Empirical Evaluation of the Genetic Similarity of Samples From Twin Registries in Australia and the Netherlands Using 359 STRP Markers

One way to achieve the large sample sizes required for genetic studies of complex traits is to combine samples collected by different groups. It is not often clear, however, whether this practice is reasonable from a genetic perspective. To assess the comparability of samples from the Australian and the Netherlands twin studies, we estimated F,, (the proportion of total genetic variability attributable to genetic differences between cohorts) based on 359 short tandem repeat polymorphisms in 1068 individuals. IF,, was estimated to be 0.30% between the Australian and the Netherlands cohorts, a smaller value than between many European groups. We conclude that it is reasonable to combine the Australian and the Netherlands samples for joint genetic analyses.

Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

Characterisation of Australian isolates of Fusarium oxysporum f. sp cubense by DNA fingerprinting analysis

Genetic variation among Australian isolates of the fungus Fusarium oxysporum f. sp. cubense (Foc), which causes Fusarium wilt in banana, was examined using DNA amplification fingerprinting (DAF). Ninety-four isolates which represented Races 1, 2, 3, and 4, and vegetative compatibility groups (VCGs) 0120, 0124, 0125, 0128, 0129, 01211, 01213/16, and 01220 were analysed. The genetic relatedness among isolates within each VCG, and between the 8 different VCGs of Foc present in Australia was determined. The DNA fingerprint patterns were VCG-specific, with each VCG representing a unique genotype. The genetic similarity among isolates within each VCG ranged from 97% to 100%. Among the different VCGs of Foc, 3 major clusters were distinguished which corresponded with race. All Race 1 and 2 isolates (VCGs 0124, 0125, 0128, and 01220) were closely related and clustered together, the Race 3 isolates from Heliconia clustered separately, and all Race 4 isolates (VCGs 0120, 0129, 01211, and 01213/16) clustered together. Fifteen isolates from Alstonville, NSW, were characterised because although they were classified as Race 2 based on their recovery from cooking banana cultivars, they belonged in VCG 0124, which had previously contained only Race 1 isolates. The occurrence of more than one race within a VCG means that vegetative compatibility grouping cannot be used to assign pathotype to pathogenic race as previously thought. It was possible to distinguish the Race 1 and Race 2 isolates within VCG 0124 using DNA fingerprinting, as each race produced a unique DNA fingerprint pattern. Among the Australian isolates, DNA fingerprinting analysis identified 9 different VCGs and genotypes of Foc.

Carapace dentition patterns, morphometrics and allozyme differentiation amongst two toothed freshwater crab species (Potamonautes warreni and P-unispinus) (Decapoda : Brachyura : Potamonautidae) from river systems in South Africa

The taxonomic relationship between two toothed South African river crabs, Potamonautes warreni and P. unispinus, is unclear. The problem stems from the widespread variation in carapace dentition patterns amongst P. warreni individuals over its biogeographic range, where single toothed individuals may appear similar in carapace morphology to P. unispinus. Ten populations of P. warreni and 18 populations of P. unispinus were collected and the morphometric and genetic differentiation between the two taxa quantified. Patterns of morphometric and genetic variation were examined using multivariate statistics and protein gel electrophoresis, respectively. Principal component analyses of carapace characters showed that the two species are morphologically indistinguishable. However, discriminate functions analyses and additional statistical results corroborate the morphological distinction between the two taxa. Allozyme electrophoresis of 17 protein coding loci, indicated a close genetic similarity between the two species (I = 0.92). A fixed allelic difference at one locus (LT-2) and extensive genetic variability at another locus (PGM-1) indicate that two gene pools are present and that the two taxa are genetically isolated. Intraspecific genetic I values for both species were > 0.97 and indicated no apparent genetic structuring on a micro or macro-geographic scale. The variation in carapace dentition among P. warreni populations possesses no genetic basis and may possibly toe the product of ecogenesis. The value of dentition patterns in the systematics of river crabs is discussed. Dentition patterns among river crab species appear to be conserved and reliable as species specific diagnostic markers, but should ideally be used in combination with other morphological data sets and genetic evidence.

