The microstratigraphy of middens: capturing daily routine in rubbish at Neolithic Çatalhöyük, Turkey

Microstratigraphy — the sequencing of detailed biological signals on site — is an important new approach being developed in the Çatalhöyük project. Here the authors show how microscopic recording of the strata and content of widespread middens on the tell are revealing daily activities and the selective employment of plants in houses and as fuel. Here we continue to witness a major advance in the practice of archaeological investigation.</jats:p

From Bad to Good: Fitness Reversals and the Ascent of Deleterious Mutations

Deleterious mutations are considered a major impediment to adaptation, and there are straightforward expectations for the rate at which they accumulate as a function of population size and mutation rate. In a simulation model of an evolving population of asexually replicating RNA molecules, initially deleterious mutations accumulated at rates nearly equal to that of initially beneficial mutations, without impeding evolutionary progress. As the mutation rate was increased within a moderate range, deleterious mutation accumulation and mean fitness improvement both increased. The fixation rates were higher than predicted by many population-genetic models. This seemingly paradoxical result was resolved in part by the observation that, during the time to fixation, the selection coefficient (s) of initially deleterious mutations reversed to confer a selective advantage. Significantly, more than half of the fixations of initially deleterious mutations involved fitness reversals. These fitness reversals had a substantial effect on the total fitness of the genome and thus contributed to its success in the population. Despite the relative importance of fitness reversals, however, the probabilities of fixation for both initially beneficial and initially deleterious mutations were exceedingly small (on the order of 10(−5) of all mutations)

Aggregation dynamics explain vegetation patch-size distributions

Vegetation patch-size distributions have been an intense area of study for theoreticians and applied ecologists alike in recent years. Of particular interest is the seemingly ubiquitous nature of power-law patch-size distributions emerging in a number of diverse ecosystems. The leading explanation of the emergence of these power-laws is due to local facilitative mechanisms. There is also a common transition from power law to exponential distribution when a system is under global pressure, such as grazing or lack of rainfall. These phenomena require a simple mechanistic explanation. Here, we study vegetation patches from a spatially implicit, patch dynamic viewpoint. We show that under minimal assumptions a power-law patch-size distribution appears as a natural consequence of aggregation. A linear death term also leads to an exponential term in the distribution for any non-zero death rate. This work shows the origin of the breakdown of the power-law under increasing pressure and shows that in general, we expect to observe a power law with an exponential cutoff (rather than pure power laws). The estimated parameters of this distribution also provide insight into the underlying ecological mechanisms of aggregation and death

Molecular genetic characterisation of probiotic bacteria: Lactobacillus acidophilus and Bifidobacterium species

Over time and concurrent development of methods to identify and characterise bacteria, the lactic acid bacteria (LAB) have undergone multiple taxonomic revisions. As a result of the revisionary nature of LAB taxonomy, the historical characterisation of Lactobacillus acidophilus has struggled with misidentification and misrepresentation. Now however, due to its global use in food products for both flavour and probiotic effect, L. acidophilus is now one of the most well physiologically characterised Lactobacillus species. Bifidobacterium bifidum and Bifidobacterium animalis subsp. lactis are also LAB that are considered to have probiotic effects. Here modern high-throughput next generation comparative genomic techniques are used alongside conventional biochemical and molecular typing methods to analyse the sub-species level diversity of these three probiotic species. Results Randomly Amplified Polymorphic DNA (RAPD) profile similarity analysis showed limited strain-level diversity of L. acidophilus. A species specific marker test was developed for L. acidophilus and used to search for L. acidophilus in wild rodent and human faeces. No L. acidophilus was detected in wild rodent faeces and its carriage in human faeces was highly variable. High-throughput next generation sequencing was used to resequence the genomes of 28 L. acidophilus isolates. Comparing these sequences indicated a high level of genomic conservation in L. acidophilus, which was reflected by limited phenotypic diversity. Comparative genomics in Bifidobacterium animalis subsp. lactis supported the hypothesis that it is a clonally monophyletic species, whereas B. bifidum strains were genomically diverse. Conclusions Methods for phenotypically characterising and typing LAB have generally been superseded in accuracy by DNA sequence based methods. Probiotic bacteria display a range of subspecies level population structures. Commercial and culture collection L. acidophilus isolates did not significantly differ phenotypically, but were distinct when their genome sequences are compared. B. bifidum was genotypically diverse at the subspecies level, while B. animalis subsp. lactis appeared to be clonally monophyletic. Comparative genomics and genome (re)sequencing of probiotic bacteria will become a “gold standard” method for characterisation and typing of isolates

