VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Chlamydial infections of fish: Diverse pathogens and emerging causes of disease in aquaculture species

Chlamydial infections of fish are emerging as an important cause of disease in new and established aquaculture industries. To date, epitheliocystis, a skin and gill disease associated with infection by these obligate intracellular pathogens, has been described in over 90 fish species, including hosts from marine and fresh water environments. Aided by advances in molecular detection and typing, recent years have seen an explosion in the description of these epitheliocystis-related chlamydial pathogens of fish, significantly broadening our knowledge of the genetic diversity of the order Chlamydiales. Remarkably, in most cases, it seems that each new piscine host studied has revealed the presence of a phylogenetically unique and novel chlamydial pathogen, providing researchers with a fascinating opportunity to understand the origin, evolution and adaptation of their traditional terrestrial chlamydial relatives. Despite the advances in this area, much still needs to be learnt about the epidemiology of chlamydial infections in fish if these pathogens are to be controlled in farmed environments. The lack of in vitro methods for culturing of chlamydial pathogens of fish is a major hindrance to this field. This review provides an update on our current knowledge of the taxonomy and diversity of chlamydial pathogens of fish, discusses the impact of these infections on the health, and highlights further areas of research required to understand the biology and epidemiology of this important emerging group of fish pathogens of aquaculture species.

Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST)

Chlamydia pecorum is globally associated with several ovine diseases including keratoconjunctivitis and polyarthritis. The exact relationship between the variety of C. pecorum strains reported and the diseases described in sheep remains unclear, challenging efforts to accurately diagnose and manage infected flocks. In the present study, we applied C. pecorum multi-locus sequence typing (MLST) to C. pecorum positive samples collected from sympatric flocks of Australian sheep presenting with conjunctivitis, conjunctivitis with polyarthritis, or polyarthritis only and with no clinical disease (NCD) in order to elucidate the exact relationships between the infecting strains and the range of diseases. Using Bayesian phylogenetic and cluster analyses on 62 C. pecorum positive ocular, vaginal and rectal swab samples from sheep presenting with a range of diseases and in a comparison to C. pecorum sequence types (STs) from other hosts, one ST (ST 23) was recognised as a globally distributed strain associated with ovine and bovine diseases such as polyarthritis and encephalomyelitis. A second ST (ST 69) presently only described in Australian animals, was detected in association with ovine as well as koala chlamydial infections. The majority of vaginal and rectal C. pecorum STs from animals with NCD and/or anatomical sites with no clinical signs of disease in diseased animals, clustered together in a separate group, by both analyses. Furthermore, 8/13 detected STs were novel. This study provides a platform for strain selection for further research into the pathogenic potential of C. pecorum in animals and highlights targets for potential strain-specific diagnostic test development.

Assistive classification for improving the efficiency of avian species richness surveys

Avian species richness surveys, which measure the total number of unique avian species, can be conducted via remote acoustic sensors. An immense quantity of data can be collected, which, although rich in useful information, places a great workload on the scientists who manually inspect the audio. To deal with this big data problem, we calculated acoustic indices from audio data at a one-minute resolution and used them to classify one-minute recordings into five classes. By filtering out the non-avian minutes, we can reduce the amount of data by about 50% and improve the efficiency of determining avian species richness. The experimental results show that, given 60 one-minute samples, our approach enables to direct ecologists to find about 10% more avian species.

Computer-assisted sampling of acoustic data for more efficient determination of bird species richness

Bird species richness survey is one of the most intriguing ecological topics for evaluating environmental health. Here, bird species richness denotes the number of unique bird species in a particular area. Factors affecting the investigation of bird species richness include weather, observation bias, and most importantly, the prohibitive costs of conducting surveys at large spatiotemporal scales. Thanks to advances in recording techniques, these problems have been alleviated by deploying sensors for acoustic data collection. Although automated detection techniques have been introduced to identify various bird species, the innate complexity of bird vocalizations, the background noise present in the recording and the escalating volumes of acoustic data pose a challenging task on determination of bird species richness. In this paper we proposed a two-step computer-assisted sampling approach for determining bird species richness in one-day acoustic data. First, a classification model is built based on acoustic indices for filtering out minutes that contain few bird species. Then the classified bird minutes are ordered by an acoustic index and the redundant temporal minutes are removed from the ranked minute sequence. The experimental results show that our method is more efficient in directing experts for determination of bird species compared with the previous methods.

