Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

Social structure and landscape genetics of the endemic New Caledonian ant Leptomyrmex pallens Emery, 1883 (Hymenoptera: Formicidae: Dolichoderinae), in the context of fire-induced rainforest fragmentation

Habitat fragmentation is a major threat to biodiversity, as it can alter ecological processes at various spatial and trophic scales. At the species level, fragmentation leading to the isolation of populations can trigger reductions in genetic diversity, potentially having detrimental effects on population fitness, adaptability and ultimately population persistence. Leptomyrmex pallens is a widespread rainforest ant endemic to New Caledonia but now confined to habitat patches that have been fragmented by anthropogenic fire regimes over the last 200 years. We investigated the social structure of L. pallens in the Aoupinié region (c.a. 4900 ha), and assessed the impacts of habitat fragmentation on its population genetic structure. Allele frequencies at 13 polymorphic microsatellite loci were compared among 411 worker ants from 21 nests distributed across the region. High within-nest relatedness (r = 0.70 ± 0.02), and a single queen found in 38 % of the nests by pedigree analysis indicate that the species is monogynous to weakly polygynous. Estimates of gene flow and genetic structure across the region were subsequently determined using a combined dataset of single workers per nest and of unrelated foraging workers. These estimates coupled with a comprehensive landscape genetic analysis revealed no evidence of significant population structure or habitat effects, suggesting that the Aoupinié region harbours a single panmictic population. In contrast, analyses of mitochondrial DNA sequence data revealed a high degree of genetic structuring, indicating limited maternal gene flow and suggesting that gene flow among nests is driven primarily by winged males. Overall these findings suggest that fire-induced habitat fragmentation has had little impact on the population dynamics of L. pallens. Additional studies of less mobile species should therefore be conducted to gain further insights into fire related disturbances on the unique biodiversity and function of New Caledonian ecosystems.

Lack of genetic divergence found with microsatellite DNA markers in the tarakihi Nemadactylus macropterus

Three classes of molecular markers are commonly employed during population genetic studies of marine taxa: allozymes, mitochondrial DNA (mtDNA), and microsatellite DNA. These markers differ in their levels of polymorphism, and the ease and cost of their application. Nemadactylus macropterus is a commercially important marine fish from New Zealand and southern Australia that has been the subject of genetic (allozyme, mtDNA) and non-genetic (otolith microchemistry, larval advection) studies of stock structure. We collected microsatellite DNA data from this species to compare the utility of these molecular markers with those genetic methods previously applied to N. macropterus. Microsatellites did not indicate significant divergence among Australian samples, or between Australian and New Zealand samples. The latter is incongruent with the allozyme and mtDNA studies, and it is suggested that allelic homoplasy has hindered the resolution of population structure when using microsatellites.

Microsatellites revealed no genetic differentiation between hatchery and contemporary wild populations of striped catfish, Pangasianodon hypophthalmus (Sauvage 1878) in Vietnam

Aquaculture of the striped catfish, Pangasianodon hypophthalmus (Sauvage 1878), in Vietnam has become one of the fastest growing primary food production sectors in the world. Although a demand on quantity of fingerlings is currently reached, it is likely that the long term quality of the stocks may be uncertain due to lacking of genetic broodstock management measures. The present study employed five microsatellite loci to investigate levels of genetic variation of the stripped catfish of the current wild stocks as well as of the selected hatcheries in Vietnam. The study included four hatchery populations and two wild populations spawned in 2005 in the Mekong and Bassac Rivers, and one wild population (spawned in 2006) in the Bassac River. The results showed no genetic differentiation among populations as revealed by F_ST and a model-based clustering method. AMOVA also showed no genetic differentiation between pooled wild and pooled hatchery populations while variation within groups was significant. Genetic variation of wild (mean number of alleles per locus, A = 4.80–6.20; allelic richness, A_r = 4.54–5.06; mean effective number of alleles per locus, A_e = 2.86–3.20; observed heterozygosity, H_o = 0.62–0.65; expected heterozygosity, H_e = 0.62–0.64) and hatchery populations (A = 4.60–5.20; A^_r = 4.10–4.83; A_e = 2.80–3.11; H_o = 0.61–0.66; H_e = 0.61–0.64) were not statistically different. There were no evidences for recent genetic bottleneck in all populations. Therefore it is implied that the hatchery stocks of striped catfish in Vietnam were founded from sufficient numbers of brooders and current population size is large. The domestication process is in an early stage.

Development of molecular techniques for the genetic analysis of abalone populations

Three DNA techniques: random amplified polymorphic DNA (RAPD), minisatellite, and microsatellite analyses, were developed for use in abalone population genetic structure studies. The techniques were assessed using sample sets of blacklip and greenlip abalone. The study identifies a potential for the application of these DNA markers in abalone fisheries management, but microsatellites are the recommended method for future studies.

Conservation genetics of the New Holland mouse Pseudomys novaehollandiae, Waterhouse, 1843 (Rodentia: Muridae) : an analysis of mitochondrial DNA control region variation

An investigation of the genetic diversity of New Holland mouse populations using DNA. Ten distinct restriction enzyme fragment patterns or haplotypes were detected. From the fragment patterns, estimates of genetic divergence between the haplotypes revealed a degree of genetic structuring within New Holland mouse with four population assemblages apparent.

