Daniel E. L. Promislow

Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster.

ABSTRACT Drosophila melanogaster is one of the most widely used model systems in biology. However, little is known about its associated bacterial community. As a first step towards understanding these communities, we compared bacterial 16S rRNA gene sequence libraries recovered from 11 natural populations of adult D. melanogaster. Bacteria from these sequence libraries were grouped into 74 distinct taxa, spanning the phyla Proteobacteria, Bacteroidetes, and Firmicutes, which were unevenly spread across host populations. Summed across populations, the distribution of abundance of genera was closely fit by a power law. We observed differences among host population locations both in bacterial community richness and in composition. Despite this significant spatial variation, no relationship was observed between species richness and a variety of abiotic factors, such as temperature and latitude. Overall, bacterial communities associated with adult D. melanogaster hosts are diverse and differ across host populations.

Quantitative evidence for conserved longevity pathways between divergent eukaryotic species

Studies in invertebrate model organisms have been a driving force in aging research, leading to the identification of many genes that influence life span. Few of these genes have been examined in the context of mammalian aging, however, and it remains an open question as to whether and to what extent the pathways that modulate longevity are conserved across different eukaryotic species. Using a comparative functional genomics approach, we have performed the first quantitative analysis of the degree to which longevity genes are conserved between two highly divergent eukaryotic species, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Here, we report the replicative life span phenotypes for single-gene deletions of the yeast orthologs of worm aging genes. We find that 15% of these yeast deletions are long-lived. In contrast, only 3.4% of a random set of deletion mutants are long-lived-a statistically significant difference. These data suggest that genes that modulate aging have been conserved not only in sequence, but also in function, over a billion years of evolution. Among the longevity determining ortholog pairs, we note a substantial enrichment for genes involved in an evolutionarily conserved pathway linking nutrient sensing and protein translation. In addition, we have identified several conserved aging genes that may represent novel longevity pathways. Together, these findings indicate that the genetic component of life span determination is significantly conserved between divergent eukaryotic species, and suggest pathways that are likely to play a similar role in mammalian aging.

Testing an 'aging gene' in long-lived Drosophila strains: increased longevity depends on sex and genetic background

Molecular advances of the past decade have led to the discovery of a myriad of ‘aging genes’ (methuselah, Indy, InR, Chico, superoxide dismutase) that extend Drosophila lifespan by up to 85%. Despite this life extension, these mutants are no longer lived than at least some recently wild‐ caught strains. Typically, long‐lived mutants are identified in relatively short‐lived genetic backgrounds, and their effects are rarely tested in genetic backgrounds other than the one in which they were isolated or derived. However, the mutants high‐longevity phenotype may be dependent on interactions with alleles that are common in short‐lived laboratory strains. Here we set out to determine whether one particular mutant could extend lifespan in long‐lived genetic backgrounds in the fruit fly, Drosophila melanogaster. We measured longevity and resistance to thermal stress in flies that were transgenically altered to overexpress human superoxide dismutase (SOD) in the motorneurones in each of 10 genotypes. Each genotype carried the genetic background from a different naturally long‐lived wild‐caught Drosophila strain. While SOD increased lifespan on average, the effect was genotype‐ and sex‐specific. Our results indicate that naturally segregating genes interact epistatically with the aging gene superoxide dismutase to modify its ability to extend longevity. This study points to the need to identify mutants that increase longevity not only in the lab strain of origin but also in naturally long‐lived genetic backgrounds.

Mate choice, sexual conflict, and evolution of senescence.

Sex-related differences in longevity are common throughout the animal kingdom. Previous studies have suggested that at least part of these differences may be due to sex-specific costs of reproduction. Recently, workers have recognized that sexual conflicts of interest between males and females may play a significant role in the evolution of sexually dimorphic traits. Here I explore the possibility that sexual conflict may explain sex-specific differences in longevity and may act as a driving force in the evolution of senescence. I present comparative evidence for this hypothesis and discuss the potential relevance of sexual conflict theory to the search for specific genes that influence longevity. One implication of a sexual conflict theory of aging is that genes that influence senescence, and in particular those that affect sex differences in aging, may evolve very rapidly and so be difficult to detect.

