A PARAMETRIC METHOD FOR ASSESSING DIVERSIFICATION‐RATE VARIATION IN PHYLOGENETIC TREES

Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification‐rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here, we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data, which showed that PRC has acceptable false‐positive rates and statistical power to detect rate variation. We apply the PRC method to the well‐studied radiation of North American Plethodon salamanders, and support the inference that the large‐bodied Plethodon glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.     

Economic evaluation of water loss saving due to the biological control of water hyacinth at New Year’s Dam,Eastern Cape province,South Africa

Water hyacinth Eichhornia crassipes is considered the most damaging aquatic weed in the world. However, few studies have quantified the impact of this weed economically and ecologically, and even fewer studies have quantified the benefits of its control. This paper focuses on water loss saving as the benefit derived from biological control of this plant between 1990 and 2013 at New Year’s Dam, Alicedale, Eastern Cape, South Africa. Estimates of water loss due to evapotranspiration from water hyacinth vary significantly; therefore, the study used three different rates, high, medium and low. A conservative raw agriculture value of R 0.26 per m³ was used to calculate the benefits derived by the water saved. The present benefit and cost values were determined using 10% and 5% discount rates. The benefit/cost ratio at the low evapotranspiration rate was less than one, implying that biological control was not economically viable but, at the higher evapotranspiration rates, the return justified the costs of biological control. However, at the marginal value product of water, the inclusion of the costs of damage to infrastructure, or the adverse effects of water hyacinth on biodiversity, would justify the use of biological control, even at the low transpiration rate.     

The Many Dimensions of Diet Breadth: Phytochemical,Genetic, Behavioral,and Physiological Perspectives on the Interaction between a Native Herbivore and an Exotic Host

From the perspective of an herbivorous insect, conspecific host plants are not identical, and intraspecific variation in host nutritional quality or defensive capacity might mediate spatially variable outcomes in plant-insect interactions. Here we explore this possibility in the context of an ongoing host breadth expansion of a native butterfly (the Melissa blue, Lycaeides melissa) onto an exotic host plant (alfalfa, Medicago sativa). We examine variation among seven alfalfa populations that differed in terms of colonization by L. melissa; specifically, we examined variation in phytochemistry, foliar protein, and plant population genetic structure, as well as responses of caterpillars and adult butterflies to foliage from the same populations. Regional patterns of alfalfa colonization by L. melissa were well predicted by phytochemical variation, and colonized patches of alfalfa showed a similar level of inter-individual phytochemical diversity. However, phytochemical variation was a poor predictor of larval performance, despite the fact that survival and weight gain differed dramatically among caterpillars reared on plants from different alfalfa populations. Moreover, we observed a mismatch between alfalfa supporting the best larval performance and alfalfa favored by ovipositing females. Thus, the axes of plant variation that mediate interactions with L. melissa depend upon herbivore life history stage, which raises important issues for our understanding of adaptation to novel resources by an organism with a complex life history.     

The Tau/A152T mutation,a risk factor for frontotemporal‐spectrum disorders,leads to NR2B receptor‐mediated excitotoxicity

We report on a novel transgenic mouse model expressing human full‐length Tau with the Tau mutation A152T (hTau^AT), a risk factor for FTD‐spectrum disorders including PSP and CBD. Brain neurons reveal pathological Tau conformation, hyperphosphorylation, mis‐sorting, aggregation, neuronal degeneration, and progressive loss, most prominently in area CA3 of the hippocampus. The mossy fiber pathway shows enhanced basal synaptic transmission without changes in short‐ or long‐term plasticity. In organotypic hippocampal slices, extracellular glutamate increases early above control levels, followed by a rise in neurotoxicity. These changes are normalized by inhibiting neurotransmitter release or by blocking voltage‐gated sodium channels. CA3 neurons show elevated intracellular calcium during rest and after activity induction which is sensitive to NR2B antagonizing drugs, demonstrating a pivotal role of extrasynaptic NMDA receptors. Slices show pronounced epileptiform activity and axonal sprouting of mossy fibers. Excitotoxic neuronal death is ameliorated by ceftriaxone, which stimulates astrocytic glutamate uptake via the transporter EAAT2/GLT1. In summary, hTau^AT causes excitotoxicity mediated by NR2B‐containing NMDA receptors due to enhanced extracellular glutamate.     

