A5023435254- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Evolution and Paleontology Studies
- Plant and animal studies
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Photosynthetic Processes and Mechanisms
- Insect Resistance and Genetics
- Mitochondrial Function and Pathology
- Evolution and Genetic Dynamics
- Insect and Arachnid Ecology and Behavior
- Glutathione Transferases and Polymorphisms
- Microbial Community Ecology and Physiology
- Insect-Plant Interactions and Control
- Algorithms and Data Compression
- Metabolomics and Mass Spectrometry Studies
- Chromosomal and Genetic Variations
- Lepidoptera: Biology and Taxonomy
- Machine Learning in Bioinformatics
- Plant Disease Resistance and Genetics
- Bat Biology and Ecology Studies
- Species Distribution and Climate Change
- Probiotics and Fermented Foods
- Pacific and Southeast Asian Studies
- Tryptophan and brain disorders
Australian National University
1998-2024
University College Dublin
2018-2024
Ollscoil na Gaillimhe – University of Galway
2024
CSIRO Land and Water
2015-2021
ACT Government
2012-2020
Earth Science Institute of the Slovak Academy of Sciences
2019
Leibniz Supercomputing Centre
2019
Commonwealth Scientific and Industrial Research Organisation
2010-2017
University of California, Los Angeles
2014-2017
National Museum of Natural History
2014-2017
Insects are the most speciose group of animals, but phylogenetic relationships many major lineages remain unresolved. We inferred phylogeny insects from 1478 protein-coding genes. Phylogenomic analyses nucleotide and amino acid sequences, with site-specific or domain-specific substitution models, produced statistically robust congruent results resolving previously controversial relations hips. dated origin to Early Ordovician [~479 million years ago (Ma)], insect flight Devonian (~406 Ma),...
A new class of glutathione transferases has been discovered by analysis the expressed sequence tag data base and alignment. Glutathione <i>S</i>-transferases (GSTs) class, named Omega, exist in several mammalian species and<i>Caenorhabditis elegans</i>. In humans, GSTO 1-1 is most tissues exhibits glutathione-dependent thiol transferase dehydroascorbate reductase activities characteristic glutaredoxins. The structure determined at 2.0-Å resolution a GST fold (Protein Data Bank entry code...
Sequence alignment and phylogenetic analysis has identified a new subgroup of glutathione S-transferase (GST)-like proteins from range species extending plants to humans. This group been termed the Zeta class. An atomic model N-terminal domain suggests that members class have similar structure other GSTs, binding in orientation G site. Recombinant human GSTZ1-1 expressed Escherichia coli characterized. The protein is dimer composed 24.2 kDa subunits minimal glutathione-conjugating activity...
We used DNA sequencing and gel blot surveys to assess the integrity of chloroplast gene infA, which codes for translation initiation factor 1, in >300 diverse angiosperms. Whereas most angiosperms appear contain an intact infA gene, has repeatedly become defunct ∼24 separate lineages angiosperms, including almost all rosid species. In four species is defunct, transferred expressed copies were found nucleus, complete with putative transit peptide sequences. The sequences nuclear genes from...
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed illuminate evolution highly insect societies. Bumblebees also invaluable natural and agricultural pollinators, there widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects bumblebee biology, including susceptibility implicated viability threats.We report high quality draft genome sequences...
Helicoverpa armigera and zea are major caterpillar pests of Old New World agriculture, respectively. Both, particularly H. armigera, extremely polyphagous, has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics resequencing elucidate the genetic basis for their properties as pests.
Abstract Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis evolution of these traits. Here we incorporated long-read sequencing state-of-the-art scaffolding protocols 1 to generate, our knowledge, first reference-quality six bat species ( Rhinolophus ferrumequinum , Rousettus aegyptiacus Phyllostomus discolor Myotis myotis Pipistrellus kuhlii Molossus molossus...
