Phylogenetic generalised dissimilarity modelling: a new approach to analysing and predicting spatial turnover in the phylogenetic composition of communities

Compared to species turnover, patterns of phylogenetic turnover provide extra information about the spatial structure of biodiversity, for example providing more informative comparisons between the biota of sites which share no species. To harness this information for broad‐scale spatial analysis, we present phylo‐GDM, a technique for interpolating the spatial structure of phylogenetic turnover between sampled locations in relation to environment, based on generalised dissimilarity modelling (GDM). Using a database of over 150 000 location records for 114 myobatrachid frog species in Australia, linked to a species‐level phylogeny inferred from 2467 base pairs of mitochondrial DNA, we calculated species and phylogenetic turnover between pairs of sites. We show how phylogenetic turnover extended the range of informative comparison of compositional turnover to more biologically and environmentally dissimilar sites. We generated GDM models which predict species and phylogenetic turnover across Australia, and tested the fit of models for different ages within the phylogeny to find the phylogenetic tree depth at which the relationship to current day environment is greatest. We also incorporated explanatory variables based on biogeographic patterns, to represent broad‐scale turnover resulting from divergent evolutionary histories. We found that while the predictive power of our models was lower for full phylogenetic turnover than for species turnover, models based on the more recent components of the phylogeny (closer to the tips) outperformed species models and full phylogenetic models. Phylo‐GDM has considerable potential as a method for incorporating phylogenetic relationships into biodiversity analyses in ways not previously possible. Because phylogenies do not require named taxa, phylo‐GDM may also provide a means of including lineages with poorly resolved taxonomy (e.g. from metagenomic sequencing) into biodiversity planning and phylogeographic analysis.     

Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches

Evolutionary and biogeographic studies increasingly rely on calibrated molecular clocks to date key events. Although there has been significant recent progress in development of the techniques used for molecular dating, many issues remain. In particular, controversies abound over the appropriate use and placement of fossils for calibrating molecular clocks. Several methods have been proposed for evaluating candidate fossils; however, few studies have compared the results obtained by different approaches. Moreover, no previous study has incorporated the effects of nucleotide saturation from different data types in the evaluation of candidate fossils. In order to address these issues, we compared three approaches for evaluating fossil calibrations: the single-fossil cross-validation method of Near, Meylan, and Shaffer (2005. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. 165:137-146), the empirical fossil coverage method of Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 171:726-742), and the Bayesian multicalibration method of Sanders and Lee (2007. Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. Biol. Lett. 3:275-279) and explicitly incorporate the effects of data type (nuclear vs. mitochondrial DNA) for identifying the most reliable or congruent fossil calibrations. We used advanced (Caenophidian) snakes as a case study; however, our results are applicable to any taxonomic group with multiple candidate fossils, provided appropriate taxon sampling and sufficient molecular sequence data are available. We found that data type strongly influenced which fossil calibrations were identified as outliers, regardless of which method was used. Despite the use of complex partitioned models of sequence evolution and multiple calibrations throughout the tree, saturation severely compressed basal branch lengths obtained from mitochondrial DNA compared with nuclear DNA. The effects of mitochondrial saturation were not ameliorated by analyzing a combined nuclear and mitochondrial data set. Although removing the third codon positions from the mitochondrial coding regions did not ameliorate saturation effects in the single-fossil cross-validations, it did in the Bayesian multicalibration analyses. Saturation significantly influenced the fossils that were selected as most reliable for all three methods evaluated. Our findings highlight the need to critically evaluate the fossils selected by data with different rates of nucleotide substitution and how data with different evolutionary rates affect the results of each method for evaluating fossils. Our empirical evaluation demonstrates that the advantages of using multiple independent fossil calibrations significantly outweigh any disadvantages.     

Flying Insect Detection and Classification with Inexpensive Sensors

An inexpensive, noninvasive system that could accurately classify flying insects would have important implications for entomological research, and allow for the development of many useful applications in vector and pest control for both medical and agricultural entomology. Given this, the last sixty years have seen many research efforts devoted to this task. To date, however, none of this research has had a lasting impact. In this work, we show that pseudo-acoustic optical sensors can produce superior data; that additional features, both intrinsic and extrinsic to the insect’s flight behavior, can be exploited to improve insect classification; that a Bayesian classification approach allows to efficiently learn classification models that are very robust to over-fitting, and a general classification framework allows to easily incorporate arbitrary number of features. We demonstrate the findings with large-scale experiments that dwarf all previous works combined, as measured by the number of insects and the number of species considered.     