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

Techniques for targeted genetic disruption in Plasmodium, the causative agent of malaria, are currently intractable for those genes that are essential for blood stage development. The ability to use RNA interference (RNAi) to silence gene expression
would provide a powerful means to gain valuable insight into the pathogenic blood stages but its functionality in Plasmodium remains controversial. Here we have used various RNA-based gene silencing approaches to test the utility of RNAi in malaria
parasites and have undertaken an extensive comparative genomics search using profile hidden Markov models to clarify whether RNAi machinery
exists in malaria. These investigative approaches revealed that Plasmodium lacks the enzymology required for RNAi-based ablation of gene expression
and indeed no experimental evidence for RNAi was observed. In its absence, the most likely explanations for previously reported RNAi-mediated knockdown are either the general toxicity of introduced RNA (with global down-regulation of gene expression) or a specific antisense effect mechanistically distinct from RNAi, which will need systematic
analysis if it is to be of use as a molecular genetic tool for malaria parasites.

Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters : implications for conservation

A population genetics approach was used to investigate the genetic diversity of the spotted seahorse (Hippocampus kuda) in Thai waters; specifically, the degree of genetic differentiation and species evolution was inferred from sequence analysis of 353 bp of the mitochondrial (mt)DNA control region. The data were then used to identify discrete populations in Thai waters for effective conservation and management. Spotted seahorses were collected from 4 regions on the east and west coasts of the Gulf of Thailand and a geographically separated region in the Andaman Sea. Of the 101 mtDNA sequences analyzed, 7 haplotypes were identified, 5 of which were shared among individuals from the east and west coasts of the Gulf of Thailand. The remaining haplotypes were restricted to individuals from the Andaman Sea. Nucleotide and haplotype diversities were similar within the Gulf of Thailand samples, whereas diversity was lower in the Andaman Sea sample. Genetic differentiation appeared between pairs of samples from the Gulf of Thailand and Andaman Sea (FST, p < 0.0001). A large genetic variance appeared among the 2 population groups (94.46%, ΦCT = 0.94464, p < 0.01). A Neighbor-joining tree indicated that individuals from the Gulf of Thailand and Andaman Sea formed 2 phylogenetically distinct groups, which were segregated into different population-based clades. While results reported here indicate that populations from the Gulf of Thailand and Andaman Sea should be treated as separate conservation units, a larger sample size from the Andaman Sea is required to confirm this genetic partitioning and low level of diversity observed in the present study.

Genetics and public health - evolution, or revolution?

During the 19th and early 20th century, public health and genetics shared common ground through similar approaches to health promotion in the population. By the mid-20th century there was a division between public health and genetics, with eugenicists estranged and clinical genetics focused on single gene disorders, usually only relevant to small numbers of people. Now through a common interest in the aetiology of complex diseases such as heart disease and cancer, there is a need for people working in public health and genetics to collaborate. This is not a comfortable convergence for many, particularly those in public health. Nine main concerns are reviewed: fear of eugenics; genetic reductionism; predictive power of genes; non-modifiable risk factors; rights of individuals compared with populations; resource allocation; commercial imperative; discrimination; and understanding and education. This paper aims to contribute to the thinking and discussion about an evolutionary, multidisciplinary approach to understanding, preventing, and treating complex diseases.

Genes and song : genetic and social connections in fragmented habitat in a woodland bird with limited dispersal

Understanding the processes leading to population declines in fragmented landscapes is essential for successful conservation management. However, isolating the influence of disparate processes, and dispersal in particular, is challenging. The Grey Shrike-thrush, Colluricincla harmonica, is a sedentary woodland-dependent songbird, with learned vocalizations whose incidence in suitable habitat patches falls disproportionally with decline in tree cover in the landscape. Although it has been suggested that gaps in tree cover might act as barriers to its dispersal, the species remains in many remnants of native vegetation in agricultural landscapes, suggesting that it may have responded to habitat removal and fragmentation by maintaining or even increasing dispersal distances. We quantified population connectivity of the Grey Shrike-thrush in a system fragmented over more than 120 years using genetic (microsatellites) and acoustic (song types) data. First, we tested for population genetic and acoustic structure at regional and local scales in search of barriers to dispersal or gene flow and signals of local spatial structuring indicative of restricted dispersal or localized acoustic similarity. Then we tested for effects of habitat loss and fragmentation on genetic and acoustic connectivity by fitting alternative models of mobility (isolation-by-distance [the null model] and reduced and increased movement models) across treeless vs. treed areas. Birds within 5 km of each other had more similar genotypes and song types than those farther away, suggesting that dispersal and song matching are limited in the region. Despite restricted dispersal detected for females (but not males), populations appeared to be connected by gene flow and displayed some cultural (acoustic) connectivity across the region. Fragmentation did not appear to impact greatly the dispersal of the Grey Shrike-thrush: none of the mobility models fit the genetic distances of males, whereas for females, an isolation-by-distance model could not be rejected in favor of the models of reduced or increased movement through treeless gaps. However, dissimilarities of the song types were more consistent with the model of reduced cultural connectivity through treeless areas, suggesting that fragmentation impedes song type sharing in the Grey Shrike-thrush. Our paper demonstrates that habitat fragmentation hinders important population processes in an Australian woodland bird even though its dispersal is not detectably impacted.