Comparative phylogeography of two open forest frogs from eastern Australia

We investigated the phylogeography of two closely related Australian frog species from open forest habitats, Limnodynastes tasmaniensis and L. peronii, using mitochondrial ND4 sequence data. Comparison of our results with previous work on Litoria fallax allowed us to test the generality of phylogeographic patterns among non-rainforest anurans along the east coast of Australia. In general, there was no strong evidence for congruence between overall patterns of genetic structure in the three species. However, phylogenetic breaks congruent with the position of the Burdekin Gap were detected at some level in all species. As previously noted for closed forest taxa, this area of dry habitat appears to have been an important influence on the evolution of several open forest taxa. There were broad geographic similarities in the phylogenetic structuring of southern populations of L. peronii and L. tasmaniensis. Contrarily, although the McPherson Range has previously been noted to coincide geographically with a major mtDNA phylogenetic break in Litoria fallax this pattern is not apparent in L. peronii or L. tasmaniensis. It appears that major phylogeographic splits within L. peronii and L. tasmaniensis may predate the Quaternary. We conclude that phylogeographies of open forest frogs are complex and more difficult to predict than for rainforest taxa, mainly due to an absence of palaeomodels for historical distributions of non-rainforest habitats. (C) 2001 The Linnean Society of London.

The phylogeography and connectivity of the latitudinally widespread scleractinian coral Plesiastrea versipora in the Western Pacific

Whereas terrestrial animal populations might show genetic connectivity within a continent, marine species, such as hermatypic corals, may have connectivity stretching to all corners of the planet. We quantified the genetic variability within and among populations of the widespread scleractinian coral, Plesiastrea versipora along the eastern Australian seaboard (4145 km) and the Ryukyu Archipelago (Japan, 681 km) using sequences of internal transcribed spacers (ITS1-2) from ribosomal DNA. Geographic patterns in genetic variability were deduced from a nested clade analysis (NCA) performed on a parsimony network haplotype. This analysis allowed the establishment of geographical associations in the distribution of haplotypes within the network cladogram, therefore allowing us to deduce phylogeographical patterns based under models of restricted gene flow, fragmentation and range expansion. No significant structure was found among Ryukyu Archipelago populations. The lack of an association between the positions of haplotypes in the cladogram with geographical location of these populations may be accounted for by a high level of gene flow of P. versipora within this region, probably due to the strong Kuroshio Current. In contrast, strong geographical associations were apparent among populations of P. versipora along the south-east coast of Australia. This pattern of restricted genetic connectivity among populations of P. versipora on the eastern seaboard of Australia seems to be associated with the present surface ocean current (the East Australian Current) on this side of the south-western Pacific Ocean.

Faeces as a source of DNA for molecular studies in a threatened population of great bustards

With recent advances in molecular biology, it is now possible to use the trace amounts of DNA in faeces to non-invasively sample endangered species for genetic studies. A highly vulnerable population of approximately 100 great bustards (Otis tarda) exists in Morocco necessitating the use of non-invasive protocols to study their genetic structure. Here we report a reliable silica-based method to extract DNA from great bustard faeces. We found that successful extraction and amplification correlated strongly with faeces freshness and composition. We could not extract amplifiable DNA from 30% of our samples as they were dry or contained insect material. However 100% of our fresh faecal samples containing no obvious insect material worked, allowing us to assess the levels of genetic variation among 25 individuals using a 542 bp control region sequence. We were able to extract DNA from four out of five other avian species, demonstrating that faeces represents a suitable source of DNA for population genetics studies in a broad range of species.

