Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (FST = 0· 09 − 0· 49; P < 0· 05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

Albert Einstein; Princeton, New Jersey Portraits; Men

Digital Image

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10−8). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Genetic studies of body mass index yield new insights for obesity biology

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10−8), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ~2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

Solutions for archiving data in long-term studies: A reply to Whitlock et al.

In our recent paper [1], we discussed some potential undesirable consequences of public data archiving (PDA) with specific reference to long-term studies and proposed solutions to manage these issues. We reaffirm our commitment to data sharing and collaboration, both of which have been common and fruitful practices supported for many decades by researchers involved in long-term studies. We acknowledge the potential benefits of PDA (e.g., [2]), but believe that several potential negative consequences for science have been underestimated [1] (see also 3 and 4). The objective of our recent paper [1] was to define practices to simultaneously maximize the benefits and minimize the potential unwanted consequences of PDA.

Assessment of novel gear designs to reduce interactions between species

This project tested modified gillnets designed by commercial net fishers in the Queensland East Coast Inshore Finfish Fishery (ECIFF) to try and identify gears that would mitigate and/or improve interactions between fishing nets and Species of Conservation Interest (SOCI). The study also documents previously unrecognised initiatives by pro-active commercial net fishers that reflect a conservation-minded approach to their fishing practices, which is the opposite of what is perceived publicly. Between 2011 and 2014, scientists from James Cook University and the Queensland Department of Agriculture and Fisheries teamed with commercial fishers representing the Queensland Seafood Industry Association and the Moreton Bay Seafood Industry Association to conduct field trials of various modified net designs under normal fishery conditions. Trials were conducted in Moreton Bay (southern part of the fishery) and Bowling Green Bay (northern) and tested different net designs developed by fishers to improve the nature of interactions between net fishing gear and SOCI.

Albert Einstein; Princeton, New Jersey Portraits; Men

Digital Image

Spatial variation in life history reveals insight into connectivity and geographic population structure of a tropical estuarine teleost: king threadfin, Polydactylus macrochir

Understanding the life history of exploited fish species is not only critical in developing stock assessments and productivity models, but has a dual function in the delineation of connectivity and geographical population structure. In this study, patterns in growth and length and age at sex change of Polydactylus macrochir, an ecologically and economically important protandrous estuarine teleost, were examined to provide preliminary information on the species' connectivity and geographic structure across northern Australia. Considerable variation in life history parameters was observed among the 18 locations sampled. Both unconstrained and constrained (t(0) = 0) estimates of von Bertalanffy growth function parameters differed significantly among all neighbouring locations with the exception of two locations in Queensland's east coast and two in Queensland's Gulf of Carpentaria waters, respectively. Comparisons of back-calculated length-at-age 2 provided additional evidence for growth differences among some locations, but were not significantly different among locations in the south-eastern Gulf of Carpentaria or on Queensland's east coast. The length and age at sex change differed markedly among locations, with fish from the east coast of Australia changing sex from males to females at significantly greater lengths and ages than elsewhere. Sex change occurred earliest at locations within Queensland's Gulf of Carpentaria, where a large proportion of small, young females were recorded. The observed differences suggest that P. macrochir likely form a number of geographically and/or reproductively distinct groups in Australian waters and suggest that future studies examining connectivity and geographic population structure of estuarine fishes will likely benefit from the inclusion of comparisons of life history parameters. (C) 2012 Elsevier B.V. All rights reserved.

Parasites as indicators of movement and population connectivity of a non-diadromous, tropical estuarine teleost: king threadfin Polydactylus macrochir

Temporal and spatial patterns in parasite assemblages were examined to evaluate the degree of movement and connectivity of post-recruitment life-history stages of a large, non-diadromous tropical estuarine teleost, king threadfin Polydactylus macrochir, collected from 18 locations across northern Australia. Ten parasites types (juvenile stages of two nematodes and seven cestodes, and adults of an acanthocephalan) were deemed to be suitable for use as biological tags, in that they were considered to have a long residence time in the fish, were relatively easy to find and were morphologically very different to each other which aided discrimination. Univariate and discriminant function analysis of these parasites revealed little difference in temporal replicates collected from five locations, suggesting that the parasite communities were stable over the timeframes explored. Univariate, discriminant function, and BrayCurtis similarity analyses indicated significant spatial heterogeneity, with BrayCurtis classification accuracies ranging from 55 to 100% for locations in north-western and northern Australia, 24 to 88% in the Gulf of Carpentaria, and 39 to 88% on the east coast of Queensland. Few differences were observed among locations separated by <200 km. The observed patterns of parasite infection are in agreement with concurrent studies of movement and connectivity of P. macrochir in that they indicate a complex population structure across northern Australia. These results should be considered when reviewing the management arrangements for this species.

Evidence for a new metastable crystalline compound in Ge---Te system

Pressure dependence of the electrical resistivity of bulk, melt quenched GexTe100−x glasses (15 less-than-or-equals, slant x less-than-or-equals, slant 28) has been studied up to 8GPa pressure. All the glasses exhibit a sharp, discontinuous glass to crystal transition under pressure. The high pressure crystalline phases are identified to have a face centered cubic structure. The value of the cell constant is 0.779nm for 15 less-than-or-equals, slant x less-than-or-equals, slant 17, 0.642nm for x=20 and 0.55lnm for 22 ≤ x ≤ 28 samples respectively. The cell constants of the high pressure crystalline phases suggest the possible existance of a new metastable crystalline compound in the Ge---Te system with F.C.C. structure and cell constant equal to 1.109nm as reported by Moore et al.