A phylogeny for the genus Isoodon and a range extension for I-obesulus peninsulae based on mtDNA control region and morphology

Short-nosed bandicoots, Isoodon, have undergone marked range contractions since European colonisation of Australia and are currently divided into many subspecies, the validity of which is debated. Discriminant function analysis of morphology and a phylogeny of Isoodon based on mtDNA control region sequences indicate a clear split between two of the three recognised species, I. macrourus and I. obesulus/auratus. However, while all previously recognised taxa within the I. obesulus/auratus group are morphologically distinct, I. auratus and I. obesulus are not phylogenetically distinct for mtDNA. The genetic divergence between I. obesulus and I. auratus (2.6%) is similar to that found among geographic isolates of the former (I. o. obesulus and I. o. peninsulae: 2.7%). Further, the divergence between geographically close populations of two different species (I. o. obesulus from Western Australia and I. a. barrowensis: 1.2%) is smaller than that among subspecies within I. auratus (I. a. barrowensis and I. auratus from northern Western Australia: 1.7%). A newly discovered population of Isoodon in the Lamb Range, far north Queensland, sympatric with a population of I. m. torosus, is shown to represent a range extension of I. o. peninsulae (350 km). It seems plausible that what is currently considered as two species, I. obesulus and I. auratus, was once one continuous species now represented by isolated populations that have diverged morphologically as a consequence of adaptation to the diverse environments that occur throughout their range. The taxonomy of these populations is discussed in relation to their morphological distinctiveness and genetic similarity.

Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani

We assayed mtDNA haplotype [300 base pairs (bp) control region] geography and genealogy in the Indo-Pacific tasselfish, Polynemus sheridani from its contiguous estuarine distribution across northern Australia (n = 169). Eight estuaries were sampled from three oceanographic regions (Timor Sea, Gulf of Carpentaria and the Coral Sea) to assess the impact of Pleistocene sea level changes on the historical connectivity among P. sheridani populations. Specifically, we investigated the genetic consequences of disruption to Indian-Pacific Ocean connectivity brought about by the closure of the Torres Strait. Overall there was significant population subdivision among estuaries (F-ST = 0.161, (Phi(ST) = 0.187). Despite a linear distribution, P. sheridani did not show isolation by distance over the entire sampled range because of genetic similarity of estuaries greater than 3000 km apart. However, significant isolation by distance was detected between estuaries separated by less than 3000 km of coastline. Unlike many genetic studies of Indo-Pacific marine species, there was no evidence for an historical division between eastern and western populations. Instead, phylogeographical patterns were dominated by a starlike intraspecific phylogeny coupled with evidence for population expansion in both the Gulf of Carpentaria and the Coral Sea but not the Timor Sea. This was interpreted as evidence for recent west to east recolonization across of northern Australia following the last postglacial marine advance. We argue that although sufficient time has elapsed postcolonization for populations to approach gene flow-drift equilibrium over smaller spatial scales (< 3000 km), the signal of historical colonization persists to obscure the expected equilibrium pattern of isolation by distance over large spatial scales (> 3000 km).

An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [ viz. S. pyramidalis P. Beauv., S. natalensis ( Steud.) Dur and Schinz, S. fertilis ( Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified polymorphic DNA ( RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD pro. ling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51(490) for S. pyramidalis and S. natalensis; UBC43(310,2000,2100) for S. fertilis and S. africanus; and OPA20(850) and UBC43(470) for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the 'S. indicus complex'. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species ( major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

Variance components analyses of multiple asthma traits in a large sample of Australian families ascertained through a twin proband

