Rapid assessment of genotype-by-environment interactions and heritability for growth rate in aquaculture species using in vitro fertilisation and DNA tagging

Commercial environments may receive only a fraction of expected genetic gains for growth rate as predicted from the selection environment This fraction is the result of undesirable genotype-by-environment interactions (G x E) and measured by the genetic correlation (r(g)) of growth between environments. Rapid estimates of genetic correlation achieved in one generation are notoriously difficult to estimate with precision. A new design is proposed where genetic correlations can be estimated by utilising artificial mating from cryopreserved semen and unfertilised eggs stripped from a single female. We compare a traditional phenotype analysis of growth to a threshold model where only the largest fish are genotyped for sire identification. The threshold model was robust to differences in family mortality differing up to 30%. The design is unique as it negates potential re-ranking of families caused by an interaction between common maternal environmental effects and growing environment. The design is suitable for rapid assessment of G x E over one generation with a true 0.70 genetic correlation yielding standard errors as low as 0.07. Different design scenarios were tested for bias and accuracy with a range of heritability values, number of half-sib families created, number of progeny within each full-sib family, number of fish genotyped, number of fish stocked, differing family survival rates and at various simulated genetic correlation levels

Trapping to monitor tephritid movement: Results, best practice, and assessment of alternatives

Movement of tephritid flies underpins their survival, reproduction, and ability to establish in new areas and is thus of importance when designing effective management strategies. Much of the knowledge currently available on tephritid movement throughout landscapes comes from the use of direct or indirect methods that rely on the trapping of individuals. Here, we review published experimental designs and methods from mark-release-recapture (MRR) studies, as well as other methods, that have been used to estimate movement of the four major tephritid pest genera (Bactrocera, Ceratitis, Anastrepha, and Rhagoletis). In doing so, we aim to illustrate the theoretical and practical considerations needed to study tephritid movement. MRR studies make use of traps to directly estimate the distance that tephritid species can move within a generation and to evaluate the ecological and physiological factors that influence dispersal patterns. MRR studies, however, require careful planning to ensure that the results obtained are not biased by the methods employed, including marking methods, trap properties, trap spacing, and spatial extent of the trapping array. Despite these obstacles, MRR remains a powerful tool for determining tephritid movement, with data particularly required for understudied species that affect developing countries. To ensure that future MRR studies are successful, we suggest that site selection be carefully considered and sufficient resources be allocated to achieve optimal spacing and placement of traps in line with the stated aims of each study. An alternative to MRR is to make use of indirect methods for determining movement, or more correctly, gene flow, which have become widely available with the development of molecular tools. Key to these methods is the trapping and sequencing of a suitable number of individuals to represent the genetic diversity of the sampled population and investigate population structuring using nuclear genomic markers or non-recombinant mitochondrial DNA markers. Microsatellites are currently the preferred marker for detecting recent population displacement and provide genetic information that may be used in assignment tests for the direct determination of contemporary movement. Neither MRR nor molecular methods, however, are able to monitor fine-scale movements of individual flies. Recent developments in the miniaturization of electronics offer the tantalising possibility to track individual movements of insects using harmonic radar. Computer vision and radio frequency identification tags may also permit the tracking of fine-scale movements by tephritid flies by automated resampling, although these methods come with the same problems as traditional traps used in MRR studies. Although all methods described in this chapter have limitations, a better understanding of tephritid movement far outweighs the drawbacks of the individual methods because of the need for this information to manage tephritid populations.

Recent developments in DNA evidence

DNA evidence has made a significant contribution to criminal investigations in Australia and around the world since it was widely adopted in the 1990s (Gans & Urbas 2002). The direct matching of DNA profiles, such as comparing one obtained from a crime scene with one obtained from a suspect or database, remains a widely used technique in criminal investigations. A range of new DNA profiling techniques continues to be developed and applied in criminal investigations around the world (Smith & Urbas 2012). This paper is the third in a series by the Australian Institute of Criminology (AIC) on DNA evidence. The first, published in 1990 when the technology was in its relative infancy, outlined the scientific background for DNA evidence, considered early issues such as scientific reliability and privacy and described its application in early criminal cases (Easteal & Easteal 1990). The second, published in 2002, expanded on the scientific background and discussed a significant number of Australian cases in a 12-year period, illustrating issues that had arisen in investigations, at trial and in the use of DNA in the review of convictions and acquittals (Gans & Urbas 2002). There have been some significant developments in the science and technology behind DNA evidence in the 13 years since 2002 that have important implications for law enforcement and the legal system. These are discussed through a review of relevant legal cases and the latest empirical evidence. This paper is structured in three sections. The first examines the scientific techniques and how they have been applied in police investigations, drawing on a number of recent cases to illustrate them. The second considers empirical research evaluating DNA evidence and databases and the impact DNA has on investigative and court outcomes. The final section discusses significant cases that establish legal precedent relating to DNA evidence in criminal trials where significant issues have arisen or new techniques have been applied that have not yet been widely discussed in the literature. The paper concludes by reflecting on implications for policy and practice.

