Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level

We tested the metabolic rate hypothesis (whereby rates of mtDNA evolution are postulated to be mediated primarily by mutagenic by-products of respiration) by examining whether mass-specific metabolic rate was correlated with root-to-tip distance on a set of mtDNA trees for the springtail Cryptopygus antarcticus travei from sub-Antarctic Marion Island

Novel Distances for Dollo Data

We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), which is consistent for data generated under a Dollo model, and show that it has some useful theoretical properties including an intriguing link to the LogDet distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, Nei Li and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process, which may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology (DArT) datasets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyse gene family presence/absence data on bacteria from the COG database and compare the results to previous phylogenies estimated using the conditioned genome reconstruction approach

Modelling gene content across a phylogeny to determine when genes become associated

In this work, we develop a stochastic model of gene gain and loss with the aim of inferring when (if at all) in evolutionary history and association between two genes arises. The data we consider is a species tree along with information on the presence or absence of two genes in each of the species. The biological motivation for our model is that if two genes are involved in the same biochemical pathway, i.e. they are both required for some function, then the rate of gain or loss of one gene in the pathway should depend upon the presence or absence of the other gene in the pathway. However, if the two genes are not functionally linked, then the rate of gain or loss of one gene should be independent of the state of another gene. We simulate data under this model to determine under what conditions a shift from the independent rates class to the dependent rates class can be detected. For example, how large a tree is required and how large a shift in the rates is needed before Akaike information criterion (AIC) supports a model with two rate classes over a simpler model with just one rate class? If a model with two rate classes is preferred, can it correctly detect where on the evolutionary tree the shift occurred?Comment: The Eleventh International Conference on Matrix-Analytic Methods in Stochastic Models (MAM11), 2022, Seoul, Republic of Kore

Maximum likelihood estimates of pairwise rearrangement distances

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog

The Emergence of Predators in Early Life: There was No Garden of Eden

BACKGROUND: Eukaryote cells are suggested to arise somewhere between 0.85~2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85~2.7 billion years ago, leads to an unexpected prediction of a long period (approximately 1-3 billion years) with no phagocytotes -- a veritable Garden of Eden. METHODOLOGY: We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms -- given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators. CONCLUSIONS: Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been 'prokaryotes', but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features

Stochastic niche-based models for the evolution of species

There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the phylogenetic comparative method some authors have argued that it is necessary to have a biologically realistic model to generate evolutionary trees that incorporates information about the ecological niche occupied by species. Price presented a simple model along these lines in 1997. He defined a two-dimensional niche space formed by two continuous-valued traits, in which new niches arise with trait values drawn from a bivariate normal distribution. When a new niche arises, it is occupied by a descendant species of whichever current species is closest in ecological niche space. In sequence, more species are then evolved from already-existing species to which they are ecologically closest. Here we explore ways of extending Price's adaptive radiation model. One extension is to increase the dimensionality of the niche space by considering more than two continuous traits. A second extension is to allow both extinction of species (which may leave unoccupied niches) and removal of niches (which causes species occupying them to go extinct). To model this problem, we consider a continuous-time stochastic process which implicitly defines a phylogeny. To explore if trees generated under such a model (or under different parametrizations of the model) are realistic we can compute a variety of summary statistics that can be compared to those of empirically observed phylogenies. For example, there are existing statistics that aim to measure: tree balance, the relative rate of diversification, and phylogenetic signal of traits.Comment: The Eleventh International Conference on Matrix-Analytic Methods in Stochastic Models (MAM11), 2022, Seoul, Republic of Kore