AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

Background  

Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites.     

Trade-offs between microhabitat selection and physiological plasticity in the Antarctic springtail, <Emphasis Type="Italic">Cryptopygus antarcticus</Emphasis> (Willem)

In the maritime Antarctic, terrestrial arthropods have recourse to two strategies to mitigate low summer temperatures: (1) physiological plasticity and (2) avoidance via microhabitat insulation. This study investigated the interaction between these strategies in the springtail, Cryptopygus antarcticus, established in situ within contrasting microcosms (buffered vs. exposed) and within two sets of habitat simulations (wet vs. dry) over diurnal scales through the Antarctic summer. Significant differences were found in the cold hardiness of springtails sampled simultaneously from each microcosm. Exposed animals showed greater plasticity in the “true” austral summer, but as field temperatures declined preceding the onset of winter, buffered animals showed greater resilience. Overall, water was found to inhibit the buffering effect of moss and there was a significantly greater discrimination between buffered and exposed microcosms in the dry treatment. Analysis of microhabitat temperatures indicate that it is thermal variability not lower temperature that is responsible for the greater plasticity of exposed animals.     

Establishment potential of the predatory mirid <Emphasis Type="Italic">Dicyphus hesperus</Emphasis> in northern Europe

The predatory mirid Dicyphus hesperus Knight (Hemiptera: Miridae) is native to North America. The species has been used for the control of glasshouse whitefly on aubergine in the Netherlands, and is currently being evaluated for continued and wider release in Europe. Field and laboratory studies were conducted on a population collected from southern California, USA, to assess the cold tolerance and potential for outdoor establishment under prevailing northern European climates. The supercooling points (whole animal freezing temperatures) of nymphal and adult insects were around −20°C. The lethal temperatures (LTemp₅₀) of non-diapausing nymphs and adults and diapausing adults were close to their respective freezing temperatures at −17.6, −17.6 and −19.2°C. At 5°C, the LTime₅₀ was 54, 101.7 and 117.5 days for fed nymphs, non-diapausing and diapausing adults respectively. When first instar nymphs were placed in the field in winter, starved samples died out after 70 days, but 5% of the fed nymphs survived until the end of winter (140 days) and developed to adult on return to the laboratory. After a similar 5-month field exposure, 50% of fed diapausing adults and 15% of fed non-diapausing adults were still alive at the end of winter, whereas starved diapausing adults died after 140 days. On return to the laboratory after 5 months in the field, both diapausing and non-diapausing adults mated and laid eggs, forming viable populations. Overall, the field and laboratory experiments indicate that this population of D. hesperus is able to enter diapause and that winter temperatures are not a barrier to establishment in northern Europe.     

Effect of UVA fluence rate on indicators of oxidative stress in human dermal fibroblasts

During the course of a day human skin is exposed to solar UV radiation that fluctuates in fluence rate within the UVA (290-315 nm) and UVB (315-400 nm) spectrum. Variables affecting the fluence rate reaching skin cells include differences in UVA and UVB penetrating ability, presence or absence of sunscreens, atmospheric conditions, and season and geographical location where the exposure occurs. Our study determined the effect of UVA fluence rate in solar-simulated (SSR) and tanning-bed radiation (TBR) on four indicators of oxidative stress---protein oxidation, glutathione, heme oxygenase-1, and reactive oxygen species--in human dermal fibroblasts after receiving equivalent UVA and UVB doses. Our results show that the higher UVA fluence rate in TBR increases the level of all four indicators of oxidative stress. In sequential exposures when cells are exposed first to SSR, the lower UVA fluence rate in SSR induces a protective response that protects against oxidative stress following a second exposure to a higher UVA fluence rate. Our studies underscore the important role of UVA fluence rate in determining how human skin cells respond to a given dose of radiation containing both UVA and UVB radiation.     

Invasion status of Florida bass Micropterus floridanus (Lesueur, 1822) in South Africa

Largemouth bass Micropterus salmoides are a popular North American angling species that was introduced into South Africa in 1928. To enhance the largemouth bass fisheries, Florida bass Micropterus floridanus were introduced into KwaZulu Natal, South Africa, in 1980. Knowledge on the status of M. floridanus in South Africa is required, because it lives longer and reaches larger sizes than M. salmoides, which may result in heightened impacts on native biota. Because M. floridanus are morphologically similar, but genetically distinct from M. salmoides, the distribution of this species was assessed by genetically screening 185 Micropterus sp. individuals sampled from 20 localities across South Africa using the mitochondrial ND2 gene. Individuals with mitochondrial DNA matching M. salmoides were recovered from 16 localities, whereas M. floridanus mitochondrial DNA was recovered from 13 localities. At nine localities (45%), the mitochondrial DNA of both species was detected. These results demonstrate M. floridanus dispersal to multiple sites across South Africa.     

