Prieurianin/endosidin 1 is an actin-stabilizing small molecule identified from a chemical genetic screen for circadian clock effectors in Arabidopsis thaliana

Chemical modulators are powerful tools to investigate biological processes. To identify circadian clock effectors, we screened a natural product library in the model plant Arabidopsis thaliana. Two compounds, prieurianin (Pri) and prieurianin acetate, were identified as causing a shorter circadian period. Recently, Pri was independently identified as a vesicle trafficking inhibitor and re-named endosidin 1 (ES1). Here we show that Pri primarily affects actin filament flexibility in vivo, later resulting in reduced severing and filament depolymerization. This stabilization of the actin cytoskeleton subsequently causes changes in vesicle trafficking. Pri also affected microfilaments in mammalian cells, indicating that its target is highly conserved; however, it did not alter actin dynamics in vitro, suggesting that its activity requires the presence of actin-associated proteins. Furthermore, well-characterized actin inhibitors shortened the period length of the Arabidopsis clock in a similar way to Pri, supporting the idea that Pri affects rhythms by altering the actin network. We conclude that actin-associated processes influence the circadian system in a light-dependent manner, but their disruption does not abolish rhythmicity. In summary, we propose that the primary effect of Pri is to stabilize the actin cytoskeleton system, thereby affecting endosome trafficking. Pri appears to stabilize actin filaments by a different mechanism from previously described inhibitors, and will be a useful tool to study actin-related cellular processes.     

Genetic indications of translocated and stocked grey partridges (Perdix perdix): does the indigenous Danish grey partridge still exist?

Non‐local population stocking can have adverse genetic effects on wild populations through loss of genetic diversity and introgressive hybridization. The grey partridge (Perdix perdix) has been an important European game species for centuries, widely subject to translocation and stocking. After c. 80 years of releasing reared grey partridges in Denmark, this study investigated whether an indigenous Danish grey partridge still existed. If so, they would (1) belong to the western European clade (W1) and (2) be more closely related to the historical, indigenous grey partridges than to farm‐bred partridges. These predictions were tested by analysing the variation in both the mitochondrial control region (CR1) and microsatellite markers in museum samples representing the ancestral indigenous Danish grey partridge, contemporary wild grey partridges and farmed grey partridges from the five largest farms in Denmark. Phylogeography and population structure analyses showed traces of the indigenous Danish grey partridges amongst recent wild partridges in certain areas and significant genetic differences between farmed partridges and historical and recent partridges. The results also showed that the indigenous Danish grey partridges belonged to the western European clade (W1 haplotype). A foreign stocking effect was detected on the remote island of Bornholm, where the current population originated from introduced Danish and Bohemian grey partridges. The loss of haplotype diversity over time in certain geographical areas probably results from serious declines in wild Danish grey partridge numbers in recent decades. This, combined with the observation that hybridization between released stocked and wild partridges can occur, may complicate recovery of partridge populations. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 694–710.     

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

Alpine species often have similar demographic responses to Pleistocene climate changes, but exhibit different spatial patterns of genetic diversity. Using a comparative phylogeographical approach, we examined the factors influencing lineage formation in three alpine carabid beetles of the genus Nebria Latreille inhabiting the California Sierra Nevada. These flightless beetles differ in altitudinal zonation and habitat preferences, but overlap spatially, have limited dispersal capacities and share life history characteristics. Species distribution modelling predicted decreasing population connectivity in relation to increasing altitudinal preferences. Diversity patterns at the cytochrome oxidase subunit I gene revealed north–south genetic structure and recent population growth in all three species. The high‐elevation‐restricted species, Nebria ingens Horn, exhibited a deep phylogeographical split, morphological divergence and evidence of limited, unidirectional gene flow towards the south. This was supported by additional data from three nuclear genes and isolation with migration analysis. Nebria spatulata Van Dyke, inhabiting an intermediate altitudinal range, exhibited fixed morphological differences between northern and southern populations, but showed limited structure. The broadly distributed Nebria ovipennis LeConte showed less structure and lacked morphological variation. Diversification of these Nebria species supports the role of altitudinal zonation in lineage formation and is consistent with the Pleistocene species pump model. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Thirty‐five years of spatial autocorrelation analysis in population genetics: an essay in honour of Robert Sokal (1926–2012)

