Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats

Coalescent model–based methods for phylogeny estimation force systematists to confront issues related to the identification of species boundaries. Unlike conventional phylogenetic analysis, where species membership can be assessed qualitatively after the phylogeny is estimated, the phylogenies that are estimated under a coalescent model treat aggregates of individuals as the operational taxonomic units and thus require a priori definition of these sets because the models assume that the alleles in a given lineage are sampled from a single panmictic population. Fortunately, the use of coalescent model–based approaches allows systematists to conduct probabilistic tests of species limits by calculating the probability of competing models of lineage composition. Here, we conduct the first exploration of the issues related to applying such tests to a complex empirical system. Sequence data from multiple loci were used to assess species limits and phylogeny in a clade of North American Myotis bats. After estimating gene trees at each locus, the likelihood of models representing all hierarchical permutations of lineage composition was calculated and Akaike information criterion scores were computed. Metrics borrowed from information theory suggest that there is strong support for several models that include multiple evolutionary lineages within the currently described species Myotis lucifugus and M. evotis. Although these results are preliminary, they illustrate the practical importance of coupled species delimitation and phylogeny estimation

First Records of the Northern Long-eared Bat, Myotis septentrionalis, in the Yukon Territory

Three adult male Northern Long-eared Bats, Myotis septentrionalis, were captured in mist nets in July 2004 in the LaBiche River Valley, southeastern Yukon. These are the first records of M. septentrionalis in the Yukon. Further survey work is needed to delineate the extent of the range and population structure of this and other species of bats in northwestern North America

Comparison of Eight Methods for the Extraction of Bacillus atrophaeus Spore DNA from Eleven Common Interferents and a Common Swab

Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit) were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum) and one solid (Underarm deodorant), the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar), and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method

Effects of early feeding on growth velocity and overweight/obesity in a cohort of HIV unexposed South African infants and children

BACKGROUND: South Africa has the highest prevalence of overweight/obesity in Sub-Saharan Africa. Assessing the effect of modifiable factors such as early infant feeding on growth velocity and overweight/obesity is therefore important. This paper aimed to assess the effect of infant feeding in the transitional period (12 weeks) on 12–24 week growth velocity amongst HIV unexposed children using WHO growth velocity standards and on the age and sex adjusted body mass index (BMI) Z-score distribution at 2 years. METHODS: Data were from 3 sites in South Africa participating in the PROMISE-EBF trial. We calculated growth velocity Z-scores using the WHO growth standards and assessed feeding practices using 24-hour and 7-day recall data. We used quantile regression to study the associations between 12 week infant feeding and 12–24 week weight velocity (WVZ) with BMI-for-age Z-score at 2 years. We included the internal sample quantiles (70th and 90th centiles) that approximated the reference cut-offs of +2 (corresponding to overweight) and +3 (corresponding to obesity) of the 2 year BMI-for-age Z-scores. RESULTS: At the 2-year visit, 641 children were analysed (median age 22 months, IQR: 17–26 months). Thirty percent were overweight while 8.7% were obese. Children not breastfed at 12 weeks had higher 12–24 week mean WVZ and were more overweight and obese at 2 years. In the quantile regression, children not breastfed at 12 weeks had a 0.37 (95% CI 0.07, 0.66) increment in BMI-for-age Z-score at the 50th sample quantile compared to breast-fed children. This difference in BMI-for-age Z-score increased to 0.46 (95% CI 0.18, 0.74) at the 70th quantile and 0.68 (95% CI 0.41, 0.94) at the 90th quantile . The 12–24 week WVZ had a uniform independent effect across the same quantiles. CONCLUSIONS: This study demonstrates that the first 6 months of life is a critical period in the development of childhood overweight and obesity. Interventions targeted at modifiable factors such as early infant feeding practices may reduce the risks of rapid weight gain and subsequent childhood overweight/obesity.Scopu

Protein-Truncating Variants at the Cholesteryl Ester Transfer Protein Gene and Risk for Coronary Heart Disease.