In vitro evaluation of native entomopathogenic fungi and neem (Azadiractha indica) extracts on Spodoptera frugiperda

The control of Spodoptera frugiperda is based on synthetic insecticides, so some alternatives are the use of entomopathogenic fungi (EF) and neem extract. The objective of the study was to evaluate in vitro effectiveness of native EF and neem extracts on S. frugiperda larvae. Six EF were identified by DNA sequencing of ITS regions from three EF (Fusarium solani, Metarrhizium robertsii, Nigrospora spherica and Penicillium citrinum). They were evaluated in concentrations of 1 × 10⁸ spores/ mL. In addition, a second bioassay was carried out evaluating only F. solani, M. robertsii and N. sphaerica and the addition of vegetable oil. On the other hand, extraction of secondary metabolites from neem seed (Azadirachta indica) was carried out by performing, mass (g) and solvent volume (mL ethanol and water) combinations, which were subjected to microwaves and ultrasound. Subsequently, these extracts were evaluated in concentrations of 3%, 4% and 5%. A survival analysis was performed for each of the bioassays. With respect to the results of the first bioassay, F. solani obtained a probability of survival of 0.476 on the seventh day, while in the second bioassay, M. robertsii obtained 0.488 survival probability. This suggests that the expected percentage of larvae that stay alive on the sixth day is 48.8%. However, in the evaluation of the neem extract the combination 1:12/70% to 4% caused 84% mortality of larvae. The use of native HE and neem extracts has potential for the control of S. frugiperda.     

Contemporary patterns in a historical context: phylogeographic history of the pipevine swallowtail,Battus philenor (Papilionidae)

Abstract We examined mitochondrial DNA (mtDNA) variation in pipevine swallowtail butterflies ( Battus philenor ) from throughout its extant range to provide a historical, phylogeographical context for ecological studies of the disjunct population in California. We evaluate current hypotheses regarding host plant use, behavior, and mimetic relationships of B. philenor populations and generate alternative hypotheses. Compared to populations throughout the rest of the species' range, California populations are ecologically distinct in that they lack mimics, lay significantly larger clutches of eggs, and exclusively use a unique, endemic larval host plant. Analysis of molecular variance, tests of population differentiation, and nested clade analysis of mtDNA variation indicate that, despite low levels of population genetic structure across the species' range, there is evidence of recent range expansion from presumed Pleistocene refuge(s) in southeastern North America. Colonization of California appears to have been a recent event. This phylogeographic investigation also suggests that the evolution of life-history adaptations to a novel larval host has occurred rapidly in California and the lack of mimics in California may be attributable to the recency of colonization.     

Bull selection and use in northern Australia. 4. Calf output and predictors of fertility of bulls in multiple-sire herds

