arXiv subjects

Paul G. Higgs

Publications and source records attributed to Paul G. Higgs.

10 recordsLinked to original sources

arXiv2018

Constraining the Time Interval for the Origin of Life on Earth

Estimates of the time at which life arose on Earth make use of two types of evidence. First, astrophysical and geophysical studies provide a timescale for the formation of Earth and the Moon, for large impact events on early Earth, and for the cooling of the early magma ocean. From this evidence, we can deduce a habitability boundary, which is the earliest point at which Earth became habitable. Second, biosignatures in geological samples, including microfossils, stromatolites, and chemical isotope ratios, provide evidence for when life was actually present. From these observations we can deduce a biosignature boundary, which is the earliest point at which there is clear evidence that life existed. Studies with molecular phylogenetics and records of the changing level of oxygen in the atmosphere give additional information that helps to determine the biosignature boundary. Here, we review the data from a wide range of disciplines to summarize current information on the timings of these two boundaries. The habitability boundary could be as early as 4.5 Ga, the earliest possible estimate of the time at which Earth had a stable crust and hydrosphere, or as late as 3.9 Ga, the end of the period of heavy meteorite bombardment. The lack of consensus on whether there was a late heavy meteorite bombardment that was significant enough to prevent life is the largest uncertainty in estimating the time of the habitability boundary. The biosignature boundary is more closely constrained. Evidence from carbon isotope ratios and stromatolite fossils both point to a time close to 3.7 Ga. Life must have emerged in the interval between these two boundaries. The time taken for life to appear could, therefore, be within 200 Myr or as long as 800 Myr.

astro-ph.EP↗

arXiv2009

A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code

Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

astro-ph.EP↗

arXiv2007

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.

q-bio.PE↗

arXiv2005

The response of amino acid frequencies to directional mutation pressure in mitochondrial genome sequences is related to the physical properties of the amino acids and to the structure of the genetic code

The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd positions, selection reduces the degree of frequency variation. Using a simple evolutionary model, we show that 1st position sites are less constrained by selection than 2nd position sites, and therefore that the frequencies of bases at 1st position are more responsive to mutation pressure than those at 2nd position. We define a similarity measure between amino acids that is a function of 8 measured physical properties. We define a proximity measure for each amino acid, which is the average similarity between an amino acid and all others that are accessible via single point mutations in the genetic code. We also define a responsiveness for each amino acid, which measures how rapidly an amino acid frequency changes as a result of mutation pressure acting on the base frequencies. There is a strong correlation between responsiveness and proximity, and both these quantities are also correlated with the mutability of amino acids estimated from the mtREV substitution rate matrix. We also consider the variation of base frequencies between strands and between genes on a strand. These trends are consistent with the patterns expected from analysis of the variation among genomes

q-bio.PE↗

arXiv2005

A Unified Model of Codon Reassignment in Alternative Genetic Codes

Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment, based on the observation that reassignment involves a gain and a loss. The loss could be the deletion or loss of function of a tRNA or release factor. The gain could be the gain of a new type of tRNA for the reassigned codon, or the gain of function of an existing tRNA due to a mutation or a base modification. In the codon disappearance mechanism, the codon disappears from the genome during the period of reassignment. In the other mechanisms, the codon does not disappear. In the ambiguous intermediate mechanism, the gain precedes the loss; in the unassigned codon mechanism, the loss precedes the gain; and in the compensatory change mechanism, the loss and gain spread through the population simultaneously. We present simulations of the gain-loss model and demonstrate that all four mechanisms are possible. The frequencies of the different mechanisms are influenced by selection strengths, number of codons undergoing reassignment, directional mutation pressure and the possibility of selection for reduced genome size.

q-bio.PE↗

arXiv2004

Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications for the Frequency of Horizontal Gene Transfer

The current picture of bacterial evolution is based largely on studies of 16S rRNA. However, this is just one gene. It is known that horizontal gene transfer can occur between bacterial species, although the frequency and implications of this are not fully understood. If horizontal transfer were frequent, there would be no single evolutionary tree for bacteria because each gene would follow a different tree. We carried out phylogenetic analyses of rRNA and tRNA genes from Proteobacteria (a diverse group for which many complete genome sequences are available) using RNA-specific phylogenetic methods that account for the conservation of the secondary structure. We compared trees for 16S rRNA and 23S rRNA with those derived from concatenated alignments of 29 tRNA genes that are found in all the genomes studied. The tRNA genes are scattered throughout the genomes, and would not follow the same evolutionary history if horizontal transfer were frequent. Nevertheless, the tRNA tree is consistent with the rRNA tree in most respects. Minor differences can almost all be attributed to uncertainty or unreliability of the phylogenetic method. We therefore conclude that tRNA genes give a coherent picture of the phylogeny of the organisms, and that horizontal transfer of tRNAs is too rare to obscure the signal of the organismal tree. Some tRNA genes are not present in all the genomes. We discuss possible explanations for the observed patterns of presence and absence of genes: these involve gene deletion, gene duplication, and mutations in the tRNA anticodons.

