sequence data generated from plasma samples of 2,029 people living with viremic HIV who participated in the population-based Rakai Community Cohort Study (RCCS). We estimated individual- and population-level probabilities of being multiply infected and assessed epidemiological risk factors using the novel Bayesian deep-phylogenetic multiple infection model (deep&#xa0;-&#xa0;phyloMI) which accounts for bias due to partial sequencing success and false-negative and false-positive detection rates. We estimated that between 2010 and 2020, 4.09% (95% highest posterior density interval (HPD) 2.95%-5.45%) of RCCS participants with viremic HIV multiple infection at time of sampling. Participants living in high-HIV prevalence communities along Lake Victoria were 2.33-fold (95% HPD 1.3-3.7) more likely to harbor a multiple infection compared to individuals in lower prevalence neighboring communities. This work introduces a high-throughput surveillance framework for identifying people with multiple HIV infections and quantifying population-level prevalence and risk factors of multiple infection for clinical and epidemiological investigations.

Humans↗
PubMed2005

Bayesian modelling of imperfect ascertainment methods in cancer studies.

Tumour registry linkage, chart review and patient self-report are all commonly used ascertainment methods in cancer epidemiology. These methods are used for estimating the incidence or prevalence of different cancer types in a population, and for investigating the effects of possible risk factors for cancer. Tumour registry linkage is often treated as a gold standard, but in fact none of these methods is error free, and failure to adjust for imperfect ascertainment can lead to biased estimates. This is true both if the goal of the study is to estimate the properties of each ascertainment type, or if it is to estimate cancer incidence or prevalence from one or more of these methods. Although rarely applied in the literature to date, when cancer is ascertained by three or more methods, standard latent class models can be used to estimate cancer incidence or prevalence while adjusting for the estimated imperfect sensitivities and specificities of each ascertainment method. These models, however, do not account for variations in these properties across different cancer sites. To address this problem, we extend latent class methodology to include a hierarchical component, which accommodates different ascertainment properties across cancer sites. We apply our model to a data set of 169 lupus patients with three ascertainment methods and eight cancer types. This allows us to estimate the properties of each ascertainment method without assuming any to be a gold standard, and to calculate a standardized incidence ratio for cancer for lupus patients compared to the general population. As our data set is small, we also illustrate the effects as more data become available. We show that our model produces parameter estimates that are substantially different from the currently most popular method of ascertainment, which uses tumour registry data alone.

Bayes Theorem↗
PubMed2006

Toward a global phylogeny of the Brassicaceae.

The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus-based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.

Animals↗
PubMed2000

Accounting for unreported and missing intercourse in human fertility studies.

In prospective studies of human fertility that attempt to identify days of ovulation, couples record each day whether they had intercourse. Depending on the design of the study, couples either (I) mark the dates of intercourse on a chart or (II) mark 'yes' or 'no' for each day of the menstrual cycle. If protocol I is used, intercourse dates that couples fail to record are indistinguishable from dates of no intercourse. Consequently, estimates of day-specific fecundability are biased upwards. If protocol II is used, data from menstrual cycles with missing intercourse information must be discarded in order to fit current fertility models. We propose methods to account for unreported and missing intercourse under the assumption that the missingness mechanism is independent of time conditional on the unobservable true intercourse status. We use probit mixture models to allow for heterogeneity among couples, both in fecundability and in the missingness and non-reporting mechanisms. Markov chain Monte Carlo (MCMC) techniques are used for Bayesian estimation. The methods are generally applicable to the analysis of aggregated Bernoulli outcomes when there is uncertainty in whether a given trial, out of a series of trials, was completed. We illustrate the methods by application to two prospective fertility studies. Published in 2000 by John Wiley & Sons, Ltd.

Algorithms↗
PubMed2004

Spatio-temporal autoregressive models defined over brain manifolds.

Multivariate Autoregressive time series models (MAR) are an increasingly used tool for exploring functional connectivity in Neuroimaging. They provide the framework for analyzing the Granger Causality of a given brain region on others. In this article, we shall limit our attention to linear MAR models, in which a set of matrices of autoregressive coefficients Ak (k = 1,...,p) describe the dependence of present values of the image on lagged values of its past. Methods for estimating the Ak and determining which elements that are zero are well-known and are the basis for directed measures of influence. However, to date, MAR models are limited in the number of time series they can handle, forcing the a priori selection of a (small) number of voxels or regions of interest for analysis. This ignores the full spatio-temporal nature of functional brain data which are, in fact, collections of time series sampled over an underlying continuous spatial manifold the brain. A fully spatio-temporal MAR model (ST-MAR) is developed within the framework of functional data analysis. For spatial data, each row of a matrix Ak is the influence field of a given voxel. A Bayesian ST-MAR model is specified in which the influence fields for all voxels are required to vary smoothly over space. This requirement is enforced by penalizing the spatial roughness of the influence fields. This roughness is calculated with a discrete version of the spatial Laplacian operator. A massive reduction in dimensionality of computations is achieved via the singular value decomposition, making an interactive exploration of the model feasible. Use of the model is illustrated with an fMRI time series that was gathered concurrently with EEG in order to analyze the origin of resting brain rhythms.