Population differentiation in the banana leaf spot pathogen Mycosphaerella musicola, examined at a global scale

Single-copy restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of the global population of Mycosphaerella musicola, the cause of Sigatoka (yellow Sigatoka) disease of banana. The isolates of M. musicola examined were grouped into four geographic populations representing Africa, Latin America and the Caribbean, Australia and Indonesia. Moderate levels of genetic diversity were observed for most of the populations (H = 0.22-0.44). The greatest genetic diversity was found in the Indonesian population (H = 0.44). Genotypic diversity was close to 50% in all populations. Population differentiation tests showed that the geographic populations of Africa, Latin America and the Caribbean, Australia and Indonesia were genetically different populations. Using F-ST tests, very high levels of genetic differentiation were detected between all the population pairs (F-ST > 0.40), with the exception of the Africa and Latin America-Caribbean population pair. These two populations differed by only 3% (F-ST = 0.03), and were significantly different (P < 0.05) from all other population pairs. The high level of genetic diversity detected in Indonesia in comparison to the other populations provides some support for the theory that M. musicola originated in South-east Asia and that M. musicola populations in other regions were founded by isolates from the South-east Asian region. The results also suggest the migration of M. musicola between Africa and the Latin America-Caribbean region.

Mutation scanning analysis of Marteilia sydneyi populations from different geographical locations in eastern Australia

Marteilia sydneyi (Paramyxea) is the causative agent of QX disease in oysters. In spite of the economic impact of this disease, its origin and the precise reason(s) for its apparent spread in Australian waters are not yet known. Given such knowledge gaps, investigating the population genetic structure(s) of M. sydneyi populations could provide insights into the epidemiology and ecology of the parasite and could assist in its prevention and control. In this study, single strand conformation polymorphism (SSCP)-based analysis of a region (195 bp) of the first internal transcribed spacer (ITS-1) of ribosomal DNA was employed to investigate genetic variation within and among five populations of M. sydneyi from oysters from five different locations in eastern Australia. The analysis showed the existence of a genetic variant of M. sydneyi common to the Great Sandy Strait, and the Richmond and Georges Rivers, as distinct from variants at the Pimpama and Clarence Rivers. Together with historical and other information relating to the QX disease outbreaks in eastern Australia, the molecular findings support the proposal that the parasite originated in the Great Sandy Strait and/or Richmond River and then extended southward along the coast. From a technical perspective, the study demonstrated the usefulness of SSCP as a tool to study the population genetics and epidemiology of M. sydneyi. (C) 2003 Elsevier Ltd. All rights reserved.

Historical and contemporary mating patterns in remnant populations of the forest tree Fraxinus excelsior L.

Genetic variation at microsatellite markers was used to quantify genetic structure and mating behavior in a severely fragmented population of the wind-pollinated, wind-dispersed temperate tree Fraxinus excelsior in a deforested catchment in Scotland. Remnants maintain high levels of genetic diversity, comparable with those reported for continuous populations in southeastern Europe, and show low interpopulation differentiation (Theta = 0.080), indicating that historical gene exchange has not been limited (Nm = 3.48). We estimated from seeds collected from all trees producing fruits in three of five remnants that F. excelsior is predominantly outcrossing (t(m). = 0.971 +/- 0.028). Use of a neighborhood model approach to describe the relative contribution of local and long-distance pollen dispersal indicates that pollen gene flow into each of the three remnants is extensive (46-95%) and pollen dispersal has two components. The first is very localized and restricted to tens of meters around the mother trees. The second is a long-distance component with dispersal occurring over several kilometers. Effective dispersal distances, accounting for the distance and directionality to mother trees of sampled pollen donors, average 328 m and are greater than values reported for a continuous population. These results suggest that the opening of the landscape facilitates airborne pollen movement and may alleviate the expected detrimental genetic effects of fragmentation.

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Isolation of polymorphic tetranucleotide microsatellite markers in the satin bowerbird, Ptilonorhynchus violaceus

We isolated 13 polymorphic microsatellite markers from the satin bowerbird, Ptilonorhynchus violaceus from a genomic library enriched in (AAGG)(n) repetitive elements and characterized them in 20 individuals. The number of alleles ranged from two to 18 per locus with the observed heterozygosity ranging from 0.15 to 1.00. These markers will be useful for analysing questions concerning parentage, population genetic structure and models of speciation.