RATIONALE: Therapies that inhibit CETP (cholesteryl ester transfer protein) have failed to demonstrate a reduction in risk for coronary heart disease (CHD). Human DNA sequence variants that truncate the CETP gene may provide insight into the efficacy of CETP inhibition. OBJECTIVE: To test whether protein-truncating variants (PTVs) at the CETP gene were associated with plasma lipid levels and CHD. METHODS AND RESULTS: We sequenced the exons of the CETP gene in 58 469 participants from 12 case-control studies (18 817 CHD cases, 39 652 CHD-free controls). We defined PTV as those that lead to a premature stop, disrupt canonical splice sites, or lead to insertions/deletions that shift frame. We also genotyped 1 Japanese-specific PTV in 27561 participants from 3 case-control studies (14 286 CHD cases, 13 275 CHD-free controls). We tested association of CETP PTV carrier status with both plasma lipids and CHD. Among 58 469 participants with CETP gene-sequencing data available, average age was 51.5 years and 43% were women; 1 in 975 participants carried a PTV at the CETP gene. Compared with noncarriers, carriers of PTV at CETP had higher high-density lipoprotein cholesterol (effect size, 22.6 mg/dL; 95% confidence interval, 18-27; P<1.0×10-4), lower low-density lipoprotein cholesterol (-12.2 mg/dL; 95% confidence interval, -23 to -0.98; P=0.033), and lower triglycerides (-6.3%; 95% confidence interval, -12 to -0.22; P=0.043). CETP PTV carrier status was associated with reduced risk for CHD (summary odds ratio, 0.70; 95% confidence interval, 0.54-0.90; P=5.1×10-3). CONCLUSIONS: Compared with noncarriers, carriers of PTV at CETP displayed higher high-density lipoprotein cholesterol, lower low-density lipoprotein cholesterol, lower triglycerides, and lower risk for CHD

Rationale, design and methods for a randomised and controlled trial to evaluate "Animal Fun" - a program designed to enhance physical and mental health in young children

Background: Children with poor motor ability have been found to engage less in physical activities than other children, and a lack of physical activity has been linked to problems such as obesity, lowered bone mineral density and cardiovascular risk factors. Furthermore, if children are confident with their fine and gross motor skills, they are more likely to engage in physical activities such as sports, crafts, dancing and other physical activity programs outside of the school curriculum which are important activities for psychosocial development. The primary objective of this project is to comprehensively evaluate a whole of class physical activity program called Animal Fun designed for Pre-Primary children. This program was designed to improve the child's movement skills, both fine and gross, and their perceptions of their movement ability, promote appropriate social skills and improve social-emotional development. Methods: The proposed randomized and controlled trial uses a multivariate nested cohort design to examine the physical (motor coordination) and psychosocial (self perceptions, anxiety, social competence) outcomes of the program. The Animal Fun program is a teacher delivered universal program incorporating animal actions to facilitate motor skill and social skill acquisition and practice. Pre-intervention scores on motor and psychosocial variables for six control schools and six intervention schools will be compared with post-intervention scores (end of Pre-Primary year) and scores taken 12 months later after the children's transition to primary school Year 1. 520 children aged 4.5 to 6 years will be recruited and it is anticipated that 360 children will be retained to the 1 year follow-up. There will be equal numbers of boys and girls.Discussion: If this program is found to improve the child's motor and psychosocial skills, this will assist in the child's transition into the first year of school. As a result of these changes, it is anticipated that children will have greater enjoyment participating in physical activities which will further promote long term physical and mental health

Data from: Speciation with gene flow in North American Myotis bats

Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification. In this investigation, we aim to infer the recent phylogenetic history of a clade of western long-eared bats while evaluating a number of different models that parameterize gene flow in a variety of ways. We utilize PHRAPL, a new tool for phylogeographic model selection, to compare the fit of a broad set of demographic models that include divergence, migration, or both among Myotis evotis, $M$. thysanodes and M. keenii. A genomic data set consisting of 808 loci of ultraconserved elements was used to explore such models in three steps using an incremental design where each successive set was informed by, and thus more focused than, the previous set of models. Specifically, the three steps were to (i) assess whether gene flow should be modeled and identify the best topologies, (ii) infer directionality of migration using the best topologies, and (iii) estimate the timing of gene flow. The best model (AIC model weight ${\sim}0.98$) included two divergence events (($M$. evotis, $M$. thysanodes), M. keenii) accompanied by gene flow at the initial stages of divergence. These results provide a striking example of speciation-with-gene-flow in an evolutionary lineage

Morales.etal.Supp_files_dryad

Data and scripts

Results from Bg sp PCR when tested against DNA extracts produced from a 100 µL (0.001% w/v) Bg aliquot (with an added 1 µL microbiological loopful of grated deodorant) and 100 µL (0.001% w/v) Bg aliquots removed from a cotton swab.

a<p>No. of PCR positives from <i>n</i> replicates.</p>b<p>C_T value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p