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Lindell Bromham

Publications and source records attributed to Lindell Bromham.

13 recordsLinked to original sources
PubMed2006

There is no universal molecular clock for invertebrates, but rate variation does not scale with body size.

The existence of a universal molecular clock has been called into question by observations that substitution rates vary widely between lineages. However, increasing empirical evidence for the systematic effects of different life history traits on the rate of molecular evolution has raised hopes that rate variation may be predictable, potentially allowing the "correction" of the molecular clock. One such example is the body size trend observed in vertebrates; smaller species tend to have faster rates of molecular evolution. This effect has led to the proposal of general predictive models correcting for rate heterogeneity and has also been invoked to explain discrepancies between molecular and paleontological dates for explosive radiations in the fossil record. Yet, there have been no tests of an effect in any nonvertebrate taxa. In this study, we have tested the generality of the body size effect by surveying a wide range of invertebrate metazoan lineages. DNA sequences and body size data were collected from the literature for 330 species across five phyla. Phylogenetic comparative methods were used to investigate a relationship between average body size and substitution rate at both interspecies and interfamily comparison levels. We demonstrate significant rate variation in all phyla and most genes examined, implying a strict molecular clock cannot be assumed for the Metazoa. Furthermore, we find no evidence of any influence of body size on invertebrate substitution rates. We conclude that the vertebrate body size effect is a special case, which cannot be simply extrapolated to the rest of the animal kingdom.

Animals↗
PubMed2005

Population size and molecular evolution on islands.

The nearly neutral theory predicts that the rate and pattern of molecular evolution will be influenced by effective population size (Ne), because in small populations more slightly deleterious mutations are expected to drift to fixation. This important prediction has not been widely empirically tested, largely because of the difficulty of comparing rates of molecular evolution in sufficient numbers of independent lineages which differ only in Ne. Island endemic species provide an ideal test of the effect of Ne on molecular evolution because species restricted to islands frequently have smaller Ne than closely related mainland species, and island endemics have arisen from mainland lineages many times in a wide range of taxa. We collated a dataset of 70 phylogenetically independent comparisons between island and mainland taxa, including vertebrates, invertebrates and plants, from 19 different island groups. The rate of molecular evolution in these lineages was estimated by maximum likelihood using two measures: overall substitution rate and the ratio of non-synonymous to synonymous substitution rates. We show that island lineages have significantly higher ratios of non-synonymous to synonymous substitution rates than mainland lineages, as predicted by the nearly neutral theory, although overall substitution rates do not differ significantly.

Base Sequence↗
PubMed2005

Nervous and muscle system development in Phascolion strombus (Sipuncula).

Recent interpretations of developmental gene expression patterns propose that the last common metazoan ancestor was segmented, although most animal phyla show no obvious signs of segmentation. Developmental studies of non-model system trochozoan taxa may shed light on this hypothesis by assessing possible cryptic segmentation patterns. In this paper, we present the first immunocytochemical data on the ontogeny of the nervous system and the musculature in the sipunculan Phascolion strombus. Myogenesis of the first anlagen of the body wall ring muscles occurs synchronously and not subsequently from anterior to posterior as in segmented spiralian taxa (i.e. annelids). The number of ring muscles remains constant during the initial stages of body axis elongation. In the anterior-posteriorly elongated larva, newly formed ring muscles originate along the entire body axis between existing myocytes, indicating that repeated muscle bands do not form from a posterior growth zone. During neurogenesis, the Phascolion larva expresses a non-metameric, paired, ventral nerve cord that fuses in the mid-body region in the late-stage elongated larva. Contrary to other trochozoans, Phascolion lacks any larval serotonergic structures. However, two to three FMRFamide-positive cells are found in the apical organ. In addition, late larvae show commissure-like neurones interconnecting the two ventral nerve cords, while early juveniles exhibit a third, medially placed FMRFamidergic ventral nerve. Although we did not find any indications for cryptic segmentation, certain neuro-developmental traits in Phascolion resemble the conditions found in polychaetes (including echiurans) and myzostomids and support a close relationship of Sipuncula and Annelida.

Animals↗
PubMed2005

Sociality and the rate of molecular evolution.

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.

Animals↗
PubMed2005

Molecular dating when rates vary.

Molecular-dating techniques potentially enable us to estimate the time of origin of any biological lineage. Such techniques were originally premised on the assumption of a 'molecular clock'; that is, the assumption that genetic change accumulated steadily over time. However, it is becoming increasingly clear that constant rates of molecular evolution might be the exception rather than the rule. Recently, new methods have appeared that enable the incorporation of variable rates into molecular dating. Direct comparisons between these methods are difficult, because they differ in so many respects. However, the assumptions about rate change on which they rely fall into a few broad categories. Improving our understanding of molecular evolution will be an important next step towards evaluating and improving these methods.

Journal Article↗
PubMed2004

Explosive radiations and the reliability of molecular clocks: island endemic radiations as a test case.