Bayes Theorem↗
PubMed2004

Phylogeny of Agrodiaetus Hübner 1822 (Lepidoptera: Lycaenidae) inferred from mtDNA sequences of COI and COII and nuclear sequences of EF1-alpha: karyotype diversification and species radiation.

Butterflies in the large Palearctic genus Agrodiaetus (Lepidoptera: Lycaenidae) are extremely uniform and exhibit few distinguishing morphological characters. However, these insects are distinctive in one respect: as a group they possess among the greatest interspecific karyotype diversity in the animal kingdom, with chromosome numbers (n) ranging from 10 to 125. The monophyly of Agrodiaetus and its systematic position relative to other groups within the section Polyommatus have been controversial. Characters from the mitochondrial genes for cytochrome oxidases I and II and from the nuclear gene for elongation factor 1 alpha were used to reconstruct the phylogeny of Agrodiaetus using maximum parsimony and Bayesian phylogenetic methods. Ninety-one individuals, encompassing most of the taxonomic diversity of Agrodiaetus, and representatives of 14 related genera were included in this analysis. Our data indicate that Agrodiaetus is monophyletic. Representatives of the genus Polyommatus (sensu stricto) are the closest relatives. The sequences of the Agrodiaetus taxa in this analysis are tentatively arranged into 12 clades, only 1 of which corresponds to a species group traditionally recognized in Agrodiaetus. Heterogeneous substitution rates across a recovered topology were homogenized with a nonparametric rate-smoothing algorithm before the application of a molecular clock. Two published estimates of substitution rates dated the origin of Agrodiaetus between 2.51 and 3.85 million years ago. During this time, there was heterogeneity in the rate and direction of karyotype evolution among lineages within the genus. Karyotype instability has evolved independently three times in the section Polyommatus, within the lineages Agrodiaetus, Lysandra, and Plebicula. Rapid karyotype diversification may have played a significant role in the radiation of the genus Agrodiaetus.

Animals↗
PubMed2004

Effect of clinical mastitis on the lactation curve: a mixed model estimation using daily milk weights.

The objective of this study was to estimate the milk production losses associated with clinical mastitis using mixed linear models and correlation structures that have not been available previously. Data used included computer-recorded daily milk yields and detailed and accurate recordings of clinical mastitis cases. Two commercial Holstein dairy farms in New York State participated in the study, one with 650 lactating cows and another that began the study with 830 lactating cows and increased to 1120 cows by the end of the study. Cows on both farms were housed in free stall barns and milked 3 times daily in milking parlors. Electrical conductivity was used as a diagnostic aid for clinical mastitis on both farms. Date of clinical onset was recorded for every episode of clinical mastitis as well as for 8 other diseases defined using standardized case definitions (dystocia, milk fever, retained placenta, metritis, ketosis, displaced abomasum, lameness, and cystic ovarian disease) during the study period of October 1, 1999 to July 31, 2001. The mixed linear model for explaining variation in the outcome variable daily milk yield relative to non-mastitic herdmates found the terms for all 9 diseases studied, including clinical mastitis, significant. The model with an autoregressive correlation structure was preferred based on -2 * log likelihood, Akaike's information criterion, and Bayesian information criterion as well as savings in degrees of freedom. Separate analyses were run for first lactation cows and for second-plus lactation cows because their lactation curves were shaped differently. Adjusting for the effects of the other 8 diseases, milk production loss from clinical mastitis during the whole lactation was estimated as approximately 598 kg for second-plus lactation cows. However, cows that contracted mastitis had a daily production advantage of 2.6 kg over their herdmates until they contracted the disease. When compared with this potentially higher milk production, the total loss from clinical mastitis was estimated as 1181 kg.

Animals↗
PubMed2003

Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials.

Relationships among the seven extant orders of marsupials remain poorly understood. Most classifications recognize a fundamental split between Ameridelphia, which contains the American orders Didelphimorphia and Paucituberculata, and Australidelphia, which contains four Australasian orders (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelina) and the South American order Microbiotheria, represented by Dromiciops gliroides. Ameridelphia and Australidelphia are each supported by key morphological characters with dichotomous character states. To date, molecular studies indexing all marsupial orders have reported inconclusive results. However, several studies have suggested that Dromiciops is nested within Australidelphia. This result has important implications for understanding the biogeographic history of living marsupials. To address questions in higher-level marsupial systematics, we sequenced portions of five nuclear genes (Apolipoprotein B gene; Breast and Ovarian cancer susceptibility gene 1; Recombination activating gene 1; Interphotoreceptor retinoid binding protein gene; and von Willebrand factor gene) for representatives of all orders of marsupials, as well as placental outgroups. The resulting 6.4kb concatenation was analyzed using maximum parsimony, distance methods, maximum likelihood, and Bayesian methods. tests were used to examine a priori hypotheses. All analyses provided robust support for the monophyly of Australidelphia (bootstrap support=99-100%; posterior probability=1.00). Ameridelphia received much lower support, although this clade was not rejected in statistical tests. Within Diprotodontia, both Vombatiformes and Phalangeriformes were supported at the 100% bootstrap level and with posterior probabilities of 1.00.

Animals↗