q-bio.PE↗

arXiv2004

RNA-based Phylogenetic Methods: Application to Mammalian Mitochondrial RNA Sequences

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA and rRNA sequences from 69 complete mammalian mitochondrial genomes. The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites. We use Bayesian phylogenetic methods and a Markov chain Monte Carlo algorithm is used to obtain the most probable trees and posterior probabilities of clades. The results are well resolved for almost all the important branches on the mammalian tree. They support the arrangement of mammalian orders within the four supra-ordinal clades that have been identified by studies of much larger data sets mainly comprising nuclear genes. Groups such as the hedgehogs and the murid rodents, which have been problematic in previous studies with mitochondrial proteins, appear in their expected position with the other members of their order. Our choice of genes and evolutionary model appears to be more reliable and less subject to biases caused by variation in base composition than previous studies with mitochondrial genomes.

q-bio.PE↗

arXiv2001

Food Web Structure and the Evolution of Ecological Communities

Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food web. The equations account for competition between species for the same resources, and for the diet choice of predators between alternative prey according to an evolutionarily stable strategy. The set of species present undergoes long-term evolution due to speciation and extinction events. We summarize results obtained on the macro-evolutionary dynamics of speciations and extinctions, and on the statistical properties of the food webs that are generated by the model. Simulations begin from small numbers of species and build up to larger webs with relatively constant species number on average. The rate of origination and extinction of species are relatively high, but remain roughly balanced throughout the simulations. When a `parent' species undergoes speciation, the `child' species usually adds to the same trophic level as the parent. The chance of the child species surviving is significantly higher if the parent is on the second or third trophic level than if it is on the first level, most likely due to a wider choice of possible prey for species on higher levels. Addition of a new species sometimes causes extinction of existing species. The parent species has a high probability of extinction because it has strong competition with the new species. Non-parental competitors of the new species also have a significantly higher extinction probability than average, as do prey of the new species. Predators of the new species are less likely than average to become extinct.

nlin.AO↗

arXiv2000

The Influence of Predator-Prey Population Dynamics on the Long-term Evolution of Food Web Structure

We develop a set of equations to describe the population dynamics of many interacting species in food webs. Predator-prey interactions are non-linear, and are based on ratio-dependent functional responses. The equations account for competition for resources between members of the same species, and between members of different species. Predators divide their total hunting/foraging effort between the available prey species according to an evolutionarily stable strategy (ESS). The ESS foraging behaviour does not correspond to the predictions of optimal foraging theory. We use the population dynamics equations in simulations of the Webworld model of evolving ecosystems. New species are added to an existing food web due to speciation events, whilst species become extinct due to coevolution and competition. We study the dynamics of species-diversity in Webworld on a macro-evolutionary timescale. Coevolutionary interactions are strong enough to cause continuous overturn of species, in contrast to our previous Webworld simulations with simpler population dynamics. Although there are significant fluctuations in species diversity because of speciation and extinction, very large scale extinction avalanches appear to be absent from the dynamics, and we find no evidence for self-organised criticality.

nlin.AO↗

arXiv1998

Modelling coevolution in multispecies communities

We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an evolutionary timescale. Species are defined as sets of characteristic features, and these features are used to determine interaction scores between species. A simple rule is used to transfer resources from the external environment through the food web to each of the species, and to determine mean population sizes. A time step in the model represents a speciation event. A new species is added with features similar to those of one of the existing species and a new food web structure is then calculated. The new species may (i) add stably to the web, (ii) become extinct immediately because it is poorly adapted, or (iii) cause one or more other species to become extinct due to competition for resources. We measure various properties of the model webs and compare these with data on real food webs. These properties include the proportions of basal, intermediate and top species, the number of links per species and the number of trophic levels. We also study the evolutionary dynamics of the model ecosystem by following the fluctuations in the total number of species in the web. Extinction avalanches occur when novel organisms arise which are significantly better adapted than existing ones. We discuss these results in relation to the observed extinction events in the fossil record, and to the theory of self-organized criticality.

adap-org↗