Matthew Spencer

OVIPOSITION HABITAT SELECTION BY MOSQUITOES (CULISETA LONGIAREOLATA) AND CONSEQUENCES FOR POPULATION SIZE

Many kinds of adaptive behavior, including responses to risk of predation, have been documented, but there have been few attempts to translate these behaviors into consequences for populations. We present one of the first models to predict the consequences of adaptive behavior for population size in a specific natural system. Larvae of the mosquito Culiseta longiareolata (Diptera: Culicidae) develop in freshwater pools. They are vulnerable to predation by the backswimmer Notonecta maculata (Hemiptera: Heteroptera), and to intraspecific competition. Adult female C. longiareolata usually avoid ovipositing in pools that contain N. maculata. This is presumably an adaptive response that increases individual fitness, but it is also likely to affect the size of the population. We take a novel approach to understanding the relationship between adaptive behavior and population dynamics in C. longiareolata. We use a nonlinear stage-structured population model to predict the evolutionarily stable oviposition strategy and its consequences for the size of the C. longiareolata population. Our model predicts that female C. longiareolata should always avoid ovipositing in pools with N. maculata. Such avoidance will increase the equilibrium size of the C. longiareolata population, relative to a population in which oviposition is indiscriminate with respect to N. maculata. The qualitative effect on population size is the same even if, as observed, C. longiareolata occasionally oviposit in pools containing N. maculata. These predictions have important practical implications for assessing the effectiveness of predators as biological control agents.

Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments

The integron/gene cassette systems identified in bacteria comprise a class of genetic elements that allow adaptation by acquisition of gene cassettes. Integron gene cassettes have been shown to facilitate the spread of drug resistance in human pathogens but their role outside a clinical setting has not been explored extensively. We sequenced 2145 integron gene cassettes from four marine sediment samples taken from the vicinity of Halifax Nova Scotia, Canada, increasing the number of gene cassettes obtained from environmental microbial communities by 10-fold. Sequence analyses reveals that the majority of these cassettes encode novel proteins and that this study is consistent with previous claims of high cassette diversity as we estimate a Chao1 diversity index of approximately 3000 cassettes from these samples. The functional distribution of environmental cassettes recovered in this study, when compared with that of cassettes from the only other source with significant sampling (Vibrio genomes) suggests that alternate selection regimes might be acting on these two gene pools. The majority of cassettes recovered in this study encode novel, unknown proteins. In instances where we obtained multiple alleles of a novel protein we demonstrate that non-synonymous versus synonymous substitution rates ratios suggest relaxed selection. Cassette-encoded proteins with known homologues represent a variety of functions and prevalent among these are isochorismatases; proteins involved in iron scavenging. Phylogenetic analysis of these isochorismatases as well as of cassette-encoded acetyltransferases reveals a patchy distribution, suggesting multiple sources for the origin of these cassettes. Finally, the two most environmentally similar sample sites considered in this study display the greatest overlap of cassette types, consistent with the hypothesis that cassette genes encode adaptive proteins.

How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence

Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the users input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA.

Community and food-web responses to the manipulation of energy input and disturbance in small ponds

We describe the effects on community and food web structure of an experimental manipulation of energy input and disturbance to a set of sixteen small artificial pools. Two levels of energy input (leaf litter) and disturbance (draining of pools) were established in a factorial design, and pools were inoculated at intervals with samples of invertebrates from a range of local sites. Artificial leaf litter was used to correct for differences in habitat structure caused by the energy manipulations. The experiment ran for 15 months, during which time small, but persistent, communities (8-19 taxa) established in the pools. In general, energy treatments had a greater effect on the communities than disturbance, though all effects were modest. Low energy treatments had slightly more species than high energy systems, this increase being disproportionately due to predators. Abundances and biomasses of some individual species were affected by one or other manipulation, but rarely both, and commonly neither. Some aspects of the structure of binary food webs constructed for each system were apparently affected by energy treatments, although food chains were not longer in higher energy systems. However, given the effect of energy on species number, and the non-independence of species number and various web characteristics, the significance of the effects that were observed is not clear. We briefly discuss some of the problems of methodology and interpretation associated with this and other similar studies.

Selection on stability across ecological scales

Much of the focus in evolutionary biology has been on the adaptive differentiation among organisms. It is equally important to understand the processes that result in similarities of structure among systems. Here, we discuss examples of similarities occurring at different ecological scales, from predator-prey relations (attack rates and handling times) through communities (food-web structures) to ecosystem properties. Selection among systemic configurations or patterns that differ in their intrinsic stability should lead generally to increased representation of relatively stable structures. Such nonadaptive, but selective processes that shape ecological communities offer an enticing mechanism for generating widely observed similarities, and have sparked new interest in stability properties. This nonadaptive systemic selection operates not in opposition to, but in parallel with, adaptive evolution.