Monitoring and Mining Animal Sounds in Visual Space

Monitoring animals by the sounds they produce is an important and challenging task, whether the application is outdoors in a natural habitat, or in the controlled environment of a laboratory setting. In the former case, the density and diversity of animal sounds can act as a measure of biodiversity. In the latter case, researchers often create control and treatment groups of animals, expose them to different interventions, and test for different outcomes. One possible manifestation of different outcomes may be changes in the bioacoustics of the animals. With such a plethora of important applications, there have been significant efforts to build bioacoustic classification tools. However, we argue that most current tools are severely limited. They often require the careful tuning of many parameters (and thus huge amounts of training data), are either too computationally expensive for deployment in resource-limited sensors, specialized for a very small group of species, or are simply not accurate enough to be useful. In this work we introduce a novel bioacoustic recognition/classification framework that mitigates or solves all of the above problems. We propose to classify animal sounds in the visual space, by treating the texture of their sonograms as an acoustic fingerprint using a recently introduced parameter-free texture measure as a distance measure. We further show that by searching for the most representative acoustic fingerprint, we can significantly outperform other techniques in terms of speed and accuracy.     

Effects of shell lesions on survival, growth, condition and reproduction in the New Zealand blackfoot abalone Haliotis iris

The pathogenicity of shell lesions in Haliotis iris Martyn was examined in a laboratory experiment in which 73 apparently healthy and 106 lesion-bearing abalone were maintained for up to 12 mo. The abalone were collected from the wild and kept in cages (1 ind. cage(-1)) for 4, 8 or 12 mo, at which times estimates of survival, growth, condition and reproductive capacity were made for each of 3 groups: 'healthy' (n = 73), 'mildly affected' (n = 61) and 'severely affected' (n = 32). Unaffected abalone showed a 2.7% mortality (n = 73) compared to 7.5% (n = 93) in lesion-bearing individuals over the entire experiment. Growth rates were significantly decreased in mildly and severely affected abalone: the relative von Bertalanffy growth coefficient (K), calculated over 12 mo, was -0.176 for unaffected, -0.079 for mildly affected and -0.048 for severely affected individuals. The asymptotic length (L(infinity)) was calculated to be 131.5 mm for unaffected, 142.1 mm for mildly affected and 150.3 mm for severely affected abalone. Significantly (p < 0.05) lower condition indices and decreased reproductive capacity (p > 0.05) were obtained for the severely affected group compared to unaffected abalone. These trends were consistent over the course of the experiment.     

The complement component C1s catalysed hydrolysis of peptide 4-nitroanilide substrates

The kinetic parameter kcat/Km has been determined for the hydrolysis of peptide 4-nitroanilides, catalysed by complement component C1s. Substrates based on the C-terminal sequence of human C4a (Leu-Gln-Arg) were synthesised. Replacement of the glutamine residue by glycine or serine increased kcat/Km. Substitution of valine for the leucine residue increased kcat/Km, while substitution of glycine or lysine for the leucine residue decreased kcat/Km slightly. D-Val-Ser-Arg 4-nitroanilide is the most reactive 4-nitroanilide substrate towards C1s, so far. These results are discussed in relation to the amino acid sequences near the bonds cleaved by C1s in C4, C2 and C1 inhibitor.     

Regulation of cytochrome P-450 dependent steroid hydroxylase activity in Manduca sexta: effects of the ecdysone agonist RH 5849 on ecdysone 20-monooxygenase activity

The non-steroidal ecdysone agonist RH 5849 (1,2-dibenzoyl-1-tert-butylhydrazine) was found to inhibit in a dose-response and apparently competitive fashion the cytochrome P-450 dependent ecdysone 20-monooxygenase activity in the midgut of wandering stage last instar larvae of the tobacco hornworn, Manduca sexta. More effectively on a per molar basis than the naturally occurring molting hormones ecdysone and 20-hydroxyecdysone, RH 5849 was also found to elicit the dramatic 50-fold increase in midgut steroid hydroxylase activity (which normally occurs with the onset of the wandering stage) when injected into competent head or thoracic ligated pre-wandering last instar larvae. These data support and extend the potential usefulness of RH 5849 as a pharmacological probe for further investigating the actions of ecdysteroids and their role(s) in the regulation of ecdysteroid monooxygenases.     

Cleavage of BID during cytotoxic drug and UV radiation-induced apoptosis occurs downstream of the point of Bcl-2 action and is catalysed by caspase-3: a potential feedback loop for amplification of apoptosis-associated mitochondrial cytochrome c release

BID, a pro-apoptotic Bcl-2 family member, promotes cytochrome c release during apoptosis initiated by CD95L or TNF. Activation of caspase-8 in the latter pathways results in cleavage of BID, translocation of activated BID to mitochondria, followed by redistribution of cytochrome c to the cytosol. However, it is unclear whether BID participates in cytochrome c release in other (non-death receptor) cell death pathways. Here, we show that BID is cleaved in response to multiple death-inducing stimuli (staurosporine, UV radiation, cycloheximide, etoposide). However BID cleavage in these contexts was blocked by Bcl-2, suggesting that proteolysis of BID occurred distal to cytochrome c release. Furthermore, addition of cytochrome c to Jurkat post-nuclear extracts triggered breakdown of BID at Asp-59 which was catalysed by caspase-3 rather than caspase-8. We provide evidence that caspase-3 catalysed cleavage of BID represents a feedback loop for the amplification of mitochondrial cytochrome c release during cytotoxic drug and UV radiation-induced apoptosis.