Species-area and species-individual relationships for tropical trees: A comparison of three 50-ha plots

1 Species-accumulation curves for woody plants were calculated in three tropical forests, based on fully mapped 50-ha plots in wet, old-growth forest in Peninsular Malaysia, in moist, old-growth forest in central Panama, and in dry, previously logged forest in southern India. A total of 610 000 stems were identified to species and mapped to < Im accuracy. Mean species number and stem number were calculated in quadrats as small as 5 m x 5 m to as large as 1000 m x 500 m, for a variety of stem sizes above 10 mm in diameter. Species-area curves were generated by plotting species number as a function of quadrat size; species-individual curves were generated from the same data, but using stem number as the independent variable rather than area. 2 Species-area curves had different forms for stems of different diameters, but species-individual curves were nearly independent of diameter class. With < 10(4) stems, species-individual curves were concave downward on log-log plots, with curves from different forests diverging, but beyond about 104 stems, the log-log curves became nearly linear, with all three sites having a similar slope. This indicates an asymptotic difference in richness between forests: the Malaysian site had 2.7 times as many species as Panama, which in turn was 3.3 times as rich as India. 3 Other details of the species-accumulation relationship were remarkably similar between the three sites. Rectangular quadrats had 5-27% more species than square quadrats of the same area, with longer and narrower quadrats increasingly diverse. Random samples of stems drawn from the entire 50 ha had 10-30% more species than square quadrats with the same number of stems. At both Pasoh and BCI, but not Mudumalai. species richness was slightly higher among intermediate-sized stems (50-100mm in diameter) than in either smaller or larger sizes, These patterns reflect aggregated distributions of individual species, plus weak density-dependent forces that tend to smooth the species abundance distribution and 'loosen' aggregations as stems grow. 4 The results provide support for the view that within each tree community, many species have their abundance and distribution guided more by random drift than deterministic interactions. The drift model predicts that the species-accumulation curve will have a declining slope on a log-log plot, reaching a slope of O.1 in about 50 ha. No other model of community structure can make such a precise prediction. 5 The results demonstrate that diversity studies based on different stem diameters can be compared by sampling identical numbers of stems. Moreover, they indicate that stem counts < 1000 in tropical forests will underestimate the percentage difference in species richness between two diverse sites. Fortunately, standard diversity indices (Fisher's sc, Shannon-Wiener) captured diversity differences in small stem samples more effectively than raw species richness, but both were sample size dependent. Two nonparametric richness estimators (Chao. jackknife) performed poorly, greatly underestimating true species richness.

Rapid assessment of genotype-by-environment interactions and heritability for growth rate in aquaculture species using in vitro fertilisation and DNA tagging

Commercial environments may receive only a fraction of expected genetic gains for growth rate as predicted from the selection environment This fraction is the result of undesirable genotype-by-environment interactions (G x E) and measured by the genetic correlation (r(g)) of growth between environments. Rapid estimates of genetic correlation achieved in one generation are notoriously difficult to estimate with precision. A new design is proposed where genetic correlations can be estimated by utilising artificial mating from cryopreserved semen and unfertilised eggs stripped from a single female. We compare a traditional phenotype analysis of growth to a threshold model where only the largest fish are genotyped for sire identification. The threshold model was robust to differences in family mortality differing up to 30%. The design is unique as it negates potential re-ranking of families caused by an interaction between common maternal environmental effects and growing environment. The design is suitable for rapid assessment of G x E over one generation with a true 0.70 genetic correlation yielding standard errors as low as 0.07. Different design scenarios were tested for bias and accuracy with a range of heritability values, number of half-sib families created, number of progeny within each full-sib family, number of fish genotyped, number of fish stocked, differing family survival rates and at various simulated genetic correlation levels

Generalised growth models for aquatic species with an application to blacklip abalone (Haliotis rubra)

This paper presents a maximum likelihood method for estimating growth parameters for an aquatic species that incorporates growth covariates, and takes into consideration multiple tag-recapture data. Individual variability in asymptotic length, age-at-tagging, and measurement error are also considered in the model structure. Using distribution theory, the log-likelihood function is derived under a generalised framework for the von Bertalanffy and Gompertz growth models. Due to the generality of the derivation, covariate effects can be included for both models with seasonality and tagging effects investigated. Method robustness is established via comparison with the Fabens, improved Fabens, James and a non-linear mixed-effects growth models, with the maximum likelihood method performing the best. The method is illustrated further with an application to blacklip abalone (Haliotis rubra) for which a strong growth-retarding tagging effect that persisted for several months was detected

Subsampling multi-species trawl catches from tropical northern Australia: Does it matter which part of the catch is sampled?