HATCHING RESPONSES OF TEMPORARY POOL INVERTEBRATES TO SIGNALS OF ENVIRONMENTAL QUALITY

Many temporary pool invertebrates survive dry periods as diapausing eggs. Theory predicts that the proportion of diapausing eggs that hatch when the pool fills with water should vary with signals of likely reproductive success, if such signals are available. Reproductive success in temporary pool invertebrates is influenced by the presence of predators and desiccation. We studied hatching responses of temporary pool invertebrates to the presence of fire salamanders (Salamandra salamandra L., an important predator in temporary pools), and to manipulations of nutrients. Nutrient manipulations may mimic the increase in conductivity associated with high evaporation and risk of desiccation, but might also affect food availability or modify signals associated with the presence of Salamandra. Fewer eggs of the conchostracan Cyzicus sp. hatched in the presence of Salamandra, and in pools to which nutrients had been added. Other taxa (bdelloid rotifers and chydorids) did not show unambiguous hatching responses to ...

Evaluating length heteroplasmy in the human mitochondrial DNA control region

We present allelic data for three known and one new C-tract in the human mitochondrial DNA (mtDNA) control region, and we measure intergenerational mutation rates at such C-tracts. In detail, in a sample of 1,172 mtDNA sequences, we demonstrate the existence of an instability threshold of eight consecutive cytosines, at and above which the phenomenon of length heteroplasmy arises. To determine mutation rates, we draw on mtDNA sequences in up to four generations of 248 pedigrees for families living in high or low-radiation environmental conditions. The high-radiation sample gives the most conservative (fastest) mutation rate likely to be encountered in any forensic context. We find that the C-tract mutation rate is up to 6% per generation, and we observe an excess of cytosine gains over losses. Case studies and guidelines for evaluating mtDNA heteroplasmy are provided.

CONFIDENCE INTERVALS AND HYPOTHESIS TESTING FOR BETA DIVERSITY

Under R. H. Whittakers “multiplicative” perspective of species diversity, regional (γ) diversity is viewed as the product of within-assemblage (α) diversity and among-assemblage (β) diversity. An additive perspective, which views α and β as complements, has recently been endorsed for the study of spatial patterns in species diversity. Here we highlight the relation between the two measures of β diversity, showing the multiplicative β as a simple summary statistic of the relation between the additive components. We provide analytical solutions for approximate confidence intervals and hypothesis tests for both measures of beta diversity. We also present results of simulation studies that can help delimit the sample sizes needed for future studies, and which suggest the effect-size likely to be detected with samples of a given size.

Data-driven models for regional coral-reef dynamics

Coral reefs have been affected by natural and anthropogenic disturbances. Coral cover has declined on many reefs, and macroalgae have increased on some. The existence of alternative stable states with high or low coral cover has been widely debated, but not clearly established. We evaluate the evidence for alternative stable states in benthic coral-reef dynamics in the Caribbean, Kenya and Great Barrier Reef (GBR), using stochastic semi-parametric models based on large numbers of time series of cover of hard corals, macroalgae and other components. Only the GBR showed a consistent short-term regional decline in coral cover. There was no evidence for regional increases in macroalgae. The equilibrium distributions of our models were close to recently observed distributions, and differed among regions. In all three regions, the equilibrium distributions were unimodal rather than bimodal, and thus did not suggest the existence of alternative stable states on a regional scale, under current conditions.

Multilocus Characterization Scheme for Shiga Toxin-Encoding Bacteriophages

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) strains are food-borne pathogens whose ability to produce Shiga toxin (Stx) is due to integration of Stx-encoding lambdoid bacteriophages. These Stx phages are both genetically and morphologically heterogeneous, and here we report the design and validation of a PCR-based multilocus typing scheme. PCR primer sets were designed for database variants of a range of key lambdoid bacteriophage genes and applied to control phages and 70 stx+ phage preparations induced from a collection of STEC isolates. The genetic diversity residing within these populations could be described, and observations were made on the heterogeneity of individual gene targets, including the unexpected predominance of short-tailed phages with a highly conserved tail spike protein gene. Purified Stx phages can be profiled using this scheme, and the lambdoid phage-borne genes in induced STEC preparations can be identified as well as those residing in the noninducible prophage complement. The ultimate goal is to enable robust and realistically applicable epidemiological studies of Stx phages and their traits. The impact of Stx phage on STEC epidemiology is currently unknown.