A comparison of DNA pools constructed following whole genome amplification for two-stage SNP genotyping designs

Genotyping in DNA pools reduces the cost and the time required to complete large genotyping projects. The aim of the present study was to evaluate pooling as part of a strategy for fine mapping in regions of significant linkage. Thirty-nine single nucleotide polymorphisms (SNPs) were analyzed in two genomic DNA pools of 384 individuals each and results compared with data after typing all individuals used in the pools. There were no significant differences using data from either 2 or 8 heterozygous individuals to correct frequency estimates for unequal allelic amplification. After correction, the mean difference between estimates from the genomic pool and individual allele frequencies was .033. A major limitation of the use of DNA pools is the time and effort required to carefully adjust the concentration of each individual DNA sample before mixing aliquots. Pools were also constructed by combining DNA after Multiple Displacement Amplification (MDA). The MDA pools gave similar results to pools constructed after careful DNA quantitation (mean difference from individual genotyping .040) and MDA provides a rapid method to generate pools suitable for some applications. Pools provide a rapid and cost-effective screen to eliminate SNPs that are not polymorphic in a test population and can detect minor allele frequencies as low as 1% in the pooled samples. With current levels of accuracy, pooling is best suited to an initial screen in the SNP validation process that can provide high-throughput comparisons between cases and controls to prioritize SNPs for subsequent individual genotyping.

The validation of profluorescent nitroxides as potential probes to monitor mitochondrial oxidative stress

In cells, the balance of oxidation and reduction reactions (redox chemistry) plays a significant role in key biological processes such as cell signaling, cell fate determination and the body's defence systems, all of which contribute significantly to the overall well-being of the body. This project served as a step forward in developing a more efficient method to monitor mitochondrial redox status. The method is based on the application of profluorescent nitroxides (PFN) that change in fluorescent intensity based on changing mitochondrial redox status. A major impact of this project is to facilitate assessment of mitochondrial redox status and thereby determine the efficacy of antioxidant treatments.

Evidence from molecules and morphology expands Podonomopsis Brundin (Diptera: Chironomidae: Podonominae) to include ‘genus Chile'

The informal taxon ‘genus Chile’ of Brundin, based solely on pupal exuviae of a podonomine Chironomidae, has remained inadequately known for half a century. New collections reveal life associations, and provide molecular data to hypothesise a precise phylogenetic placement in the austral Podonominae. A densely sampled molecular phylogeny based on two nuclear and one mitochondrial DNA markers shows ‘genus Chile’ to be the sister group to Podonomopsis Brundin, 1966. Within Podonomopsis a clade of South American species is sister to all Australian species. We discuss how to rank such a sister group taxon and treat ‘genus Chile’ as a new subgenus Araucanopsis, subg. nov. with the new species, Podonomopsis (Araucanopsis) avelasse, sp. nov. from Chile and Argentina as genotype of the monotypic subgenus. We describe P. (A.) avelasse in all stages and provide an expanded diagnosis and description of Podonomopsis to include Araucanopsis. A dated biogeographic hypothesis (chronogram) infers the most recent common ancestor (tmcra) of expanded Podonomopsis at 95 million years ago (Mya) (68–122 Mya 95% highest posterior density), ‘core’ Podonomopsis at 83 Mya (58–108) and Australian Podonomopsis at 65 Mya (44–87). All dates are before the South America–Australia geological separation through Antarctica, supporting previous conclusions that the taxon distribution is ‘Gondwanan’ in origin. Podonomopsis, even as expanded here, remains unknown from New Zealand or elsewhere on extant Zealandia.

