ORCID Profile
0000-0002-9619-3809
Current Organisation
Ollscoil na Gaillimhe – University of Galway
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Animal Systematics, Taxonomy And Phylogeny | Molecular Evolution | Genetics | Evolutionary Biology | Numerical and Computational Mathematics | Phylogeny and Comparative Analysis | Optimisation | Anthropological Genetics | Biological Mathematics | Sociobiology And Behavioural Ecology | Optics And Opto-Electronic Physics |
ANZSRC Socio-Economic Objective (SEO)
Biological sciences | Mathematical sciences | Mental health | Health related to ageing | Expanding Knowledge in the Biological Sciences | Health status (e.g. indicators of “well-being”) | Physical sciences
Related Links
Publications
Genetic and lipidomic analyses suggest that Nostoc punctiforme, a plant-symbiotic cyanobacterium, does not produce sphingolipids
Publisher: Microbiology Society
Date: 25-01-2022
Abstract: Sphingolipids, a class of amino-alcohol-based lipids, are well characterized in eukaryotes and in some anaerobic bacteria. However, the only sphingolipids so far identified in cyanobacteria are two ceramides (i.e. , an acetylsphingomyelin and a cerebroside), both based on unbranched, long-chain base (LCB) sphingolipids in Scytonema julianum and Moorea producens , respectively. The first step in de novo sphingolipid biosynthesis is the condensation of l -serine with palmitoyl-CoA to produce 3-keto-diyhydrosphingosine (KDS). This reaction is catalyzed by serine palmitoyltransferase (SPT), which belongs to a small family of pyridoxal phosphate-dependent α-oxoamine synthase (AOS) enzymes. Based on sequence similarity to molecularly characterized bacterial SPT peptides, we identified a putative SPT (Npun_R3567) from the model nitrogen-fixing, plant-symbiotic cyanobacterium, Nostoc punctiforme strain PCC 73102 (ATCC 29133). Gene expression analysis revealed that Npun_R3567 is induced during late-stage diazotrophic growth in N. punctiforme . However, Npun_R3567 could not produce the SPT reaction product, 3-keto-diyhydrosphingosine (KDS), when heterologously expressed in Escherichia coli . This agreed with a sphingolipidomic analysis of N. punctiforme cells, which revealed that no LCBs or ceramides were present. To gain a better understanding of Npun_R3567, we inferred the phylogenetic position of Npun_R3567 relative to other bacterial AOS peptides. Rather than clustering with other bacterial SPTs, Npun_R3567 and the other cyanobacterial BioF homologues formed a separate, monophyletic group. Given that N. punctiforme does not appear to possess any other gene encoding an AOS enzyme, it is altogether unlikely that N. punctiforme is capable of synthesizing sphingolipids. In the context of cross-kingdom symbiosis signalling in which sphingolipids are emerging as important regulators, it appears unlikely that sphingolipids from N. punctiforme play a regulatory role during its symbiotic association with plants.
Parallel implementation of maximum likelihood methods for phylogenetic analysis
Publisher: IEEE
Date: 2004
Evolution of the Inner Light-Harvesting Antenna Protein Family of Cyanobacteria, Algae, and Plants
Publisher: Springer Science and Business Media LLC
Date: 02-2007
DOI: 10.1007/S00239-006-0058-2
Abstract: Two hypotheses account for the evolution of the inner antenna light-harvesting proteins of oxygenic photosynthesis in cyanobacteria, algae, and plants: one in which the CP43 protein of photosytem II gave rise to the extrinsic CP43-like antennas of cyanobacteria (i.e. IsiA and Pcb proteins), as a late development, and the other in which CP43 and CP43-like proteins derive from an ancestral protein. In order to determine which of these hypotheses is most likely, we analyzed the family of antenna proteins by a variety of phylogenetic techniques, using alignments of the six common membrane-spanning helices, constructed using information on the antenna proteins' three-dimensional structure, and surveyed for evidence of factors that might confound inference of a correct phylogeny. The first hypothesis was strongly supported. As a consequence, we conclude that the ancestral photosynthetic apparatus, with 11 membrane-spanning helices, split at an early stage during evolution to form, on the one hand, the reaction center of photosystem II and, on the other hand, the ancestor of inner antenna proteins, CP43 (PsbC) and CP47 (PsbB). Only much later in evolution did the CP43 lineage give rise to the CP43' proteins (IsiA and Pcb) of cyanobacteria.
A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics
Publisher: Cold Spring Harbor Laboratory
Date: 27-08-2018
DOI: 10.1101/400648
Abstract: Molecular phylogenetics plays a key role in comparative genomics and has an increasingly-significant impacts on science, industry, government, public health, and society. In this opinion paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence our phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness-of-fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates. To the memory of Rossiter H. Crozier (1943-2009), an evolutionary biologist, who, with his great generosity and wide-reaching inquisitiveness, inspired students and scientists in Australia, and abroad.
Identifying Optimal Models of Evolution
Publisher: Springer New York
Date: 29-11-2016
DOI: 10.1007/978-1-4939-6622-6_15
Abstract: Most phylogenetic methods are model-based and depend on models of evolution designed to approximate the evolutionary processes. Several methods have been developed to identify suitable models of evolution for phylogenetic analysis of alignments of nucleotide or amino acid sequences and some of these methods are now firmly embedded in the phylogenetic protocol. However, in a disturbingly large number of cases, it appears that these models were used without acknowledgement of their inherent shortcomings. In this chapter, we discuss the problem of model selection and show how some of the inherent shortcomings may be identified and overcome.
GHOST: Recovering historical signal from heterotachously-evolved sequence alignments
Publisher: Oxford University Press (OUP)
Date: 31-07-2019
Abstract: Molecular sequence data that have evolved under the influence of heterotachous evolutionary processes are known to mislead phylogenetic inference. We introduce the General Heterogeneous evolution On a Single Topology (GHOST) model of sequence evolution, implemented under a maximum-likelihood framework in the phylogenetic program IQ-TREE (www.iqtree.org). Simulations show that using the GHOST model, IQ-TREE can accurately recover the tree topology, branch lengths, and substitution model parameters from heterotachously evolved sequences. We investigate the performance of the GHOST model on empirical data by s ling phylogenomic alignments of varying lengths from a plastome alignment. We then carry out inference under the GHOST model on a phylogenomic data set composed of 248 genes from 16 taxa, where we find the GHOST model concurs with the currently accepted view, placing turtles as a sister lineage of archosaurs, in contrast to results obtained using traditional variable rates-across-sites models. Finally, we apply the model to a data set composed of a sodium channel gene of 11 fish taxa, finding that the GHOST model is able to elucidate a subtle component of the historical signal, linked to the previously established convergent evolution of the electric organ in two geographically distinct lineages of electric fish. We compare inference under the GHOST model to partitioning by codon position and show that, owing to the minimization of model constraints, the GHOST model offers unique biological insights when applied to empirical data.
Markov invariants, plethysms, and phylogenetics
Publisher: Elsevier BV
Date: 08-2008
DOI: 10.1016/J.JTBI.2008.04.001
Abstract: We explore model-based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the Log-Det distance measure. We take as our primary tool group representation theory, and show that it provides a general framework for analyzing Markov processes on trees. From this algebraic perspective, the inherent symmetries of these processes become apparent, and focusing on plethysms, we are able to define Markov invariants and give existence proofs. We give an explicit technique for constructing the invariants, valid for any number of character states and taxa. For phylogenetic trees with three and four leaves, we demonstrate that the corresponding Markov invariants can be fruitfully exploited in applied phylogenetic studies.
Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
Publisher: Oxford University Press (OUP)
Date: 21-02-2006
DOI: 10.1093/BIOINFORMATICS/BTL064
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 the data, there is an increased probability of errors in the phylogenetic estimates. Methods to examine aligned sequences for these violations are available, but they are rarely used, possibly because they are not widely known or because they are poorly understood. Results: We describe and compare the available tests for symmetry of k-dimensional contingency tables from homologous sequences, and develop two new tests to evaluate different aspects of the evolutionary processes. For any pair of sequences, we consider a partition of the test for symmetry into a test for marginal symmetry and a test for internal symmetry. The proposed tests can be used to identify appropriate models for estimation of evolutionary relationships under a Markovian model. Simulations under more or less complex evolutionary conditions were done to display the performance of the tests. Finally, the tests were applied to an alignment of small-subunit ribosomal RNA sequences of five species of bacteria to outline the evolutionary processes under which they evolved. Availability: Programs written in R to do the tests on nucleotides are available from Contact: lars.jermiin@usyd.edu.au
Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics
Publisher: Springer Science and Business Media LLC
Date: 2014
Measuring Historical and Compositional Signals in Phylogenetic Data
Publisher: Cold Spring Harbor Laboratory
Date: 03-01-2020
DOI: 10.1101/2020.01.03.894097
Abstract: Most commonly-used molecular phylogenetic methods assume that the sequences evolved on a single bifurcating tree and that the evolutionary processes operating at the variable sites are Markovian. Typically, it is also assumed that these evolutionary processes were stationary, reversible and homogenous across the edges of the tree and that the multiple substitutions at variable sites occurred so infrequently that the historical signal (i.e., the signal in DNA that is due to the order and time of ergence event) in phylogenetic data has been retained, allowing for accurate phylogenetic estimates to be obtained from the data. Here, we present two metrics, λ and δ CFS , to quantify the strength of the historical and compositional signals in phylogenetic data. λ quantifies loss of historical signal , with λ = 0.0 indicating evidence of a strong historical signal and λ = 1.0 indicating evidence of a fully eroded historical signal. δ CFS quantifies compositional distance from full symmetry of a ergence matrix generated by comparing two sequences, with δ CFS = 0.0 indicating no evidence of evolution under dissimilar conditions and δ CFS 0.0 indicating increasing evidence of lineages erging under different conditions. The metrics are implemented in methods intended for use after multiple sequence alignment and before model selection and phylogenetic analysis. Results generated using these methods allow users of phylogenetic tools to select phylogenetic data more wisely than it previously was possible. The merits of these metrics and methods are illustrated using simulated data and multi-gene alignments obtained from 144 insect genomes.
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta
Publisher: Elsevier BV
Date: 09-2016
Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
Publisher: Elsevier BV
Date: 12-2007
DOI: 10.1016/J.YMPEV.2007.08.018
Abstract: The delineation and phylogenetic relationships of the pulmonate family Helicarionidae are currently poorly understood. We have undertaken a phylogenetic analysis of Australian members of Helicarionidae. Three consecutive mitochondrial genes (COI, tRNA-val and 16S rRNA) were sequenced for 36 species from Helicarionidae and related groups. Helicarionidae grouped with Ariophantidae and Urocyclidae with good support in all trees, as did Microcystinae with Trochomorphidae, corresponding to the results of a previous morphological study, but the relationships of Euconulinae and Limacidae could not be resolved. Cystopeltidae never grouped with Helicarionidae and should be regarded as a separate family. The position of tRNA-val in the mitochondrial genome provided a new synapomorphy for Microcystinae. In addition, the COI and 16S rRNA sequences showed a high degree of compositional heterogeneity and incompatibility of phylogenetic signals, highlighting the importance of testing for the decay of the historical signal prior to the phylogenetic analysis.
Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone
Publisher: MDPI AG
Date: 26-04-2022
Abstract: Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest ergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto uns led laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.
Reverse engineering
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7GC02343J
Abstract: The use of ancestral sequence reconstruction to design novel biocatalysts with improved catalytic properties for the production of polyamide precursors.
Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini)
Publisher: Springer Science and Business Media LLC
Date: 26-06-2017
A minimum reporting standard for multiple sequence alignments
Publisher: Oxford University Press (OUP)
Date: 14-04-2020
Abstract: Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.
Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages
Publisher: Oxford University Press (OUP)
Date: 12-07-2014
Abstract: Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.
A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?
Publisher: Oxford University Press (OUP)
Date: 08-09-2021
Abstract: In molecular phylogenetics, it is typically assumed that the evolutionary process for DNA can be approximated by independent and identically distributed Markovian processes at the variable sites and that these processes erge over the edges of a rooted bifurcating tree. Sometimes the nucleotides are transformed from a 4-state alphabet to a 3- or 2-state alphabet by a procedure that is called recoding, lumping, or grouping of states. Here, we introduce a likelihood-ratio test for lumpability for DNA that has erged under different Markovian conditions, which assesses the assumption that the Markovian property of the evolutionary process over each edge is retained after recoding of the nucleotides. The test is derived and validated numerically on simulated data. To demonstrate the insights that can be gained by using the test, we assessed two published data sets, one of mitochondrial DNA from a phylogenetic study of the ratites and the other of nuclear DNA from a phylogenetic study of yeast. Our analysis of these data sets revealed that recoding of the DNA eliminated some of the compositional heterogeneity detected over the sequences. However, the Markovian property of the original evolutionary process was not retained by the recoding, leading to some significant distortions of edge lengths in reconstructed trees.[Evolutionary processes likelihood-ratio test lumpability Markovian processes Markov models phylogeny recoding of nucleotides.]
Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications may have facilitated adaptation to different environmental conditions
Publisher: Cold Spring Harbor Laboratory
Date: 26-03-2019
DOI: 10.1101/585232
Abstract: Wheat ( Triticum aestivum ) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging climate and cultivation conditions, facilitating wheat breeding by fine-tuning important traits such as stress resistance, yield and plant architecture is of great importance. Since they are involved in virtually all aspects of plant development and stress responses, prime candidates for improving these traits are MIKC-type (type II) MADS-box genes. We present a detailed overview of number, phylogeny, and expression of 201 wheat MIKC-type MADS-box genes, which can be assigned to 15 subfamilies. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We find the extensive expansion of some MIKC-type subfamilies to be correlated with their chromosomal location and propose a link between MADS-box gene duplications and the adaptability of wheat. A number of MIKC-type genes encode for truncated proteins that lack either the DNA-binding or protein-protein interaction domain and occasionally show novel expression patterns, possibly pointing towards neofunctionalization. Conserved and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a ersity of conditions, hence contributing to its importance as a global staple food. Therefore, we propose that MIKC-type MADS-box genes are especially well suited for targeted breeding approaches and phenotypic fine tuning.
Genome‐wide analysis of MIKC ‐type MADS ‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization
Publisher: Wiley
Date: 10-2019
DOI: 10.1111/NPH.16122
Abstract: 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 important traits is of great importance. MADS ‐box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC ‐type MADS ‐box genes. Homoeolog retention is significantly above the average genome‐wide retention rate for wheat genes, indicating that many MIKC ‐type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily‐specific expression pattern, indicating broad conservation of function of MIKC ‐type genes during wheat evolution. We also found extensive expansion of some MIKC ‐type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC ‐type genes show novel expression patterns and respond, for ex le, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC ‐type genes may have played an important role in the adaptation of wheat to a ersity of conditions, hence contributing to the importance of wheat as a global staple food.
Improving the analysis of dinoflagellate phylogeny based on rDNA
Publisher: Elsevier BV
Date: 11-2005
DOI: 10.1016/J.PROTIS.2005.05.003
Abstract: Phylogenetic studies of dinoflagellates are often conducted using rDNA sequences. In analyses to date, the monophyly of some of the major lineages of dinoflagellates remain to be demonstrated. There are several reasons for this uncertainty, one of which may be the use of models of evolution that may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non-independently evolving sites, high levels of compositional heterogeneity among some of the sequences, high levels of incompatibility (homoplasy), and rate heterogeneity among sites. Taking into account these confounding factors, we analysed the data and found that the Gonyaulacales, a well-supported clade, may be the most recently erged order. Other supported orders were, in the analysis based on SSU, the Suessiales and the Dinophysiales however, the Gymnodiniales and Prorocentrales appeared to be polyphyletic. The Peridiniales without Heterocapsa species appeared as a monophyletic group in the analysis based on LSU however, the support was low. The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments.
Intramolecular epistasis and the evolution of a new enzymatic function
Publisher: Public Library of Science (PLoS)
Date: 29-06-2012
Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours
Publisher: The Royal Society
Date: 15-09-2005
Abstract: Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize ex les of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused.
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species
Publisher: Springer Science and Business Media LLC
Date: 31-07-2017
Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?
Publisher: Elsevier BV
Date: 02-2016
DOI: 10.1016/J.COIS.2015.12.001
Abstract: The size of gene families associated with xenobiotic detoxification in insects may be associated with the complexity of their diets and their propensities to develop insecticide resistance. We test these hypotheses by collating the annotations of cytochrome P450, carboxyl/cholinesterase and glutathione S-transferase genes in 65 insect species with data on their host use and history of insecticide resistance. We find 2-4 fold variation across the species in the numbers of these genes and, in some orders, especially the Hymenoptera, there is a clear relationship between the numbers of genes and feeding preferences. However in other orders, in particular the Lepidoptera, no such relationship is apparent. The size of these three gene families also tend to correlate with insecticide resistance propensity but this may not be an independent effect because species with broader host ranges are more likely to be pests that are heavily sprayed with insecticides.
A modern soft-bottom, shallow-water crinoid fauna (Echinodermata) from the Great Barrier Reef, Australia
Publisher: Springer Science and Business Media LLC
Date: 06-12-2005
Phylogenetic Model Evaluation
Publisher: Humana Press
Date: 2008
DOI: 10.1007/978-1-60327-159-2_16
Abstract: Most phylogenetic methods are model-based and depend on Markov models designed to approximate the evolutionary rates between nucleotides or amino acids. When Markov models are selected for analysis of alignments of these characters, it is assumed that they are close approximations of the evolutionary processes that gave rise to the data. A variety of methods have been developed for estimating the fit of Markov models, and some of these methods are now frequently used for the selection of Markov models. In a growing number of cases, however, it appears that the investigators have used the model-selection methods without acknowledging their inherent shortcomings. This chapter reviews the issue of model selection and model evaluation.
Generation of the Exact Distribution and Simulation of Matched Nucleotide Sequences on a Phylogenetic Tree
Publisher: Springer Science and Business Media LLC
Date: 28-02-2006
Multi-objective evolutionary algorithms and phylogenetic inference with multiple data sets
Publisher: Springer Science and Business Media LLC
Date: 10-05-2005
A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants
Publisher: Springer Science and Business Media LLC
Date: 09-2021
DOI: 10.1186/S12859-021-04337-8
Abstract: Variation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only the hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phylogenetic lineages or haplogroups. This lack of resolution can limit functional and clinical interpretation of a substantial body of existing mtDNA data. To address this limitation, we developed and evaluated a large, curated reference alignment of complete mtDNA sequences as part of a pipeline for imputing missing mtDNA single nucleotide variants (mtSNVs). We call our reference alignment and pipeline MitoImpute. We aligned the sequences of 36,960 complete human mitochondrial genomes downloaded from GenBank, filtered and controlled for quality. These sequences were reformatted for use in imputation software, IMPUTE2. We assessed the imputation accuracy of MitoImpute by measuring haplogroup and genotype concordance in data from the 1000 Genomes Project and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). The mean improvement of haplogroup assignment in the 1000 Genomes s les was 42.7% (Matthew’s correlation coefficient = 0.64). In the ADNI cohort, we imputed missing single nucleotide variants. These results show that our reference alignment and panel can be used to impute missing mtSNVs in existing data obtained from using microarrays, thereby broadening the scope of functional and clinical investigation of mtDNA. This improvement may be particularly useful in studies where participants have been recruited over time and mtDNA data obtained using different methods, enabling better integration of early data collected using less accurate methods with more recent sequence data.
Improved Consensus Network Techniques for Genome-Scale Phylogeny
Publisher: Oxford University Press (OUP)
Date: 22-02-2006
Abstract: Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.
SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.
Publisher: Oxford University Press (OUP)
Date: 09-06-2006
DOI: 10.1093/BIOINFORMATICS/BTL283
Abstract: Summary: Most phylogenetic methods assume that the sequences evolved under homogeneous, stationary and reversible conditions. Compositional heterogeneity in data intended for studies of phylogeny suggests that the data did not evolve under these conditions. SeqVis, a Java application for analysis of nucleotide content, reads sequence alignments in several formats and plots the nucleotide content in a tetrahedron. Once plotted, outliers can be identified, thus allowing for decisions on the applicability of the data for phylogenetic analysis. Availability: Contact: lars.jermiin@usyd.edu.au
Population Genetic Structure and Potential Incursion Pathways of the Bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) in Australia
Publisher: Public Library of Science (PLoS)
Date: 15-01-2016
A minimum reporting standard for multiple sequence alignments
Publisher: Cold Spring Harbor Laboratory
Date: 15-01-2020
DOI: 10.1101/2020.01.15.907733
Abstract: Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely-specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.
Erratum to: Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species
Publisher: Springer Science and Business Media LLC
Date: 15-08-2017
Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates
Publisher: Cold Spring Harbor Laboratory
Date: 04-11-2019
DOI: 10.1101/828996
Abstract: Most model-based molecular phylogenetic methods assume that the sequences erged on a tree under homogeneous conditions. If evolution occurred under these conditions, then it is unlikely that the sequences would become compositionally heterogeneous. Conversely, if the sequences are compositionally heterogeneous, then it is unlikely that they have evolved under homogeneous conditions. We present methods to detect and analyse heterogeneous evolution in aligned sequence data and to examine—visually and numerically—its effect on phylogenetic estimates. The methods are implemented in three programs, allowing users to better examine under what conditions their phylogenetic data may have evolved.
Mind the gaps: Evidence of bias in estimates of multiple sequence alignments
Publisher: Oxford University Press (OUP)
Date: 16-08-2007
Abstract: Multiple sequence alignment (MSA) is a crucial first step in the analysis of genomic and proteomic data. Commonly occurring sequence features, such as deletions and insertions, are known to affect the accuracy of MSA programs, but the extent to which alignment accuracy is affected by the positions of insertions and deletions has not been examined independently of other sources of sequence variation. We assessed the performance of 6 popular MSA programs (ClustalW, DIALIGN-T, MAFFT, MUSCLE, PROBCONS, and T-COFFEE) and one experimental program, PRANK, on amino acid sequences that differed only by short regions of deleted residues. The analysis showed that the absence of residues often led to an incorrect placement of gaps in the alignments, even though the sequences were otherwise identical. In data sets containing sequences with partially overlapping deletions, most MSA programs preferentially aligned the gaps vertically at the expense of incorrectly aligning residues in the flanking regions. Of the programs assessed, only DIALIGN-T was able to place overlapping gaps correctly relative to one another, but this was usually context dependent and was observed only in some of the data sets. In data sets containing sequences with non-overlapping deletions, both DIALIGN-T and MAFFT (G-INS-I) were able to align gaps with near-perfect accuracy, but only MAFFT produced the correct alignment consistently. The same was true for data sets that comprised isoforms of alternatively spliced gene products: both DIALIGN-T and MAFFT produced highly accurate alignments, with MAFFT being the more consistent of the 2 programs. Other programs, notably T-COFFEE and ClustalW, were less accurate. For all data sets, alignments produced by different MSA programs differed markedly, indicating that reliance on a single MSA program may give misleading results. It is therefore advisable to use more than one MSA program when dealing with sequences that may contain deletions or insertions, particularly for high-throughput and pipeline applications where manual refinement of each alignment is not practicable.
Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family inTriticum aestivum
Publisher: Oxford University Press (OUP)
Date: 08-2019
Abstract: The serine protease inhibitor (serpin) gene family is the largest family of protease inhibitors. Serine protease inhibitors have an active, but under-characterized, role in grain development and defense against pathogen attack in cereal crops. By exploiting publicly available genomic, transcriptomic and proteomic data for wheat (Triticum aestivum), we have identified and annotated the entire ’serpinome’ of wheat and constructed a high-quality and robust phylogenetic tree of the gene family, identifying paralogous and homeologous clades from the hexaploid wheat genome, including the Serpin-Z group that have been well characterized in barley. Using publicly available RNAseq data (www.wheat-expression.com/), expression profiles of the wheat serpins were explored across a variety of tissues from the developing grain, spikelet and spike. We show that the SERPIN-Z clade, among others, are highly expressed during grain development, and that there is homeologous and paralogous functional redundancy in this gene family. Further to their role in grain development, serpins play an important but under-explored role in response to fungal pathogens. Using 13 RNAseq datasets of wheat tissues infected by fungal pathogens, we identified 37 serpins with a significant disease response. The majority of the disease-responsive serpins were upregulated by Fusarium graminearum, a destructive fungal pathogen that attacks the spike and developing grain of wheat. As serpins are ubiquitous in wheat grain, the genes encoding serpins may be linked to grain development, with their disease response a result of pleiotropy.
Evolution of Vertebrate Genes Related to Prion and Shadoo Proteins—Clues from Comparative Genomic Analysis
Publisher: Oxford University Press (OUP)
Date: 09-2004
ModelFinder: fast model selection for accurate phylogenetic estimates
Publisher: Springer Science and Business Media LLC
Date: 08-05-2017
DOI: 10.1038/NMETH.4285
The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
Publisher: Oxford University Press (OUP)
Date: 08-2004
Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil
Publisher: Springer Science and Business Media LLC
Date: 28-03-2017
DOI: 10.1038/SREP45302
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 to the patchiness of available data. Using international agricultural/horticultural commodity trade data and mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and cytochrome b (Cyt b ) gene markers, we inferred the origins and incursion pathways into Brazil. We detected 20 mtDNA haplotypes from six Brazilian states, eight of which were new to our 97 global COI-Cyt b haplotype database. Direct sequence matches indicated five Brazilian haplotypes had Asian, African, and European origins. We identified 45 parsimoniously informative sites and multiple substitutions per site within the concatenated (945 bp) nucleotide dataset, implying that probabilistic phylogenetic analysis methods are needed. High ersity and signatures of uniquely shared haplotypes with erse localities combined with the trade data suggested multiple incursions and introduction origins in Brazil. Increasing agricultural/horticultural trade activities between the Old and New Worlds represents a significant biosecurity risk factor. Identifying pest origins will enable resistance profiling that reflects countries of origin to be included when developing a resistance management strategy, while identifying incursion pathways will improve biosecurity protocols and risk analysis at biosecurity hotspots including national ports.
Six reference-quality genomes reveal evolution of bat adaptations
Publisher: Springer Science and Business Media LLC
Date: 22-07-2020
DOI: 10.1038/S41586-020-2486-3
Abstract: Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols 1 to generate, to our knowledge, the first reference-quality genomes of six bat species ( Rhinolophus ferrumequinum , Rousettus aegyptiacus , Phyllostomus discolor , Myotis myotis , Pipistrellus kuhlii and Molossus molossus ). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of erse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease 1 .
Phylogenomics resolves the timing and pattern of insect evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 07-11-2014
Abstract: Insects are the most erse group of animals, with the largest number of species. However, many of the evolutionary relationships between insect species have been controversial and difficult to resolve. Misof et al. performed a phylogenomic analysis of protein-coding genes from all major insect orders and close relatives, resolving the placement of taxa. The authors used this resolved phylogenetic tree together with fossil analysis to date the origin of insects to ~479 million years ago and to resolve long-controversial subjects in insect phylogeny. Science , this issue p. 763
Is the Big Bang in Animal Evolution Real?
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-12-2005
Characterization of the type I interferon locus and identification of novel genes
Publisher: Elsevier BV
Date: 08-2004
The molecular structure of the IsiA–Photosystem I supercomplex, modelled from high-resolution, crystal structures of Photosystem I and the CP43 protein
Publisher: Elsevier BV
Date: 04-2010
DOI: 10.1016/J.BBABIO.2010.01.002
Abstract: We present the molecular structure of the IsiA-Photosystem I (PSI) supercomplex, inferred from high-resolution, crystal structures of PSI and the CP43 protein. The structure of iron-stress-induced A protein (IsiA) is similar to that of CP43, albeit with the difference that IsiA is associated with 15 chlorophylls (Chls), one more than previously assumed. The membrane-spanning helices of IsiA contain hydrophilic residues many of which bind Chl. The optimal structure of the IsiA-PSI supercomplex was inferred by systematically rearranging the IsiA monomers and PSI trimer in relation to each other. For each of the 6,969,600 structural configurations considered, we counted the number of optimal Chl-Chl connections (i.e., cases where Chl-bound Mg atoms are <or=25A apart). Fifty of these configurations were found to have optimal energy-transfer potential. The 50 configurations could be ided into three variants one of these, comprising 36 similar configurations, was found to be superior to the other configurations in terms of its potential to transfer excitation energy to the reaction centres under low-light conditions and its potential to dissipate excess energy under high-light conditions. Compared to the assumed model [Biochemistry 42 (2003) 3180-3188], the new Chl increases by 7% the ability of IsiA to harvest sunlight while the rearrangement of the constituent components of the IsiA-PSI supercomplex increases by 228% the energy-transfer potential. In conclusion, our model allows us to explain how the IsiA-PSI supercomplex may act as an efficient light-harvesting structure under low-light conditions and as an efficient dissipater of excess energy under high-light conditions.