Isolation of polymorphic tetranucleotide microsatellite for the large-billed scrubwren (Sericomis magnirostris)

We isolated 12 polymorphic microsatellite markers for the large-billed scrubwren Sericornis magnirostris from genomic libraries enriched for (AAGG)(n) and (AACC)(n) repetitive elements and characterized them in 11 individuals. The number of alleles ranged from four to 15 per locus with the observed heterozygosity ranging from 0.14 to 0.91. These markers will be useful to address questions concerning population genetic structure and models of speciation.

Isolation of polymorphic tetranucleotide microsatellite markers for the grey-headed robin (Poecilodryas albispecularis)

We isolated 12 polymorphic microsatellite markers for the grey-headed robin Poecilodryas albispecularis from genomic libraries enriched for (AAGG)n and (AACC)n repetitive elements and characterized them in 12 individuals. The number of alleles ranges from three to nine per locus with the observed heterozygosity ranging from 0.33 to 0.90. These markers will be useful for analysis of questions concerning population genetic structure and testing models of speciation.

Phylogeography of the scarab beetle Antitrogus parvulus Britton (Coleoptera : Scarabaeidae) in south-eastern Queensland, Australia

This study surveys the population genetic structure of Childers canegrub, Antitrogus parvulus, to elucidate its population dynamics and gene flow. Antitrogus parvulus is a pest of sugarcane in the Bundaberg region and this knowledge can be used to optimise integrated pest management practices. Here, base-pair differences in the cytochrome oxidase II gene (COII) were used to characterise haplotypic diversity, infer levels of gene flow, and phylogenetic relationships of alleles and their phylogeographical structure. There were 28 unique haplotypes among the 70 sequenced individuals from the seven locations. All three variance components (among regions, among populations, within populations) are highly significant, with highest genetic diversity among regions and lowest among populations within regions. A positive correlation between migration rates and geographical distance and significant phylogeographical structure between four main geographical regions. The main implication of these findings for pest management is that if a grower can eliminate an existing infestation within a field, then reinvasion will be slow and further outbreaks within that field are unlikely to occur. The low dispersal ability of females also means that any resistance to insecticides that develops is likely to remain localised, but will rapidly become dominant within the affected population.

An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination

Several pathogenic strains of Escherichia coli exploit type III secretion to inject effector proteins into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of > 60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into > 20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in > 20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage metagenome, acting as a crucible for the evolution of pathogenicity.

Isolation of polymorphic tetranucleotide microsatellite markers for the green-eyed tree frog (Litoria genimaculata)

We have isolated 16 polymorphic microsatellite markers for the green-eyed tree frog, Litoria genimaculata, from genomic libraries enriched for (AAGG)(n) and (AAAG)(n) repetitive elements. The number of alleles ranges from four to 14 per locus with the observed heterozygosity ranging from 0.36 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and speciation.

Spatial structure and habitat variation in a grasshopper hybrid zone

A hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae) in northern Spain has been analyzed for variation in morphology and ecology. These species are readily distinguished by the number of stridulatory pegs on the hind femur. Both sexes are fully winged and inhabit disturbed habitats throughout the study area. We develop a maximum-likelihood approach to fitting a two-dimensional cline to geographical variation in quantitative traits and for estimating associations of population mean with local habitat. This method reveals a cline in peg number approximately 30 km south of the Picos de Europa Mountains that shows substantial deviations in population mean compared with the expectations of simple tension zone models. The inclusion of variation in local vegetation in the model explains a significant proportion of the residual variation in peg number, indicating that habitat-genotype associations contribute to the observed spatial pattern. However, this association is weak, and a number of populations continue to show strong deviations in mean even after habitat is included in the final model. These outliers may be the result of long-distance colonization of sites distant from the cline center or may be due to a patchy pattern of initial contact during postglacial expansion. As well as contrasting with the smooth hybrid zones described for Chorthippus parallelus, this situation also contrasts with the mosaic hybrid zones observed in Gryllus crickets and in parts of the hybrid zone between Bombina toad species, where habitat-genotype associations account for substantial amounts of among-site variation.