Background: Intermediate phenotypes are often measured as a proxy for asthma. It is largely unclear to what extent the same set of environmental or genetic factors regulate these traits. Objective: Estimate the environmental and genetic correlations between self-reported and clinical asthma traits. Methods: A total of 3073 subjects from 802 families were ascertained through a twin proband. Traits measured included self-reported asthma, airway histamine responsiveness (AHR), skin prick response to common allergens including house dust mite (Dermatophagoides pteronyssinus [D. pter]), baseline lung function, total serum immunoglobulin E (IgE) and eosinophilia. Bivariate and multivariate analyses of eight traits were performed with adjustment for ascertainment and significant covariates. Results: Overall 2716 participants completed an asthma questionnaire and 2087 were clinically tested, including 1289 self-reported asthmatics (92% previously diagnosed by a doctor). Asthma, AHR, markers of allergic sensitization and eosinophilia had significant environmental correlations with each other (range: 0.23-0.89). Baseline forced expiratory volume in 1 s (FEV1) showed low environmental correlations with most traits. Fewer genetic correlations were significantly different from zero. Phenotypes with greatest genetic similarity were asthma and atopy (0.46), IgE and eosinophilia (0.44), AHR and D. pter (0.43) and AHR and airway obstruction (-0.43). Traits with greatest genetic dissimilarity were FEV1 and atopy (0.05), airway obstruction and IgE (0.07) and FEV1 and D. pter (0.11). Conclusion: These results suggest that the same set of environmental factors regulates the variation of many asthma traits. In addition, although most traits are regulated to great extent by specific genetic factors, there is still some degree of genetic overlap that could be exploited by multivariate linkage approaches.

Assortative Mating for Cigarette Smoking and for Alcohol Consumption in Female Australian Twins and their Spouses

Background Non-random mating affects population variation for substance use and dependence. Developmentally, mate selection leading to positive spousal correlations for genetic similarity may result in increased risk for substance use and misuse in offspring. Mate selection varies by cohort and thus, assortative mating in one generation may produce marked changes in rates of substance use in the next. We aim to clarify the mechanisms contributing to spousal similarity for cigarette smoking and alcohol consumption. Methods Using data from female twins and their male spouses, we fit univariate and bivariate twin models to examine the contribution of primary assortative mating and reciprocal marital interaction to spousal resemblance for regular cigarette smoking and nicotine dependence, and for regular alcohol use and alcohol dependence. Results We found that assortative mating significantly influenced regular smoking, regular alcohol use, nicotine dependence and alcohol dependence. The bivariate models for cigarette smoking and alcohol consumption also highlighted the importance of primary assortative mating on all stages of cigarette smoking and alcohol consumption, with additional evidence for assortative mating across the two stages of alcohol consumption. Conclusions Women who regularly used, and subsequently were dependent on cigarettes or alcohol were more likely to marry men with similar behaviors. After mate selection had occurred, one partner's cigarette or alcohol involvement did not significantly modify the other partner's involvement with these psychoactive substances.

Strong genetic structuring in a habitat specialist, the Oxleyan Pygmy Perch Nannoperca oxleyana

This study used allozyme and mitochondrial DNA variation to examine genetic structure in the Oxleyan Pygmy Perch Nannoperca oxleyana. This small-bodied freshwater fish has a very restricted distribution occurring only in some small coastal streams in south-east Queensland and northern New South Wales. It was expected that subpopulations may contain little genetic variation and be highly differentiated from one another. The results, based on allozyme and mitochondrial DNA control region variation were in agreement with these expectations. Allozyme variation was very low overall, with only one locus showing variation at most sites. The high differentiation was because a different locus tended to be polymorphic at each site. Mitochondrial variation within sites was also low, but some sites had unique haplotypes. The patterns of similarity among mitochondrial DNA haplotypes were not as expected from geographical proximity alone. In particular, although some northern sites had unique haplotypes, four sites spread along 200 km of coastline were remarkably similar, sharing the same common haplotype at similar frequencies. We suggest that these four streams may have had a confluence relatively recently, possibly when sea levels were lower, 8000-10 000 BP.

