Temporal genetic structure patterns in tropical maize populations under reciprocal recurrent selection.

In order to investigate the effect of long term recurrent selection on the pattern of gene diversity, thirty randomly-selected individuals from the progenitors (p) and four selection cycles (C0, C3, C6 and C11) were sampled for DNA analysis from the tropical maize (Zea mays L.) breeding populations, Atherton 1 (AT1) and Atherton 2 (AT2). Fifteen polymorphic Simple Sequence Repeat markers amplified a total of 284 and 257 alleles in AT1 and AT2 populations, respectively. Reductions in the number of alleles were observed at advanced selection cycles. About 11 and 12% of the alleles in AT1 and AT2 populations respectively, were near to fixation. However, a higher number of alleles (37% in AT1 and 33% in AT2) were close to extinction. Fisher's exact test and analysis of molecular variance (AMOVA) showed significant population differentiations. Gene diversity estimates and AMOVA revealed increased genetic differentiations at the expense of loss of heterozygosity. Population differentiations were mainly due to fixation of complementary alleles at a locus in the two breeding populations. The estimates of effective population at an advanced selection cycle were close to the population size predicted by the breeding method.

Using harvest statistics to monitor temporal variation in kangaroo density and harvest rate

Management of the commercial harvest of kangaroos relies on quotas set annually as a proportion of regular estimates of population size. Surveys to generate these estimates are expensive and, in the larger states, logistically difficult; a cheaper alternative is desirable. Rainfall is a disappointingly poor predictor of kangaroo rate of increase in many areas, but harvest statistics (sex ratio, carcass weight, skin size and animals shot per unit time) potentially offer cost-effective indirect monitoring of population abundance (and therefore trend) and status (i.e. under-or overharvest). Furthermore, because harvest data are collected continuously and throughout the harvested areas, they offer the promise of more intensive and more representative coverage of harvest areas than aerial surveys do. To be useful, harvest statistics would need to have a close and known relationship with either population size or harvest rate. We assessed this using longterm (11-22 years) data for three kangaroo species (Macropus rufus, M. giganteus and M. fuliginosus) and common wallaroos (M. robustus) across South Australia, New South Wales and Queensland. Regional variation in kangaroo body size, population composition, shooter efficiency and selectivity required separate analyses in different regions. Two approaches were taken. First, monthly harvest statistics were modelled as a function of a number of explanatory variables, including kangaroo density, harvest rate and rainfall. Second, density and harvest rate were modelled as a function of harvest statistics. Both approaches incorporated a correlated error structure. Many but not all regions had relationships with sufficient precision to be useful for indirect monitoring. However, there was no single relationship that could be applied across an entire state or across species. Combined with rainfall-driven population models and applied at a regional level, these relationships could be used to reduce the frequency of aerial surveys without compromising decisions about harvest management.

Stock structure of Grey Mackerel, Scomberomorus semifasciatus (Pisces: Scombridae) across northern Australia, based on otolith stable isotope chemistry

The stable isotopes of delta O-18 and delta C-13 in sagittal otolith carbonates were used to determine the stock structure of Grey Mackerel, Scomberomorus semifasciatus. Otoliths were collected from Grey Mackerel at ten locations representing much of their distributional and fisheries range across northern Australia from 2005 to 2007. Across this broad range (similar to 6500 km), fish from four broad locations-Western Australia (S1), Northern Territory and Gulf of Carpentaria (S2, S3, S4, S5, S6, S7), Queensland east coast mid and north sites (S8, S9) and Queensland east coast south site (S10)-had stable isotope values that were significantly different indicating stock separation. Otolith stable isotopes differed more between locations than among years within a location, indicating temporal stability across years. The spatial separation of these populations indicates a complex stock structure across northern Australia. Stocks of S. semifasciatus appear to be associated with large coastal embayments. These results indicate that optimal fisheries management may require a review of the current spatial arrangements, particularly in relation to the evidence of shared stocks in the Gulf of Carpentaria. Furthermore, as the population of S. semifasciatus in Western Australia exhibited high spatial separation from those at all the other locations examined, further research activities should focus on investigating additional locations within Western Australia for an enhanced determination of stock delineation. From the issue entitled "Proceedings of the 4th International Otolith Symposium, 24-28 August 2009, Monterey, California"

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.

Characterising population structure and diversity of Australian Eimeria

Develop microsatellite markers to distinguish strains of Eimeria acervulina, E. brunetti and E. maxima. Conduct nationwide sampling of chicken faeces to build baseline of Eimeria population genetic diversity for 5 economically important speces (3 species above plus E. tenella and E. necatrix). Conduct focused local screening to assess temporal changes in populations historically sampled.

Temporal and Spatial Patterns in Recruitment of Three Penaeid Prawns in Moreton Bay, Queensland, Australia

The size at recruitment, temporal and spatial distribution, and abiotic factors influencing abundance of three commercially important species of penaeid prawns in the sublittoral trawl grounds of Moreton Bay (Queensland, Australia) were compared. Metapenaeus bennettae and Penaeus plebejus recruit to the trawl grounds at sizes which are relatively small (14-15 mm carapace length, CL) and below that at which prawns are selected for, and retained, in the fleet's cod-ends. In contrast, Penaeus esculenlus recruit at the relatively large size of 27 mm CL from February to May, well above the size ranges selected for. Recruitment of M. bennettae extends over several months, September-October and February March, and was thus likely to be bi-annual, while the recruitment period of P. plebejus was distinct, peaking in October-November each year. Size classes of M . bennettae were the most spatially stratified of the three species. Catch rates of recruits were negatively correlated with depth for all three species, and were also negatively correlated with salinity for M. bennettae.

4,6,8,10,16-Penta- and 4,6,8,10,16,18-hexamethyldocosanes from the cane beetle Antitrogus parvulus - Cuticular hydrocarbons with unprecedented structure and stereochemistry

The major cuticular hydrocarbons from the cane beetle species Antitrogus parvulus were deduced to be 4,6,8,10,16,18-hexa- and 4,6,8,10,16- pentamethyldocosanes 2 and 3, respectively. Isomers of 2,4,6,8-tetramethylundecanal 27, 36, and 37, derived from 2,4,6-trimethylphenol, were coupled with the phosphoranes 28 and 29 to furnish alkenes and, by reduction, diastereomers of 2 and 3. Chromatographic and spectroscopic comparisons confirmed 2 as either 6a or 6b and 3 as either 34a or 34b.

Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle

The East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long-lived, fecund snapper species that is distributed throughout the East Indies and Indo-Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67-0.82), as was intraspecific sequence divergence (range 0-5.8%). FST between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; FST was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents

Structure of Raster in Melolonthine Larvae

Ultrastructural and electrophysiological investigations carried out on larval rasters of Rhopaea magnicomis Blackburn, Lepidiota frerzclzi Black, and Antitr-ogus consanguineus Blackburn revealed that the raster is a complex of mechanoreceptive setae. Chemical and morphological investigations provide no evidence that the raster is a site for chemical emissions; however, species differences in hydrocarbon profiles were found among larval cuticle samples. Ultrastructure of the setae (pali) show that each seta is innervated by a single dendrite which ends in a tubular body at the base of the seta. The connection with the seta is on the proximal side, which corresponds to the production of a phasic-tonic electrophysiological signal on downward deflection. The dendrite is surrounded by a granular, electron-dense sheath which has inwardly directed arms distally and outwardly directed arms proximally. Two sheath cells are present, 1 forming a large receptor lymph cavity which is lamellate and lined with electron-dense material.

Chemical synthesis and structure elucidation of bovine K-casein (1-44)

The caseins (αs1, αs2, β, and κ) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1–44) of bovine κ-casein, the protein which maintains the micellar structure of the caseins. κ-Casein (1–44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro8 to Arg34. This is the first report which demonstrates extensive secondary structure within the casein class of proteins.

Evaluation of aerial photography for predicting trends in structural attributes of Australian woodland including comparison with ground-based monitoring data

The accurate assessment of trends in the woody structure of savannas has important implications for greenhouse accounting and land-use industries such as pastoralism. Two recent assessments of live woody biomass change from north-east Australian eucalypt woodland between the 1980s and 1990s present divergent results. The first estimate is derived from a network of permanent monitoring plots and the second from woody cover assessments from aerial photography. The differences between the studies are reviewed and include sample density, spatial scale and design. Further analyses targeting potential biases in the indirect aerial photography technique are conducted including a comparison of basal area estimates derived from 28 permanent monitoring sites with basal area estimates derived by the aerial photography technique. It is concluded that the effect of photo-scale; or the failure to include appropriate back-transformation of biomass estimates in the aerial photography study are not likely to have contributed significantly to the discrepancy. However, temporal changes in the structure of woodlands, for example, woodlands maturing from many smaller trees to fewer larger trees or seasonal changes, which affect the relationship between cover and basal area could impact on the detection of trends using the aerial photography technique. It is also possible that issues concerning photo-quality may bias assessments through time, and that the limited sample of the permanent monitoring network may inadequately represent change at regional scales

Temporal expression of G-protein-coupled receptor 54 (GPR54), gonadotropin-releasing hormones (GnRH), and dopamine receptor D2 (drd2) in pubertal female grey mullet, Mugil cephalus.

The G-protein-coupled receptor 54 (muGPR54) cDNA was cloned from the brain of the grey mullet, and its expression level, as well as those of the gonadotropin-releasing hormones (GnRH1, GnRH2, GnRH3) and dopamine receptor D2 (drd2), in the brain, pituitary and ovary of pubertal fish (early, intermediate, advanced) were determined by real-time quantitative RT-PCR (QPCR). The muGPR54 cDNA has an open reading frame of 1140 bp with a predicted 380 amino acid peptide, containing seven putative transmembrane domains and putative N-glycosylation and protein kinase C phosphorylation sites. QPCR results showed that the early stage of puberty in grey mullet is characterized by significantly high levels of expression of GPR54, GnRH and drd2 in the brain relative to the intermediate and advanced stages, except for GnRH1 that increased at the advanced stage of puberty. In the pituitary, drd2 expression declined significantly at the advanced stage relative to levels at the intermediate stage. Ovarian expression of GPR54 significantly increased from the intermediate stage of puberty relative to the early stage while that of GnRH1 acutely increased at the advanced stage of puberty. The ovarian expression of drd2 decreased as puberty progressed, but the changes were not significant. The results suggest the possible role of GPR54 and GnRH in positively regulating pubertal development in grey mullet and the dopaminergic inhibition of reproductive function mediated by drd2.