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning traits great importance. MADS-box genes are prime candidates for this, as they involved in virtually all aspects plant development. Here, we present detailed overview phylogeny and expression 201 MIKC-type genes. Homoeolog retention significantly above average genome-wide rate genes,...
Abstract Molecular sequence data that have evolved under the influence of heterotachous evolutionary processes are known to mislead phylogenetic inference. We introduce General Heterogeneous evolution On a Single Topology (GHOST) model evolution, implemented maximum-likelihood framework in program IQ-TREE (http://www.iqtree.org). Simulations show using GHOST model, can accurately recover tree topology, branch lengths, and substitution parameters from heterotachously sequences. investigate...
The effect of compositional heterogeneity in sequence data on phylogenetic inference was first identified as a potential problem the late 1980s and early 1990s (Chang Campbell, 2000; Conant Lewis, 2001; Foster Hickey, 1999; Hasegawa et al., 1993; Klenk 1994; Lockhart 1992a, 1992b; Loomis Smith, 1990; Olsen Woese, Penny Sogin Tarrio Van Den Bussche 1998; Weisburg 1989), by 1993 methods had been developed to measure extent (Lockhart 1993, Steel 1995) or overcome it (Foster, 2004; Galtier Gouy,...
DNA from ancient human remains provides perspectives on the origin of our species and relationship between molecular morphological variation. We report analysis mtDNA 10 Australians. These include morphologically gracile Lake Mungo 3 [ approximately 60 thousand years (ka) before present] three other individuals Holocene deposits at Willandra Lakes (<10 ka), all within skeletal range living Australians, six Pleistocene/early (15 to <8 ka) Kow Swamp with robust morphologies outside...
Abstract The extent to which alleles can disperse across a hybrid zone depends on the selection they are subjected in genetic background or, for those that selectively neutral, their ability escape from unfavourable environment by recombination. Three markers spanning 45 cM segment center of X chromosome were used investigate degree against linked genes helps maintain barrier gene flow between Mus musculus domesticus and M. m. Denmark. introgression all sex specific was more limited than...
Alignments of nucleotide or amino acid sequences may contain a variety different signals, one which is the historical signal that we often try to recover by phylogenetic analysis. Other such as those arising due compositional heterogeneities, among-lineage and among-site rate invariant sites, covariotides, interfere adversely with recovery signal. The effect interaction these signals on inference not well understood may, in many cases, even be underappreciated. In this study, investigate...
Abstract Motivation: Most phylogenetic methods assume that the sequences of nucleotides or amino acids have evolved under stationary, reversible and homogeneous conditions. When these assumptions are violated by data, there is an increased probability errors in estimates. Methods to examine aligned for violations available, but they rarely used, possibly because not widely known poorly understood. Results: We describe compare available tests symmetry k-dimensional contingency tables from...
Multiple sequence alignment (MSA) is a crucial first step in the analysis of genomic and proteomic data. Commonly occurring features, such as deletions insertions, are known to affect accuracy MSA programs, but extent which affected by positions insertions has not been examined independently other sources variation. We assessed performance 6 popular programs (ClustalW, DIALIGN-T, MAFFT, MUSCLE, PROBCONS, T-COFFEE) one experimental program, PRANK, on amino acid sequences that differed only...
Molecular phylogenetic studies of homologous sequences nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), a model evolution with one or more site-specific time-reversible rate matrices (e.g., GTR matrix) is enough to accurately data over whole tree. However, an increasing body suggests under these conditions exception, rather than norm. To address this issue, several non-SRH models molecular have been proposed, but...
Abstract The Old World bollworm Helicoverpa armigera is now established in Brazil but efforts to identify incursion origin(s) and pathway(s) have met with limited success due the patchiness of available data. Using international agricultural/horticultural commodity trade data mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) b (Cyt ) gene markers, we inferred origins pathways into Brazil. We detected 20 mtDNA haplotypes from six Brazilian states, eight which were new our 97 global COI-Cyt...