Genetic differentiation between Australian and North American populations of the monarch butterfly Danaus plexippus (L.) (Lepidoptera : Nymphalidae): an exploration using allozyme electrophoresis

Allozyme analysis was used to address the question of the source of the Australian populations of the monarch butterfly Danaus plexippus (L.). The study had three major aims: (1) To compare the levels of diversity of Australian and Hawaiian populations with potential source populations. (2) To determine whether eastern and western North American populations were sufficiently divergent for the Australian populations to be aligned to a source population. (3) To compare the differentiation among regions in Australia and North America to test the prediction of greater genetic structure in Australia, as a consequence of reduced migratory behaviour. The reverse was found, with F-ST values an order of magnitude lower in Australia than in North America. Predictably, Australian and Hawaiian populations had lower allelic diversity, but unexpected higher heterozygosity values than North American populations. It was not possible to assign the Australian populations to a definitive source, although the high levels of similarity of Australian populations to each other suggest a single colonization event. The possibility that the Australian populations have not been here long enough to reach equilibrium is discussed. (C) 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75, 437-452.

Analysis of genetic diversity in Cassia brewsteri with randomly amplified DNA fingerprints (RAFS)

Genetic diversity in Cassia brewsteri (F. Muell.) F. Muell. ex Benth. was assessed with Randomly Amplified DNA Fingerprints (RAFs). Thirty accessions of C. brewsteri collected from throughout its natural distribution were analysed with three random decamer primers, along with three accessions of C. tomentella (Benth.) Domin and a single accession of each of C. queenslandica C. T. White and C. marksiana (F. M. Bailey) Domin. The three primers yielded a reproducible amplification profile of 265 scorable polymorphic fragments for the 35 accessions. These molecular markers were used to calculate Nei and Li similarity coefficients between each pair of individuals. A matrix of dissimilarity of each pair of individuals was examined by multidimensional scaling (MDS). The analysis supports the division of C. brewsteri into two subspecies and the suggestion that intergradation of C. brewsteri and C. tomentella can occur where the distributions of these species meet.

Orientation of the genetic variance-covariance matrix and the fitness surface for multiple male sexually selected traits

Stabilizing selection has been predicted to change genetic variances and covariances so that the orientation of the genetic variance-covariance matrix (G) becomes aligned with the orientation of the fitness surface, but it is less clear how directional selection may change G. Here we develop statistical approaches to the comparison of G with vectors of linear and nonlinear selection. We apply these approaches to a set of male sexually selected cuticular hydrocarbons (CHCs) of Drosophila serrata. Even though male CHCs displayed substantial additive genetic variance, more than 99% of the genetic variance was orientated 74.9degrees away from the vector of linear sexual selection, suggesting that open-ended female preferences may greatly reduce genetic variation in male display traits. Although the orientation of G and the fitness surface were found to differ significantly, the similarity present in eigenstructure was a consequence of traits under weak linear selection and strong nonlinear ( convex) selection. Associating the eigenstructure of G with vectors of linear and nonlinear selection may provide a way of determining what long-term changes in G may be generated by the processes of natural and sexual selection.

Antigenic and genetic typing of Whataroa viruses in Australia

We recently characterized three novel alphaviruses isolated from mosquitoes captured in New South Wales, Australia. Initial cross-neutralization studies revealed antigenic similarity to the Sindbis virus (SINV)-like Whataroa virus (WHAV), heretofore found only in New Zealand. Nucleotide sequence analysis showed that the WHAV-Iike viruses shared >99% nucleotide sequence similarity with each other, and 96-97% similarity with prototype WHAV. Enzyme-linked immunosorbent assay reactions of a panel of monoclonal antibodies to SINV showed that the novel WHAV-Iike viruses displayed identical binding patterns and were antigenically distinct from all SINV isolates examined. Although these viruses displayed a similar binding pattern to prototype WHAV, three monoclonal antibodies discriminated them from the New Zealand virus. Our results suggest that these novel alphaviruses are antigenic variants of WHAV and represent the first reported isolations of this virus from outside New Zealand. The monoclonal antibodies used in this study will be useful for typing new SINV and SINV-like isolates.