Spatio-temporal patterns in maturation of the chokka squid (Loligo vulgaris reynaudii) off the coast of South Africa

Knowledge of the temporal and spatial characteristics of chokka squid (Loligo vulgaris reynaudii) biology in South African waters is limited, so the possibility of there being a geographically fragmented stock was examined by investigating the distribution of maturity patterns for the species, covering all known spawning areas and using both historical and recent data. Gonadosomatic indices (GSI) varied between year-round consistency and apparent seasonal peaks in both summer and winter; there was no clear spatial pattern. Monthly percentage maturity provided further evidence for two peak reproductive periods each year, although mature squid were present throughout. Sex ratios demonstrated great variability between different areas and life history stages. Male-biased sex ratios were only apparent on the inshore spawning grounds and ranged between 1.118:1 and 4.267:1. Size at sexual maturity was also seasonal, squid maturing smaller in winter/spring than in summer/autumn. Also, squid in the east matured smaller than squid in the west. Although the results from the present study do not provide conclusive evidence of distinct geographic populations, squid likely spawn over a significantly larger area of the Agulhas Bank than previously estimated, and squid on the west coast of South Africa may return to spawn on the western portion of the Agulhas Bank. It remains likely, however, that the east and west coast populations are a single stock and that migration of juveniles to the west coast and their subsequent return as sub-adults is an integral but non-essential and variable part of the life history.

The genetic structure of Australasian green turtles (Chelonia mydas): Exploring the geographical scale of genetic exchange

Ecological and genetic studies of marine turtles generally support the hypothesis of natal homing, but leave open the question of the geographical scale of genetic exchange and the capacity of turtles to shift breeding sites. Here we combine analyses of mitochondrial DNA (mtDNA) variation and recapture data to assess the geographical scale of individual breeding populations and the distribution of such populations through Australasia. We conducted multiscale assessments of mtDNA variation among 714 samples from 27 green turtle rookeries and of adult female dispersal among nesting sites in eastern Australia. Many of these rookeries are on shelves that were flooded by rising sea levels less than 10 000 years (c. 450 generations) ago. Analyses of sequence variation among the mtDNA control region revealed 25 haplotypes, and their frequency distributions indicated 17 genetically distinct breeding stocks (Management Units) consisting either of individual rookeries or groups of rookeries in general that are separated by more than 500 km. The population structure inferred from mtDNA was consistent with the scale of movements observed in long-term mark-recapture studies of east Australian rookeries. Phylogenetic analysis of the haplotypes revealed five clades with significant partitioning of sequence diversity (Φ = 68.4) between Pacific Ocean and Southeast Asian/Indian Ocean rookeries. Isolation by distance was indicated for rookeries separated by up to 2000 km but explained only 12% of the genetic structure. The emerging general picture is one of dynamic population structure influenced by the capacity of females to relocate among proximal breeding sites, although this may be conditional on large population sizes as existed historically across this region.

Genetic population structure of red snappers (Lutjanus malabaricus Bloch & Schneider, 1801 and Lutjanus erythropterus Bloch, 1790) in central and eastern Indonesia and northern Australia

The genetic population structure of red snapper Lutjanus malabaricus and Lutjanus erythropterus in eastern Indonesia and northern Australia was investigated by allozyme electrophoresis and sequence variation in the control region of mtDNA. Samples were collected from eight sites in Indonesia and four sites in northern Australia for both species. A total of 13 allozyme loci were scored. More variable loci were observed in L. malabaricus than in L. erythropterus. Sequence variation in the control region (left domain) of the mitochondrial genome was assessed by RFLP and direct sequencing. MtDNA haplotype diversity was high (L. erythropterus, 0.95 and L. malabaricus, 0.97), as was intraspecific sequence divergence, (L. erythropterus, 0.0-12.5% and L. malabaricus, 0.0-9.5%). The pattern of mtDNA haplotype frequencies grouped both species into two broad fisheries stocks with a genetic boundary either between Kupang and Sape (L. malabaricus) or between Kupang and Australian Timor Sea (L. erythropertus). The allozyme analyses revealed similar boundaries for L. erythropterus. Seven allozymes stocks compared to two mtDNA stocks of L. malabaricus including Ambon, which was not sampled with mtDNA, however, were reported. Possible reasons for differences in discrimination between the methods include: i) increased power of multiple allozyme loci over the single mtDNA locus, ii) insufficient gene sampling in the mtDNA control region and iii) relative evolutionary dynamics of nuclear (allozyme loci) and mitochondrial DNA in these taxa. Allozyme and haplotype data did not distinguish separate stocks among the four Australian locations nor the central Indonesian (Bali and Sape locations) for both L. malabaricus and L. erythropterus.