175 research outputs found
Online Data Supplement: Longevity is linked to mitochondrial mutation rates in rockfish: a test using Poisson regression
No full text<p>This is the online supplement for:</p>
<p>Xia Hua, Peter Cowman, Dan Warren, and Lindell Bromham</p>
<p><em>Longevity is linked to mitochondrial mutation rates in rockfish: a test using Poisson regression.</em> Mol Biol Evol first published online June 5, 2015 doi:10.1093/molbev/msv137</p>
<p> </p>
<p>It contains scripts, files and alignments assoicated with the paper to reproduce the branch length estimation analyses</p
PlantRateEstimation
No full textThis online data supplement contains the assoicated data and replicatable analyses to estimate branch rates for sister-pair analyses from the paper "Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants" Bromham, Lindell, Hua, Xia, Lanfear, Robert, Cowman, Peter F
Sociality and the rate of molecular evolution
No full textCopyright © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of "nearly neutral" mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs, and nontranslated sequences). By including a wide range of social taxa, we were able to test whether there is a general influence of sociality on rates of molecular evolution and to test specific predictions of the hypothesis: (1) that social species have faster rates because they have reduced effective population sizes; (2) that mitochondrial genes would show a greater effect of sociality than nuclear genes; and (3) that rates of molecular evolution should be correlated with the degree of sociality. We find no consistent pattern in rates of molecular evolution between social and nonsocial lineages and no evidence that mitochondrial genes show faster rates in social taxa. However, we show that the most highly eusocial Hymenoptera do have faster rates than their nonsocial relatives. We also find that social parasites (that utilize the workers from related species to produce their own offspring) have faster rates than their social relatives, which is consistent with an effect of lower effective population size on rate of molecular evolution. Our results illustrate the importance of allowing for phylogenetic nonindependence when conducting investigations of determinants of variation in rate of molecular evolution.Lindell Bromham and Remko Ley
Why do species vary in their rate of molecular evolution?
No full textDespite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses
Comparability in evolutionary biology: The case of Darwin’s barnacles
No full textLanguage change and biological evolution are sufficiently similar that biologists and linguists often face similar challenges in reconstructing paths of historical change connecting different species or languages. Tracing evolutionary change over time requires us to consider how shared features have been modified in different lineages since they shared a common ancestor, and this means we have to be able to establish meaningful comparability between traits. In some cases, we may wish to understand how the same ancestral trait has been modified in each lineage in response to different pressures. But in other cases, we may wish to ask whether particular traits often arise in response to certain circumstances. Biologists must therefore consider different reasons for similarities between species, and choose to compare those traits that are relevant to the story they want to tell. To reconstruct histories of change, we need to compare homologous traits (those similar due to shared ancestry). But comparing analogous traits (independently derived but similar traits) highlights how separate evolutionary lineages can find similar solutions to common problems. I will illustrate the importance of comparability in constructing evolutionary explanations using one of the more obscure yet fascinating examples of Charles Darwin's scientific researches, his multi-volume taxonomic treatise on barnacles. Darwin faced the challenge of how to explain the evolutionary trajectory of unique and highly modified traits that appear to have no equivalents in related taxa. He did this by tracing the development of unique traits within growing individuals, looking for variation in these strange adaptations between individuals, and comparing them across species that varied in their degree of modification from their ancestor. Using meticulous observations to establish comparability, even in such an incomparable animal as the barnacle, he could reconstruct plausible evolutionary explanations for even the most bizarrely modified traits, such as the presence of parasitic males and the invention of the cement that sticks barnacles to rocks, boats and whales. Nowadays, scientists increasingly rely on DNA evidence to trace evolutionary paths, which brings both advantages and challenges in establishing comparability. Even if you, like most people, are not particularly interested in barnacles, Darwin's underappreciated taxonomic work is a surprisingly good place to go to if you want to think about the issue of comparability and why it matters to understanding evolution
Online Data Supplement: Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants
No full text<p>This online data supplement contains the assoicated data and replicatable analyses to estimate branch rates for sister-pair analyses from the paper "Exploring the relationships between mutation rates, life history, genome size, environment and species richness in flowering plants" American Naturalist, by Bromham L, Hua X, Cowman PF, Lanfear R</p>
<p> </p
Molecular clocks in reptiles: Life history influences rate of molecular evolution
No full textLife history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between bode size and substitution rate for many Molecular data sets. Both the generality and the cause of the negative bode size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles. lizards. snakes, crocodile, and tuatara. Although this Study was limited by the number of comparisons for which both sequence and lite-history data were available, the results, suggest that a negative bode size trend in rate of molecular evloution may be a general feature of reptile molecular evolution. consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences
The human zoo: Endogenous retroviruses in the human genome
No full textThe main focus of the human genome sequencing project has been gene discovery, but a great additional benefit is that it offers the chance to examine the large proportion of the genome that does not contain human genes. The nature of this ‘noncoding’ DNA is poorly understood, both as an evolutionary question (how did it get there?) and in the functional sense (what is it doing now?). Much of the noncoding DNA is derived from retroviruses that have inserted their DNA into the genome. The availability of complete genomic sequences will revolutionize studies of the number and location of endogenous retroviruses, their role in genome evolution, and their contribution to human disease
Substitution Rate Analysis and Molecular Evolution
No full textThe study of the tempo and mode of molecular evolution has played a key role in evolutionary biology, both as a stimulant for theoretical enrichment and as the foundation of useful analytical
tools. When protein and DNA sequences were first produced, the surprising constancy of rates of change brought molecular evolution into conflict with mainstream evolutionary biology,
but also stimulated the formation of new theoretical understanding of the processes of genetic change, including the recognition of the role of neutral mutations and genetic drift in genomic evolution. As more data were collected, it became clear that there were systematic differences in the substitution rate between species, which prompted further elaboration of ideas such as the generation time effect and the nearly neutral theory. Comparing substitution rates between species continues to provide a window on fundamental evolutionary processes. However, investigating patterns of substitution rates requires attention to potential complicating factors such as the phylogenetic non-independence of rates estimates and the time-dependence of measurement error. This chapter compares different analytical approaches to study the tempo and mode
of molecular evolution, and considers the way a richer biological understanding of the causes of variation in substitution rate might inform our attempts to use molecular data to uncover
evolutionary history
Wandering drunks and general lawlessness in biology: does diversity and complexity tend to increase in evolutionary systems?
No full text- …