Protein networks, pleiotropy and the evolution of senescence.

The number of interactions, or connectivity, among proteins in the yeast protein interaction network follows a power law. I compare patterns of connectivity for subsets of yeast proteins associated with senescence and with five other traits. I find that proteins associated with ageing have significantly higher connectivity than expected by chance, a pattern not seen for most other datasets. The pattern holds even when controlling for other factors also associated with connectivity, such as localization of protein expression within the cell. I suggest that these observations are consistent with the antagonistic pleiotropy theory for the evolution of senescence. In further support of this argument, I find that a proteins connectivity is positively correlated with the number of traits it influences or its degree of pleiotropy, and further show that the average degree of pleiotropy is greatest for proteins associated with senescence. I explain these results with a simple mathematical model combining assumptions of the antagonistic pleiotropy theory for the evolution of senescence with data on network topology. These findings integrate molecular and evolutionary models of senescence, and should aid in the search for new ageing genes.

THE ROLE OF PARENTAL AGE EFFECTS ON THE EVOLUTION OF AGING

Abstract Any studies have found that older parents have shorter‐lived offspring. However, the evolutionary significance of these findings is poorly understood. We carried out large‐scale demographic experiments to examine the direct effect of maternal age and paternal age on offspring aging in inbred and outbred strains of the fruit fly Drosophila melanogaster. We found that the age of mothers and, to a lesser extent, the age of fathers can have a large influence on both offspring longevity and the shape of the age‐specific mortality trajectory. In two independent experiments we found that older mothers generally produced shorter‐lived offspring, although the exact effect of maternal age on offspring longevity differed among strains. These results suggest that maternal age effects on progeny aging may influence the evolution of aging.

PHYLOGENETIC PERSPECTIVES IN THE EVOLUTION OF PARENTAL CARE IN RAY-FINNED FISHES

Abstract Among major vertebrate groups, ray‐finned fishes (Actinopterygii) collectively display a nearly unrivaled diversity of parental care activities. This fact, coupled with a growing body of phylogenetic data for Actinopterygii, makes these fishes a logical model system for analyzing the evolutionary histories of alternative parental care modes and associated reproductive behaviors. From an extensive literature review, we constructed a supertree for ray‐finned fishes and used its phylogenetic topology to investigate the evolution of several key reproductive states including type of parental care (maternal, paternal, or biparental), internal versus external fertilization, internal versus external gestation, nest construction behavior, and presence versus absence of sexual dichromatism (as an indicator of sexual selection). Using a comparative phylogenetic approach, we critically evaluate several hypotheses regarding evolutionary pathways toward parental care. Results from maximum parsimony reconstructions indicate that all forms of parental care, including paternal, biparental, and maternal (both external and internal to the female reproductive tract) have arisen repeatedly and independently during ray‐finned fish evolution. The most common evolutionary transitions were from external fertilization directly to paternal care and from external fertilization to maternal care via the intermediate step of internal fertilization. We also used maximum likelihood phylogenetic methods to test for statistical correlations and contingencies in the evolution of pairs of reproductive traits. Sexual dichromatism and nest construction proved to be positively correlated with the evolution of male parental care in species with external fertilization. Sexual dichromatism was also positively correlated with female‐internal fertilization and gestation. No clear indication emerged that female‐only care or biparental care were evolutionary outgrowths of male‐only care, or that biparental care has been a common evolutionary stepping stone between paternal and maternal care. Results are discussed in the context of prior thought about the evolution of alternative parental care modes in vertebrates.