Pheromone of the banana-spotting bug, Amblypelta lutescens lutescens Distant (Heteroptera: Coreidae): Identification, synthesis, and field bioassay

The banana-spotting bug, Amblypelta lutescens lutescens Distant (Heteroptera: Coreidae), is one of the principal pests of tree fruits and nuts across northern and eastern Australia. Apart from visual damage assessment, there are currently no reliable methods for monitoring bug activity to aid management decisions. An attractant pheromone for this species that could be used as a trap lure could potentially fill this void. Earlier, two male-specific compounds were identified in airborne extracts from A. lutescens lutescens, (E,E)-α-farnesene and (R,E)-nerolidol; an unknown compound with a molecular weight 220 was also detected. We now report the identification of this hitherto unknown compound as (R,E,E)-α-farnesene-10,11-oxide. Synthesis of this epoxide was conducted using a regioselective asymmetric dihydroxylation of a sulfolene. A blend mimicking the natural proportions of (E,E)-α-farnesene, (R,E)-nerolidol, and (R,E,E)-α-farnesene-10,11- oxide attracted male and female A. lutescens lutescens as well as nymphs in the field, verifying that the aggregation pheromone comprises or is contained within this group of compounds. Copyright © 2012 Ashot Khrimian et al.

Prediction of mortality and conception rates of beef breeding cattle in northern Australia

In current simulation packages for the management of extensive beef-cattle enterprises, the relationships for the key biological rates (namely conception and mortality) are quite rudimentary. To better estimate these relationships, cohort-level data covering 17 100 cow-years from six sites across northern Australia were collated and analysed. Further validation data, from 7200 cow-years, were then used to test these relationships. Analytical problems included incomplete and non-standardised data, considerable levels of correlation among the 'independent' variables, and the close similarity of alternate possible models. In addition to formal statistical analyses of these data, the theoretical equations for predicting mortality and conception rates in the current simulation models were reviewed, and then reparameterised and recalibrated where appropriate. The final models explained up to 80% of the variation in the data. These are now proposed as more accurate and useful models to be used in the prediction of biological rates in simulation studies for northern Australia. © The State of Queensland (through the Department of Agriculture, Fisheries and Forestry) 2012. © CSIRO.

Sperm protamine deficiency correlates with sperm DNA damage in Bos indicus bulls

The primary purpose of spermatozoa is to deliver the paternal DNA to the oocyte at fertilization. During the complex events of fertilization, if the spermatozoon penetrating the oocyte contains compromised or damaged sperm chromatin, the subsequent progression of embryogenesis and foetal development may be affected. Variation in sperm DNA damage and protamine content in ejaculated spermatozoa was reported in the cattle, with potential consequences to bull fertility. Protamines are sperm-specific nuclear proteins that are essential to packaging of the condensed paternal genome in spermatozoa. Sperm DNA damage is thought to be repaired during the process of protamination. This study investigates the potential correlation between sperm protamine content, sperm DNA damage and the subsequent relationships between sperm chromatin and commonly measured reproductive phenotypes. Bos indicus sperm samples (n = 133) were assessed by two flow cytometric methods: the sperm chromatin structure assay (SCSA) and an optimized sperm protamine deficiency assay (SPDA). To verify the SPDA assay for bovine sperm protamine content, samples collected from testis, caput and cauda epididymidis were analyzed. As expected, mature spermatozoa in the cauda epididymidis had higher protamine content when compared with sperm samples from testis and caput epididymidis (p < 0.01). The DNA fragmentation index (DFI), determined by SCSA, was positively correlated (r = 0.33 ± 0.08, p < 0.05) with the percentage of spermatozoa that showed low protamine content using SPDA. Also, DFI was negatively correlated (r = -0.21 ± 0.09, p < 0.05) with the percentage of spermatozoa with high protamine content. Larger scrotal circumference contributes to higher sperm protamine content and lower content of sperm DNA damage (p < 0.05). In conclusion, sperm protamine content and sperm DNA damage are closely associated. Protamine deficiency is likely to be one of the contributing factors to DNA instability and damage, which can affect bull fertility. © 2014 American Society of Andrology and European Academy of Andrology.

Integrated pest management in cotton: exploiting behaviour-modifying (semiochemical) compounds for managing cotton pests

We review here research on semiochemicals for cotton pest management carried out in successive Cotton Co-operative Research Centres from 1998 to 2012. Australian cotton is now dominated by transgenic (Bt) varieties, which provide a strong platform for integrated pest management of key pests such as Helicoverpa spp., but new technologies are required to manage the development of resistance in Helicoverpa spp. to transgenic cotton and the problems posed by emerging and secondary pests, especially sucking insects. A long-range attractant for Helicoverpa moths, based on plant volatiles, has been commercialised as Magnet®. The product has substantial area-wide impacts on moth populations, and only limited effects on beneficial insects. Potential roles are being investigated for this product in resistance management of Helicoverpa spp. on transgenic cotton. Short-range, non-volatile compounds on organ surfaces of plants that do not support development of Helicoverpa spp. have been identified; these compounds deter feeding or oviposition, or are toxic to insect pests. One such product, Sero X®, is effective on Helicoverpa spp. and sucking pests such as whiteflies (Bemisia tabaci), green mirids (Creontiades dilutus), and other hemipteran insects, and is in the advanced stages of commercialisation.