The domestication of the probiotic bacterium Lactobacillus acidophilus

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population

Disease transmission promotes evolution of host spatial patterns

Ecological dynamics can produce a variety of striking patterns. On ecological time scales, pattern formation has been hypothesized to be due to the interaction between a species and its local environment. On longer time scales, evolutionary factors must be taken into account. To examine the evolutionary robustness of spatial pattern formation, we construct a spatially explicit model of vegetation in the presence of a pathogen. Initially, we compare the dynamics for vegetation parameters that lead to competition induced spatial patterns and those that do not. Over ecological time scales, banded spatial patterns dramatically reduced the ability of the pathogen to spread, lowered its endemic density and hence increased the persistence of the vegetation. To gain an evolutionary understanding, each plant was given a heritable trait defining its resilience to competition; greater competition leads to lower vegetation density but stronger spatial patterns. When a disease is introduced, the selective pressure on the plant's resilience to the competition parameter is determined by the transmission of the disease. For high transmission, vegetation that has low resilience to competition and hence strong spatial patterning is an evolutionarily stable strategy. This demonstrates a novel mechanism by which striking spatial patterns can be maintained by disease-driven selection

Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles.

Burkholderia gladioli is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective abilities and antibiotic biosynthesis. We explored the genomic diversity and specialized metabolic potential of 206 B. gladioli strains, phylogenomically defining 5 clades. Historical disease pathovars (pv.) B. gladioli pv. allicola and B. gladioli pv. cocovenenans were distinct, while B. gladioli pv. gladioli and B. gladioli pv. agaricicola were indistinguishable; soft-rot disease and CF infection were conserved across all pathovars. Biosynthetic gene clusters (BGCs) for toxoflavin, caryoynencin and enacyloxin were dispersed across B. gladioli, but bongkrekic acid and gladiolin production were clade-specific. Strikingly, 13 % of CF infection strains characterized were bongkrekic acid-positive, uniquely linking this food-poisoning toxin to this aspect of B. gladioli disease. Mapping the population biology and metabolite production of B. gladioli has shed light on its diverse ecology, and by demonstrating that the antibiotic trimethoprim suppresses bongkrekic acid production, a potential therapeutic strategy to minimize poisoning risk in CF has been identified

Experimental evolution of UV resistance in a phage

The dsDNA bacteriophage T7 was subjected to 30 cycles of lethal ultraviolet light (UV) exposure to select increased resistance to UV. The exposure effected a 0.9999 kill of the ancestral population, and survival of the ending population was nearly 50-fold improved. At the end point, a 2.1 kb deletion of early genes and three substitutions in structural-genes were the only changes observed at high frequency throughout the 40 kb genome; no changes were observed in genes affecting DNA metabolism. The deletion accounted for only a two-fold improvement in survival. One possible explanation of its benefit is that it represents an error catastrophe, whereby the genome experiences a reduced mutation rate. The mechanism of benefit provided by the three structural-gene mutations remains unknown. The results offer some hope of artificially evolving greater protection against sunlight damage in applications of phage therapy to plants, but the response of T7 is weak compared to that observed in bacteria selected to resist ionizing radiation. Because of the weak response, mathematical analysis of the selection process was performed to determine how the protocol might have been modified to achieve a greater response, but the greatest protection may well come from evolving phages to bind materials that block the UV

Evaluation of the implementation of a state government community design policy aimed at increasing local walking: Design issues and baseline results from RESIDE, Perth Western Australia

Objectives. To describe the design and baseline results of an evaluation of the Western Australian government's pedestrian-friendly subdivision design code (Liveable Neighborhood (LN) Guidelines). Methods. Baseline results (2003–2005) from a longitudinal study of people (n=1813) moving into new housing developments: 18 Liveable, 11 Hybrid and 45 Conventional (i.e., LDs, HDs and CDs respectively) are presented including usual recreational and transport related walking undertaken within and outside the neighborhood, and 7-day pedometer steps. Results. At baseline, more participants walked for recreation and transport within the neighborhood (52.6%; 36.1% respectively), than outside the neighborhood (17.7%; 13.2% respectively). Notably, only 20% of average total duration of walking (128.4 min/week (SD159.8)) was transport related and within the neighborhood. There were few differences between the groups' demographic, psychosocial and perceived neighborhood environmental characteristics, pedometer steps, or the type, amount and location of self-reported walking ( pN0.05). However, asked what factors influenced their choice of housing development, more participants moving into LDs reported aspects of their new neighborhood's walkability as important ( pb0.05). Conclusions. The baseline results underscore the desirability of incorporating behavior and context-specific measures and value of longitudinal designs to enable changes in behavior, attitudes, and urban form to be monitored, while adjusting for baseline residential location preferences