The reliability of molecular clocks has been questioned for several key evolutionary radiations on the basis that the clock might run fast in explosive radiations. Molecular date estimates for the radiations of metazoan phyla (the Cambrian explosion) and modern orders of mammals and birds are in many cases twice as old as the palaeontological evidence would suggest. Could some aspect of explosive radiations speed the molecular clock, making molecular date estimates too old? Here we use 19 independent instances of recent explosive radiations of island endemic taxa as a model system for testing the proposed influence of rapid adaptive radiation on the rate of molecular evolution. These radiations are often characterized by many of the potential mechanisms for fast rates in explosive radiations--such as small population size, elevated speciation rate, rapid rate of morphological change, release from previous ecological constraints, and adaptation to new niches--and represent a wide variety of species, islands, and genes. However, we find no evidence of a consistent increase in rates in island taxa compared to their mainland relatives, and therefore find no support for the hypothesis that the molecular clock runs fast in explosive radiations.

Adaptation, Biological↗
PubMed2004

Selection pressure-driven evolution of the Epstein-Barr virus-encoded oncogene LMP1 in virus isolates from Southeast Asia.

The geographically constrained distribution of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in southeast Asian populations suggests that both viral and host genetics may influence disease risk. Although susceptibility loci have been mapped within the human genome, the role of viral genetics in the focal distribution of NPC remains an enigma. Here we report a molecular phylogenetic analysis of an NPC-associated viral oncogene, LMP1, in a large panel of EBV isolates from southeast Asia and from Papua New Guinea, Africa, and Australia, regions of the world where NPC is and is not endemic, respectively. This analysis revealed that LMP1 sequences show a distinct geographic structure, indicating that the southeast Asian isolates have evolved as a lineage distinct from those of Papua New Guinea, African, and Australian isolates. Furthermore, a likelihood ratio test revealed that the C termini of the LMP1 sequences of the southeast Asian lineage are under significant positive selection pressure, particularly at some sites within the C-terminal activator regions. We also present evidence that although the N terminus and transmembrane region of LMP1 have undergone recombination, the C-terminal region of the gene has evolved without any history of recombination. Based on these observations, we speculate that selection pressure may be driving the LMP1 sequences in virus isolates from southeast Asia towards a more malignant phenotype, thereby influencing the endemic distribution of NPC in this region.

Amino Acid Sequence↗
PubMed2003

Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes.

Mutualistic, maternally transmitted endosymbiotic microorganisms undergo severe population bottlenecks at each host generation, resulting in a reduction in effective population size (Ne). Previous studies of Buchnera, the primary endosymbiont of aphids, and of several other species of endosymbiotic bacteria have shown that these species exhibit an increase in the rate of substitution of slightly deleterious mutations, among other predicted effects of increased drift due to small Ne, such as reduced codon bias. However, these studies have been limited in taxonomic scope, and it was therefore not clear whether the increase in rate is a general feature of endosymbiont lineages. Here, we test the prediction that a long-term reduction in Ne causes an increase in substitution rate using DNA sequences of the 16S rRNA gene from 13 phylogenetically independent comparisons between taxonomically diverse endosymbiotic microorganisms and their free-living relatives. Maximum likelihood and distance-based methods both indicate a significant increase in substitution rate in a wide range of bacterial and fungal endosymbionts compared to closely related free-living lineages. We use the same data set to test whether 16S genes from endosymbionts display increased A + T content, another indicator of increased genetic drift, and find that there is no significant difference in base composition between endosymbiont and nonendosymbiont 16S genes. However, analysis of an additional data set of whole bacterial genomes demonstrates that, while host-dependent bacteria have significantly increased genomic A + T content, the base content of the 16S gene tends to vary less than that of the whole genome. It is possible that selection for stability of rRNA is strong enough to overcome the effects of drift toward increased A + T content in endosymbiont 16S genes, despite the reduced effective population sizes of these organisms.

Animals↗
PubMed2003

Molecular clocks and explosive radiations.

Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--using available empirical evidence on patterns of variation in rate of molecular evolution.

Animals↗
PubMed2003

The modern molecular clock.

The discovery of the molecular clock--a relatively constant rate of molecular evolution--provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explained by assuming that most changes to genes are effectively neutral. Theory predicts several sources of variation in the rate of molecular evolution. However, even an approximate clock allows time estimates of events in evolutionary history, which provides a method for testing a wide range of biological hypotheses ranging from the origins of the animal kingdom to the emergence of new viral epidemics.

Animals↗
PubMed2002

Molecular clocks in reptiles: life history influences rate of molecular evolution.

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between body size and substitution rate for many molecular data sets. Both the generality and the cause of the negative body 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 life-history data were available, the results suggest that a negative body size trend in rate of molecular evolution 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.

Aging↗
PubMed2002

Testing the relationship between morphological and molecular rates of change along phylogenies.

Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for "total-evidence" phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.

Animals↗