Subsampling is a common method for estimating the abundance of species in trawl catches. However, the accuracy of subsampling in representing the total catch has not been assessed. To estimate one possible source of bias due to subsampling, we tested whether the position on trawler sorting trays from which subsamples were taken affected their ability to represent species in catches. This was done by sorting catches into 10 kg subsamples and comparing subsamples taken from different positions on the sorting tray. Comparisons were made after species were grouped into three categories of abundance, either 'rare', 'common' or 'abundant'. A generalised linear model analysis showed that taking subsamples from different positions on the sorting tray had no major effect on estimating the total numbers or weights of fish or invertebrates, or the total number of fish or invertebrate taxa, recorded in each position. Some individual taxa showed differences between positions on the sorting tray (11.5% of taxa ina three-position design; 25% in a five-position design). But consistent and meaningful patterns in the position of these taxa on the sorting tray could only be seen for the pony fish Leiognathus moretoniensis and the saucer scallop Amusium pleuronectes. Because most bycatch laxa are well mixed throughout the catch, subsamples can be taken from any position on trawler sorting trays without introducing bias.

Ecology of uncultivated oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches

The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.

Female Reproductive Biology and Spawning Periodicity of Two Species of King Prawns, Penaeus longistylus Kubo and Penaeus latisulcatus Kishinouye, from Queensland's East Coast Fishery

In the coastal region of central Queensland female red-spot king prawns, P. longistylus, and the western or blue-leg king prawns, P. latisulcatus, had high mean ovary weights and high proportions of advanced ovary development during the winter months of July and August of 1985 and 1986. On the basis of insemination, both species began copulating at the size of 26-27 mm CL, but P. longistylus matured and spawned at a smaller size than P. latisulcatus. Abundance of P. longistylus was generally three to four times greater than that of P. latisulcatus but the latter was subject to greater variation in abundance. Low mean ovary weight and low proportions of females with advanced ovaries were associated with the maximum mean bottom sea-water temperature (28.5ºC) for both species. Population fecundity indices indicated that peaks in yolk or egg production (a) displayed a similar pattern for both species, (b) varied in timing from year to year for both species and (c) were strongly influenced by abundance. Generally, sample estimates of abundance and commercial catch rates (CPUE) showed similar trends. Differences between the two may have been due to changes in targeted commercial effort in this multi-species fishery.

First record of a smut fungus on Byblidaceae: Yelsemia lowrieana, a new species from Australia.

Yelsemia lowrieana sp . nov. (Ustilaginomycetes) is described and illustrated from Byblis rorida collected in northwestern Western Australia. Infected plants had galls filled with spores on stems and pedicels. The spores were unusual in that each could be separated from a dark outer spore wall. This is the first record of a smut fungus on the dicotyledonous host family Byblidaceae.

Spoilage pattern of five species of Australian prawns: Deterioration is influenced by environment of capture and mode of storage

Five species of commercial prawns Penaeus plebejus, P. merguiensis, P. semisulcatus/P. esculentus and M. bennettae, were obtained from South-East and North Queensland, chilled soon after capture and then stored either whole or deheaded on ice and ice slurry, until spoilage. Total bacterial counts, total volatile nitrogen, K-values and total demerit scores were assessed at regular intervals. Their shelf lives ranged from 10-17 days on ice and >20 days on ice slurry. Initial bacterial flora on prawns from shallower waters (4-15m) were dominated by Gram-positives and had lag periods around 7 days, whereas prawns from deeper waters (100m) were dominant in Pseudomonas spp. with no lag periods in bacterial growth. The dominant spoiler in ice was mainly Pseudomonas fragi whereas the main spoiler in ice slurry was Shewanella putrefaciens. Bacterial interactions seem to play a major role in the patterns of spoilage in relation to capture environment and pattern of storage