Inducible knockdown of pregnancy‐associated plasma protein‐A gene expression in adult female mice extends life span

Pregnancy‐associated plasma protein‐A (PAPP‐A) knockout (KO) mice, generated through homologous recombination in embryonic stem cells, have a significantly increased lifespan compared to wild‐type littermates. However, it is unknown whether this longevity advantage would pertain to PAPP‐A gene deletion in adult animals. In the present study, we used tamoxifen (Tam)‐inducible Cre recombinase‐mediated excision of the floxed PAPP‐A (fPAPP‐A) gene in mice at 5 months of age. fPAPP‐A mice, which were either positive (pos) or negative (neg) for Tam‐Cre, received Tam treatment with quarterly boosters. Only female mice could be used with this experimental design. fPAPP‐A/neg and fPAPP‐A/pos mice had similar weights at the start of the experiment and showed equivalent weight gain. We found that fPAPP‐A/pos mice had a significant extension of life span (P = 0.005). The median life span was increased by 21% for fPAPP‐A/pos compared to fPAPP‐A/neg mice. Analysis of mortality in life span quartiles indicated that the proportion of deaths of fPAPP‐A/pos mice were lower than fPAPP‐A/neg mice at young adult ages (P = 0.002 for 601–800 days) and higher than fPAPP‐A/neg mice at older ages (P = 0.004 for >1000 days). Thus, survival curves and age‐specific mortality indicate that female mice with knockdown of PAPP‐A gene expression as adults have an extended healthy life span.     

Effects of temperature on the establishment potential in the U.K. of the non-native glasshouse biocontrol agent Macrolophus caliginosus

Abstract This study investigated the effect of temperature on the development and winter survival of the predatory mirid Macrolophus caliginosus Wagner, recently introduced into the U.K. as a biocontrol agent for glasshouse whitefly Trialeurodes vaporariorum . The developmental threshold for M. caliginosus calculated by three methods was between 7.3 and 8.4 °C, with a day-degree requirement per generation varying between 472 and 524 day-degrees. It was estimated that under outdoor conditions M. caliginosus could complete two generations per year in the U.K. All life stages of M. caliginosus had supercooling points around −20 °C, with some pre-freeze mortality evident in both acute and chronic low temperature exposures. Acclimation increased survival of nymphal M. caliginosus from approximately 24–52 days when exposed to a constant 0 °C. Provision of prey extended survival of nymphs in the laboratory at a constant 5 °C from 39 to 64 days and in the field by c . 150 days. The results are discussed in the context of the occurrence and establishment of M. caliginosus in the U.K. and the need to develop a reliable risk assessment system for non-native species used in glasshouse biocontrol.     

Herbivory in global climate change research: direct effects of rising temperature on insect herbivores

This review examines the direct effects of climate change on insect herbivores. Temperature is identified as the dominant abiotic factor directly affecting herbivorous insects. There is little evidence of any direct effects of CO₂ or UVB. Direct impacts of precipitation have been largely neglected in current research on climate change. Temperature directly affects development, survival, range and abundance. Species with a large geographical range will tend to be less affected. The main effect of temperature in temperate regions is to influence winter survival; at more northerly latitudes, higher temperatures extend the summer season, increasing the available thermal budget for growth and reproduction. Photoperiod is the dominant cue for the seasonal synchrony of temperate insects, but their thermal requirements may differ at different times of year. Interactions between photoperiod and temperature determine phenology; the two factors do not necessarily operate in tandem. Insect herbivores show a number of distinct life‐history strategies to exploit plants with different growth forms and strategies, which will be differentially affected by climate warming. There are still many challenges facing biologists in predicting and monitoring the impacts of climate change. Future research needs to consider insect herbivore phenotypic and genotypic flexibility, their responses to global change parameters operating in concert, and awareness that some patterns may only become apparent in the longer term.     

Effects of host plant drought stress on the performance of the bird cherry-oat aphid, Rhopalosiphum padi (L.): a mechanistic analysis

Abstract.  1. The growth (increase in height and leaf number) of four grass species was reduced by a −0.5 MPa drought stress, but the performance of an associated herbivore, Rhopalosiphum padi (L.), was not affected consistently. The intrinsic rate of increase of R. padi was reduced by drought stress on three grass species, including Dactylis glomerata (L.), but was unaffected on Arrhenatherum elatius (L.). Therefore, there is no general relationship in the effect of plant drought on an insect herbivore, even among closely related host plant species.
2. Drought stress increased the quality of plant phloem sap, as indicated by increased sieve element osmotic pressure and essential amino acid concentrations. Thus, diet quality could not account for the reduced performance of R. padi under drought stress. The concentration of essential amino acids in the phloem of well-watered A. elatius was, however, lower than that of well-watered D. glomerata , correlating with the decreased performance of aphids on well-watered A. elatius .
3. There were no differences in aphid feeding duration between watering treatments or plant species but sap ingestion rates were reduced significantly under drought stress.
4. Using the measure of dietary amino acid concentrations and the estimate of sap ingestion, the essential amino acid flux through aphids was calculated. Compared with the flux through aphids feeding on well-watered D. glomerata , there was a reduction in aphids feeding on drought-stressed D. glomerata and drought-stressed A. elatius due to lower sap ingestion rates. The flux through aphids on well-watered A. elatius was also reduced due to low phloem essential amino acid concentrations. Thus, the performance of an aphid is correlated with the availability and accessibility of essential amino acids.