Mutation and senescence: where genetics and demography meet

Two evolutionary genetic models–mutation accumulation and antagonistic pleiotropy–have been proposed to explain the origin and maintenance of senescence. In this paper, we focus our attention on the mutation accumulation model. We re-examine previous evidence for mutation accumulation in light of new information from large-scale demographic experiments. After discussing evidence for the predictions that have been put forth from models of mutation accumulation, we discuss two critical issues at length. First, we discuss the possibility that classical fruit fly stock maintenance regimes may give rise to spurious results in selection studies of aging. Second, we consider evidence for the assumptions underlying evolutionary models of aging. These models assume that mutations act additively on age-specific survival rate, that there exist mutations whose effects are confined to late age-classes, and that all mutations have equal effects. Recent empirical evidence suggests that each of these three assumptions is unlikely to be true. On the basis of these results, we do not conclude that mutation accumulation is no longer a valid explanation for the evolution of aging. Rather, we suggest that we now need to begin developing more biologically realistic genetic models for the evolution of aging.

Functional and evolutionary inference in gene networks: does topology matter?

The relationship between the topology of a biological network and its functional or evolutionary properties has attracted much recent interest. It has been suggested that most, if not all, biological networks are ‘scale free.’ That is, their connections follow power-law distributions, such that there are very few nodes with very many connections and vice versa. The number of target genes of known transcriptional regulators in the yeast, Saccharomyces cerevisiae, appears to follow such a distribution, as do other networks, such as the yeast network of protein–protein interactions. These findings have inspired attempts to draw biological inferences from general properties associated with scale-free network topology. One often cited general property is that, when compromised, highly connected nodes will tend to have a larger effect on network function than sparsely connected nodes. For example, more highly connected proteins are more likely to be lethal when knocked out. However, the correlation between lethality and connectivity is relatively weak, and some highly connected proteins can be removed without noticeable phenotypic effect. Similarly, network topology only weakly predicts the response of gene expression to environmental perturbations. Evolutionary simulations of gene-regulatory networks, presented here, suggest that such weak or non-existent correlations are to be expected, and are likely not due to inadequacy of experimental data. We argue that ‘top-down’ inferences of biological properties based on simple measures of network topology are of limited utility, and we present simulation results suggesting that much more detailed information about a gene’s location in a regulatory network, as well as dynamic gene-expression data, are needed to make more meaningful functional and evolutionary predictions. Specifically, we find in our simulations that: (1) the relationship between a gene’s connectivity and its fitness effect upon knockout depends on its equilibrium expression level; (2) correlation between connectivity and genetic variation is virtually non-existent, yet upon independent evolution of networks with identical topologies, some nodes exhibit consistently low or high polymorphism; and (3) certain genes show low polymorphism yet high divergence among independent evolutionary runs. This latter pattern is generally taken as a signature of positive selection, but in our simulations its cause is often neutral coevolution of regulatory inputs to the same gene.

The functional costs and benefits of dietary restriction in Drosophila

Dietary restriction (DR) extends lifespan in an impressively wide array of species spanning three eukaryotic kingdoms. In sharp contrast, relatively little is known about the effects of DR on functional senescence, with most of the work having been done on mice and rats. Here we used Drosophila melanogaster to test the assumption that lifespan extension through DR slows down age‐related functional deterioration. Adult virgin females were kept on one of three diets, with sucrose and yeast concentrations ranging from 7% to 11% to 16% (w/v). Besides age‐specific survival and fecundity, we measured starvation resistance, oxidative stress resistance, immunity, and cold‐stress resilience at ages 1, 3, 5, and 7 weeks. We confirmed that DR extends lifespan: median lifespans ranged from 38 days (16% diet) to 46 days (11% diet) to 54 days (7% diet). We also confirmed that DR reduces fecundity, although the shortest‐lived flies only had the highest fecundity when males were infrequently available. The most striking result was that DR initially increased starvation resistance, but strongly decreased starvation resistance later in life. Generally, the effects of DR varied across traits and were age dependent. We conclude that DR does not universally slow down functional deterioration in Drosophila. The effects of DR on physiological function might not be as evolutionarily conserved as its effect on lifespan. Given the age‐specific effects of DR on functional state, imposing DR late in life might not provide the same functional benefits as when applied at early ages.