DNA sequences and austral taxa indicate generic synonymy of Paratrichocladius Santos-Abreu with Cricotopus Wulp (Diptera: Chironomidae)

In the century since the description of the orthoclad genus Paratrichocladius Santos-Abreu (Diptera: Chironomidae), separation in any life stage from the cosmopolitan, diverse Cricotopus Wulp has been problematic. Molecular analysis reveals the presence of two species in Australia that conform in morphology to Paratrichocladius and which form a well-supported clade including Paratrichocladius micans (Kieffer) from Africa and a distinct southern African larva. This clade clusters with taxa allied with Cricotopus albitibia (Walker), in turn nested within all other sampled Australian Cricotopus. Relevant nodes strongly support Cricotopus as nonmonophyletic without inclusion of Paratrichocladius. We synonymize Paratrichocladius with Cricotopus syn.n, treating Paratrichocladius as a subgenus. Cricotopus (Paratrichocladius) australiensis Cranston sp.n. is described for Trichocladius pluriserialis Freeman from Australia, which is not the same species under that name in New Zealand. Cricotopus (Paratrichocladius) bifenestrus Cranston sp.n. from Australia is described, also in all life stages. The many new combinations, listed in an Appendix, include three replacement names for new secondary homonyms, namely: Cricotopus (Paratrichocladius) sinobicinctus Cranston & Krosch nom.n. for Paratrichocladius bicinctus Fu, Sæther & Wang, Cricotopus draysoni Cranston & Krosch nom.n. for Cricotopus brevicornis Drayson, Krosch & Cranston, and Cricotopus (Paratrichocladius) sikhotealinus Makarchenko & Makarchenko nom.n. for Cricotopus orientalis Kieffer. We conclude with comments on wider issues in the taxonomy of Paratrichocladius, especially concerning New Zealand species.

Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia

Recent advances in DNA sequencing have enabled mapping of genes for monogenic traits in families with small pedigrees and even in unrelated cases. We report the identification of disease-causing mutations in a rare, severe, skeletal dysplasia, studying a family of two healthy unrelated parents and two affected children using whole-exome sequencing. The two affected daughters have clinical and radiographic features suggestive of anauxetic dysplasia (OMIM 607095), a rare form of dwarfism caused by mutations of RMRP. However, mutations of RMRP were excluded in this family by direct sequencing. Our studies identified two novel compound heterozygous loss-of-function mutations in POP1, which encodes a core component of the RNase mitochondrial RNA processing (RNase MRP) complex that directly interacts with the RMRP RNA domains that are affected in anauxetic dysplasia. We demonstrate that these mutations impair the integrity and activity of this complex and that they impair cell proliferation, providing likely molecular and cellular mechanisms by which POP1 mutations cause this severe skeletal dysplasia. © 2011 Glazov et al.

Genome-wide DNA methylation profiling of CD8+ T cells shows a distinct epigenetic signature to CD4+ T cells in multiple sclerosis patients

Background Multiple sclerosis (MS) is thought to be a T cell-mediated autoimmune disorder. MS pathogenesis is likely due to a genetic predisposition triggered by a variety of environmental factors. Epigenetics, particularly DNA methylation, provide a logical interface for environmental factors to influence the genome. In this study we aim to identify DNA methylation changes associated with MS in CD8+ T cells in 30 relapsing remitting MS patients and 28 healthy blood donors using Illumina 450K methylation arrays. Findings Seventy-nine differentially methylated CpGs were associated with MS. The methylation profile of CD8+ T cells was distinctive from our previously published data on CD4+ T cells in the same cohort. Most notably, there was no major CpG effect at the MS risk gene HLA-DRB1 locus in the CD8+ T cells. Conclusion CD8+ T cells and CD4+ T cells have distinct DNA methylation profiles. This case–control study highlights the importance of distinctive cell subtypes when investigating epigenetic changes in MS and other complex diseases.

Avian diversification patterns across the K-Pg boundary: Influence of calibrations, datasets, and model misspecification

Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.

Epigenetics Underpinning DNA Damage Repair

Epigenetics is the study of heritable changes in gene expression that are not the result of genetic alterations. These changes include DNA methylation, histone modifications, or indeed microRNA expression. Chromatin is a tightly compacted DNA–protein complex that allows approximately two meters of DNA to be packaged inside a cell, only a few micrometers across. Although the resulting DNA structure is very stable, it is not very amiable to DNA-dependent processes, so mechanisms have to exist to allow processes such as transcription, replication, and DNA repair to occur. This chapter will look at how a cell responds to and deals with genomic instability at the epigenetic level and highlight how critical chromatin remodeling is for correct DNA repair and cell survival following DNA damage. This chapter will initially look at the DNA repair pathways that function in human cells and then at how the repair of DNA damage is controlled by epigenetics.

The phylogeny and evolutionary timescale of muscoide (Diptera: Brachycera: Calyptratae) inferred from mitochondrial genomes

Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene