James Mcinerney

• 301Impact points

• 64Publications

• 63Followers

Education

Contact Details

Other

Publications

• The public goods hypothesis for the evolution of life on Earth.

  Authors: James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell

  Biology direct. 6(1):41.

  ABSTRACT: It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. InABSTRACT: It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.

• Planctomycetes and eukaryotes: A case of analogy not homology.

  Authors: James O McInerney, William F Martin, Eugene V Koonin, John F Allen, Michael Y Galperin, Nick Lane, John M Archibald, T Martin Embley

  BioEssays : news and reviews in molecular, cellular and developmental biology.

  Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular,Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.

• A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases.

  Authors: Carla A Cummins, James O McInerney

  Systematic biology.

  Current phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combinedCurrent phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combined with dense sampling of large numbers of characters. However, systematic biases and superimposed substitutions make this task very difficult. Model adequacy can sometimes be achieved at the cost of adding large numbers of free parameters, with each parameter being optimized according to some criterion, resulting in increased computation times and large variances in the model estimates. In this study, we develop a simple approach that estimates the relative evolutionary rate of each homologous character. The method that we describe uses the similarity between characters as a proxy for evolutionary rate. In this article, we work on the premise that if the character-state distribution of a homologous character is similar to many other characters, then this character is likely to be relatively slowly evolving. If the character-state distribution of a homologous character is not similar to many or any of the rest of the characters in a data set, then it is likely to be the result of rapid evolution. We show that in some test cases, at least, the premise can hold and the inferences are robust. Importantly, the method does not use a "starting tree" to make the inference and therefore is tree independent. We demonstrate that this approach can work as well as a maximum likelihood (ML) approach, though the ML method needs to have a known phylogeny, or at least a very good estimate of that phylogeny. We then demonstrate some uses for this method of analysis, including the improvement in phylogeny reconstruction for both deep-level and recent relationships and overcoming systematic biases such as base composition bias. Furthermore, we compare this approach to two well-established methods for reweighting or removing characters. These other methods are tree-based and we show that they can be systematically biased. We feel this method can be useful for phylogeny reconstruction, understanding evolutionary rate variation, and for understanding selection variation on different characters.

• The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.

  Authors: David Alvarez-Ponce, James O McInerney

  Genome biology and evolution.

  Eukaryotes are generally thought to stem from a fusion event involving an archaebacterium and a eubacterium. As a result of this event, contemporaneous eukaryotic genomes are chimaeras of genesEukaryotes are generally thought to stem from a fusion event involving an archaebacterium and a eubacterium. As a result of this event, contemporaneous eukaryotic genomes are chimaeras of genes inherited from both endosymbiotic partners. These two coexisting gene repertoires have been shown to differ in a number of ways in yeast. Here we combine genomic and functional data in order to determine if and how human genes that have been inherited from both prokaryotic ancestors remain distinguishable. We show that, despite being fewer in number, human genes of archaebacterial origin are more highly and broadly expressed across tissues, are more likely to have lethal mouse orthologs, tend to be involved in informational processes, are more selectively constrained, and encode shorter and more central proteins in the protein-protein interaction network than eubacterium-like genes. Furthermore, consistent with Endosymbiotic Theory, we show that proteins tend to interact with those encoded by genes of the same ancestry. Most interestingly from a human health perspective, archaebacterial genes are less likely to be involved in heritable human disease. Taken together, these results illustrate that after more than two billion years of evolution the human genome maintains at least two somewhat distinct communities of genes.

  Download

• Planctomycetes and eukaryotes: A case of analogy not homology

  Authors: J. O. McInerney, W. F. Martin, E. V. Koonin, J. F. Allen, M. Y. Galperin, N. Lane, J. M. Archibald, T. M. Embley

  Bioessays.

  Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular,Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.

  Download

• A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

  Authors: C. A. Cummins, J. O. McInerney

  Syst Biol.

  Current phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combinedCurrent phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combined with dense sampling of large numbers of characters. However, systematic biases and superimposed substitutions make this task very difficult. Model adequacy can sometimes be achieved at the cost of adding large numbers of free parameters, with each parameter being optimized according to some criterion, resulting in increased computation times and large variances in the model estimates. In this study, we develop a simple approach that estimates the relative evolutionary rate of each homologous character. The method that we describe uses the similarity between characters as a proxy for evolutionary rate. In this article, we work on the premise that if the character-state distribution of a homologous character is similar to many other characters, then this character is likely to be relatively slowly evolving. If the character-state distribution of a homologous character is not similar to many or any of the rest of the characters in a data set, then it is likely to be the result of rapid evolution. We show that in some test cases, at least, the premise can hold and the inferences are robust. Importantly, the method does not use a "starting tree" to make the inference and therefore is tree independent. We demonstrate that this approach can work as well as a maximum likelihood (ML) approach, though the ML method needs to have a known phylogeny, or at least a very good estimate of that phylogeny. We then demonstrate some uses for this method of analysis, including the improvement in phylogeny reconstruction for both deep-level and recent relationships and overcoming systematic biases such as base composition bias. Furthermore, we compare this approach to two well-established methods for reweighting or removing characters. These other methods are tree-based and we show that they can be systematically biased. We feel this method can be useful for phylogeny reconstruction, understanding evolutionary rate variation, and for understanding selection variation on different characters.

• The public goods hypothesis for the evolution of life on Earth

  Authors: J. O. McInerney, D. Pisani, E. Bapteste, M. J. O'Connell

  Biol Direct. 6(1):41.

  ABSTRACT: It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. InABSTRACT: It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.

  Download

• Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.

  Authors: James A Cotton, James O McInerney

  Proceedings of the National Academy of Sciences of the United States of America.

  The traditional tree of life shows eukaryotes as a distinct lineage of living things, but many studies have suggested that the first eukaryotic cells were chimeric, descended from both EubacteriaThe traditional tree of life shows eukaryotes as a distinct lineage of living things, but many studies have suggested that the first eukaryotic cells were chimeric, descended from both Eubacteria (through the mitochondrion) and Archaebacteria. Eukaryote nuclei thus contain genes of both eubacterial and archaebacterial origins, and these genes have different functions within eukaryotic cells. Here we report that archaebacterium-derived genes are significantly more likely to be essential to yeast viability, are more highly expressed, and are significantly more highly connected and more central in the yeast protein interaction network. These findings hold irrespective of whether the genes have an informational or operational function, so that many features of eukaryotic genes with prokaryotic homologs can be explained by their origin, rather than their function. Taken together, our results show that genes of archaebacterial origin are in some senses more important to yeast metabolism than genes of eubacterial origin. This importance reflects these genes' origin as the ancestral nuclear component of the eukaryotic genome.

• Gene and genome trees conflict at many levels.

  Authors: Leanne S Haggerty, Fergal J Martin, David A Fitzpatrick, James O McInerney

  Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 364(1527):2209-19.

  Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodelHorizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a diverse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.

• The network of life: genome beginnings and evolution. Introduction.

  Authors: Mark A. Ragan, James O. McInerney, James A. Lake

  Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 364(1527):2169-75.

• Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae).

  Authors: Luciane Mendes Hatadani, James O McInerney, Hermes Fonseca de Medeiros, Ana Carolina Martins Junqueira, Ana Maria de Azeredo-Espin, Louis Bernard Klaczko

  Molecular phylogenetics and evolution.

  We suggest a new phylogenetic hypothesis for the tripunctata radiation based on sequences of mitochondrial genes. Phylogenetic trees were reconstructed by parsimony, maximum likelihood and BayesianWe suggest a new phylogenetic hypothesis for the tripunctata radiation based on sequences of mitochondrial genes. Phylogenetic trees were reconstructed by parsimony, maximum likelihood and Bayesian methods. We performed tests for hypotheses of monophyly for taxonomic groups and other specific hypotheses. Results reject the monophyly for the tripunctata group whereas monophyly is not rejected for the tripunctata radiation and other specific groups within the radiation. Although most of the basal nodes were unresolved we were able to identify four clusters within the tripunctata radiation. These results suggest the collection of additional data before a proper taxonomic revision could be proposed.

• Recurring cluster and operon assembly for Phenylacetate degradation genes.

  Authors: Fergal Martin, James McInerney

  BMC evolutionary biology. 9(1):36.

  ABSTRACT: BACKGROUND: A large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. Most of these theories have beenABSTRACT: BACKGROUND: A large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. Most of these theories have been dismissed because empirical data do not match the expectations of the models. In this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process. RESULTS: We have selected an exemplar well-characterised biochemical pathway, the phenylacetate degradation pathway, and we show that its complex history is only compatible with a model where a selective advantage accrues from moving genes closer together. This selective pressure is likely to be reasonably weak and only twice in our dataset of 102 genomes do we see independent formation of a complete cluster containing all the catabolic genes in the pathway. Additionally, de novo clustering of genes clearly occurs repeatedly, even though recombination should result in the random dispersal of such genes in their respective genomes. Interspecies gene transfer has frequently replaced in situ copies of genes resulting in clusters that have similar content but very different evolutionary histories. CONCLUSIONS: Our model for cluster formation in prokaryotes, therefore, consists of a two-stage selection process. The first stage is selection to move genes closer together, either because of macromolecular crowding, chromatin relaxation or transcriptional regulation pressure. This proximity opportunity sets up a separate selection for co-transcription.

• Trees from trees: construction of phylogenetic supertrees using clann.

  Authors: Christopher J Creevey, James O McInerney

  Methods in molecular biology (Clifton, N.J.). 537:139-61.

  Supertree methods combine multiple phylogenetic trees to produce the overall best "supertree." They can be used to combine phylogenetic information from datasets only partially overlapping and fromSupertree methods combine multiple phylogenetic trees to produce the overall best "supertree." They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down problems thought to be computationally intractable. Some of the longest standing phylogenetic conundrums are now being brought to light using supertree approaches. We describe the most widely used supertree methods implemented in the software program "clann" and provide a step by step tutorial for investigating phylogenetic information and reconstructing the best supertree. Clann is freely available for Windows, Mac and Unix/Linux operating systems under the GNU public licence at http://bioinf.nuim.ie/software/clann .

• The tree of genomes: An empirical comparison of genome phylogeny reconstruction methods.

  Authors: Angela McCann, James Cotton, James McInerney

  BMC evolutionary biology. 8(1):312.

  ABSTRACT: BACKGROUND: In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completedABSTRACT: BACKGROUND: In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present. RESULTS: We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods. CONCLUSIONS: We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.

• The prokaryotic tree of life: past, present... and future?

  Authors: James O McInerney, James A Cotton, Davide Pisani

  Trends in ecology & evolution (Personal edition). 23(5):276-81.

  No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data wereNo accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.

  Download

• Genetics. Paradigm for life.

  Authors: James O McInerney, Davide Pisani

  Science (New York, N.Y.). 318(5855):1390-1.

• Supertrees disentangle the chimerical origin of eukaryotic genomes.

  Authors: Davide Pisani, James A Cotton, James O McInerney

  Molecular biology and evolution. 24(8):1752-60.

  Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes ofEukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.

• MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

  Authors: Thomas M Keane, Thomas J Naughton, James O McInerney

  Nucleic acids research. 35(Web Server issue):W33-7.

  With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. MaximumWith the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods. However, it can still take a long time to analyse the evolutionary history of many gene families using a single computer. Distributed computing refers to a method of combining the computing power of multiple computers in order to perform some larger overall calculation. In this article, we present the first high-throughput implementation of a distributed phylogenetics platform, MultiPhyl, capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching and bootstrapping of each of the alignments using many desktop machines. The program implements a set of 88 amino acid models and 56 nucleotide maximum likelihood models and a variety of statistical methods for choosing between alternative models. A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php.

• TOPD/FMTS: a new software to compare phylogenetic trees.

  Authors: Pere Puigbò, Santiago Garcia-Vallvé, James O McInerney

  Bioinformatics (Oxford, England). 23(12):1556-8.

  SUMMARY: TOPD/FMTS has been developed to evaluate similarities and differences between phylogenetic trees. The software implements several new algorithms (including the Disagree method that returnsSUMMARY: TOPD/FMTS has been developed to evaluate similarities and differences between phylogenetic trees. The software implements several new algorithms (including the Disagree method that returns the taxa, that disagree between two trees and the Nodal method that compares two trees using nodal information) and several previously described methods (such as the Partition method, Triplets or Quartets) to compare phylogenetic trees. One of the novelties of this software is that the FMTS (From Multiple to Single) program allows the comparison of trees that contain both orthologs and paralogs. Each option is also complemented with a randomization analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation. AVAILABILITY: The Perl source code of TOPD/FMTS is available at http://genomes.urv.es/topd.

• Of clades and clans: terms for phylogenetic relationships in unrooted trees.

  Authors: Mark Wilkinson, James O McInerney, Robert P Hirt, Peter G Foster, T Martin Embley

  Trends in ecology & evolution (Personal edition). 22(3):114-5.