Fixed, free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian–Triassic origin
Publisher: Elsevier BV
Date: 2013
DOI: 10.1016/J.YMPEV.2012.09.018
Abstract: Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian-Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid ersity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231-252mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian-Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon s ling are needed to recover a more robust phylogeny of the group.
Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”
Publisher: American Association for the Advancement of Science (AAAS)
Date: 31-07-2015
Abstract: Tong et al . comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a “roachoid” fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate.
Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
Publisher: Oxford University Press (OUP)
Date: 27-08-2020
DOI: 10.1093/GBE/EVAA137
Abstract: We examine the genetic history and population status of Hawaiian hoary bats (Lasiurus semotus), the most isolated bats on Earth, and their relationship to northern hoary bats (Lasiurus cinereus), through whole-genome analysis of single-nucleotide polymorphisms mapped to a de novo-assembled reference genome. Profiles of genomic ersity and ergence indicate that Hawaiian hoary bats are distinct from northern hoary bats, and form a monophyletic group, indicating a single ancestral colonization event 1.34 Ma, followed by substantial ergence between islands beginning 0.51 Ma. Phylogenetic analysis indicates Maui is central to the radiation across the archipelago, with the southward expansion to Hawai‘i and westward to O‘ahu and Kaua‘i. Because this endangered species is of conservation concern, a clearer understanding of the population genetic structure of this bat in the Hawaiian Islands is of timely importance.
Isolation and characterization of the mouse ubiquitin-specific protease Usp15
Publisher: Springer Science and Business Media LLC
Date: 2003
DOI: 10.1007/S00335-002-3035-0
Abstract: We have characterized the mouse ortholog of the human ubiquitin-specific protease USP15. Mouse Usp15 consists of 981 amino acids with a predicted molecular mass of 112 kDa, contains the highly conserved Cys and His boxes present in all members of the UBP family of deubiquitinating enzymes, and is 98% identical/99% similar to human USP15. Usp15 shares 59.5% identity/75.5% sequence similarity with the mouse Unp(Usp4) oncoprotein. Recombinant Usp15 demonstrated ubiquitin-specific protease activity against engineered linear fusions of ubiquitin to glutathione S-transferase. Usp15 can also cleave the ubiquitin-proline bond, as can USP15 and Usp4. Alignment of mouse and human Usp15 and Usp4 protein sequences suggested that Usp15/USP15 may be alternately spliced in a manner analogous to Usp4. Sequence analysis of RT-PCR products from several human and mouse cell lines and tissues revealed alternate splicing in all cells studied. Northern blot analysis of both mouse and human Usp15 revealed two differently sized mRNAs in all tissues examined, owing to alternate polyadenylation sites spaced by 1.5 kb. Chromosomal mapping by interspecific backcross analysis localized the Usp15 gene to the distal region of mouse Chromosome (Chr) 10. This region is syntenic with human Chr 12q24, the location of human USP15, and a different location to Unp(Usp4) (Chr 9). Identification of the mouse Usp15 gene (>69.5 kb) and human USP15 gene (145 kb) sequences in genome databases reveals that both are composed of 22 exons with identical splice sites, and both have an exon/intron structure identical to the mouse Usp4 gene, including the alternately spliced exon. Phylogenetic studies suggest that a sequence currently identified as a chicken Usp4 ortholog is in fact a USP15 ortholog, while bona-fide chicken, cow, and rat Usp4 orthologs can be identified in EST databases.
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
Publisher: F1000 Research Ltd
Date: 15-05-2023
DOI: 10.12688/F1000RESEARCH.133724.1
Abstract: Bio ersity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of bio ersity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate bio ersity preservation and restoration. This white paper, prepared by the ELIXIR Bio ersity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the bio ersity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Bio ersity Community in ELIXIR and is an appeal to identify and involve new stakeholders.
Tracing the Decay of the Historical Signal in Biological Sequence Data
Publisher: Oxford University Press (OUP)
Date: 08-2004
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