On 10 northern Australian properties, the number of calves sired (calf output) by individual bulls in multiple-sire matings was measured by DNA typing for paternity. There were 235 bulls (92 Santa Gertrudis, 25 5/8 Brahman and 119 Brahman) from 37 multiple-sire mating groups. Number of bulls in groups ranged from 2 to 25 and ages of bulls ranged from 2 to 5 years. Mating periods were for 3-12 months and bull mating percentages were 2.5-6%. In all, there were 4251 calves tested and the resolution of paternity ranged from 92.5 to 100% and averaged 97.7% across all sites. This included 9.9% of calves with no potential sires in any of the mating groups. Of the 235 bulls mated, 58% sired 10% or less calves in each of their respective mating groups with 6% not siring any calves. In contrast, 14% sired over 30% of the calves in each of the respective mating groups. When bulls were mated in groups of 8-24, the maximum percent of calves sired by individual bulls was 26+/-7% (mean+/-S.D.) with a range 11-36%. However, when bulls were mated in groups of 2-7, the maximum percent of calves sired by individual bulls was 59+/-19% with a range 24-94%. Calf output of bulls was moderately repeatable across years at four of five sites. Multiple regression models relating pre-mating measures of physical, seminal and behavioural traits to calf output were developed for the three breed groups. In all, only 138 of the 235 bulls were included in the models (40 Santa Gertrudis, 24 5/8 Brahman and 74 Brahman). Sheath and testicular traits, such as scrotal circumference and testicular tone, were generally not related to calf output, the exceptions being sheath depth in Brahman bulls which was negatively related (P<0.05) and scrotal circumference in 5/8 Brahmans which was positively related (P=0.08) to calf output. Dominance was only included in the 5/8 Brahman model but there was no significant relationship between dominance hierarchy and calf output. Semen motility was only related (P<0.05) to calf output in 5/8 Brahmans. However, measures of semen quality based on spermatozoa morphology were important contributors to calf output in the Santa Gertrudis and Brahman models where percent normal spermatozoa was positively related (P<0.01) to calf output. In Santa Gertrudis and Brahman bulls, measures of sexual behaviour in the serving capacity test were related to calf output. In Santa Gertrudis, these were for the number of displays of sexual interest (P<0.05), and mounts (P<0.01), but not number of serves, whilst in Brahman bulls, libido score was positively related to calf output (P<0.05). The models only explained 35-57% of the variation in calf output.     

Bull selection and use in northern Australia. Part 2. Semen traits

Detailed semen evaluations were carried out on approximately 363 Santa Gertrudis, 5/8 Brahman and Brahman bulls on 12 different properties across northern Australia, as part of systematic breeding soundness examinations. A subset of bulls (n=245) were subsequently mated in groups, to cows and heifers at bull:female ratios of 2.5-6.0%, with the paternity of resulting calves being determined by microsatellite DNA testing. Motility traits of semen and spermatozoa were moderately repeatable and correlated with each other, but were unrelated to calf output. The percentage of morphologically normal spermatozoa in ejaculates was moderately to highly repeatable (e.g. r=0.10-0.64). The most common morphological abnormalities seen were mid-piece abnormalities, in particular, distal mid-piece reflex associated with a cytoplasmic droplet. Semen quality, particularly percent normal spermatozoa, was consistently related to calf output. In general, bulls with <50% normal spermatozoa sired few calves while bulls with the highest calf outputs had >70% normal spermatozoa. The presence or absence of heparin binding proteins in semen did not influence calf output. Semen from 93% of tested bulls was positive for heparin binding proteins. These results confirm that examination of semen, in particular, evaluation of percent morphologically normal spermatozoa, should be included in the breeding soundness examination of bulls.     

Chemiluminescent measurement of telomere DNA content in biopsies

Telomeres are nucleoprotein complexes that protect the ends of chromosomes from fusion and degradation. They are typically shorter in tumor cells than in paired normal cells, and shorter telomeres are associated with poor outcome in cancer. We previously described a slot blot-based methodfor measuring telomere DNA content, a proxy for telomere length. Although this method represented an improvement over existing methods, its 30-ng limit of sensitivity was insufficient for use with biopsy or other scant tissues. Here we describe a chemiluminescent slot blot assay for telomere DNA content that has the sensitivity required for use with biopsy materials. The results obtained with DNA derived from human placental, HeLa, human peripheral blood lymphocytes, sham-needle core prostate biopsies, and archival prostatectomy tissues demonstrated that telomere DNA content can be reliably and reproducibly measured in 5 ng, and sometimes as little as 2 ng, genomic DNA. Sham-needle core prostate biopsy and prostatectomy specimens processed in parallel produced comparable results. The contribution of truncated telomeres in admixtures containing as much as 75% normal placental DNA could be established. We also demonstrated that the treatment of tissue with formalin before DNA purification does not decrease the efficacy of the assay.