We could not start this review, literally from the beginning, without expressing our sadness over the passing of Professor Robert R. Sokal. We are sure, nevertheless, that the importance of his scientific achievements will ensure he is long remembered. In this modest tribute to Professor Sokal, we highlight his contributions to the field of population genetics and spatial statistical methods. Specifically, we discuss how two papers, co‐authored with Professor N. L. Oden and published in the pages of the Biological Journal of the Linnean Society in 1978, revolutionized the field of analytical population genetics. In these papers, Sokal and Oden created an elegant framework for inferring evolutionary processes (e.g. isolation‐by‐distance, demic diffusion, selection gradients, genetic drift) from the spatial autocorrelation analysis of genetic variation patterns. We also highlight the pivotal importance of Sokal's work to the development of emerging fields (e.g. landscape and conservation genetics). We hope this virtual issue containing the papers that Professor Sokal published in BJLS, and later, related papers by other researchers, will help to remember his work and maintain his legacy of spatial analysis in genetics, ecology, and evolutionary biology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Getting a head start: the importance of personal genetics education in high schools

With advances in sequencing technology, widespread and affordable genome sequencing will soon be a reality. However, studies suggest that "genetic literacy" of the general public is inadequate to prepare our society for this unprecedented access to our genetic information. As the current generation of high school students will come of age in an era when personal genetic information is increasingly utilized in health care, it is of vital importance to ensure these students understand the genetic concepts necessary to make informed medical decisions. These concepts include not only basic scientific knowledge, but also considerations of the ethical, legal, and social issues that will arise in the age of personal genomics. In this article, we review the current state of genetics education, highlight issues that we believe need to be addressed in a comprehensive genetics education curriculum, and describe our education efforts at the Harvard Medical School-based Personal Genetics Education Project.     

Sequence Thyself: Personalized Medicine and Therapies for the Future: 2012 Yale Healthcare Conference

Now in its 8th year, the Yale Healthcare Conference has arguably come upon its most exciting and dramatic time within the U.S. health care system. Dynamic speakers from all over the country came together in April 2012 at Yale University to question, debate, creatively think, and examine challenges within health care organizations and institutions. One of the most prominent issues concerned the aftermath of sequencing the human genome and the explosion of information concerning gene polymorphisms and biomarkers in health and disease. Clinicians, scientists, and pharmaceuticals are looking to innovative individually tailored treatments for patients. During the conference breakout session, speakers Thomas Lynch, MD, director of the Yale Cancer Center and physician-in-chief of the Smilow Cancer Hospital, and Zen Chu, MBA, co-founder of Accelerated Medical Ventures and entrepreneur-in-residence at Massachusetts Institute of Technology, provided enriching discussion on the delivery of science and genetic care of the individual.     

Genotypic diversity enhances invasive ability of Spartina alterniflora

Although genetic diversity is very important for alien species, which have to cope with new environments, little is known about the role that genetic diversity plays in their invasive success. In this study, we set up a manipulation experiment including three levels of genotypic diversity to test whether genotypic diversity can enhance the invasive ability of alien species, in our case the invasive Spartina alterniflora in China, and to infer the underlying mechanisms. There was no significant relationship between genotypic diversity and parameters of performance in the first year; however, from the summer of the second year onwards, genotypic diversity enhanced four of the six parameters of performance. After two growing seasons, there were significant positive relationships between genotypic diversity and maximum spread distance, patch size, shoot number per patch, and aboveground biomass. Moreover, abundance of the native dominant species Scirpus mariqueter was marginally significantly decreased with genotypic diversity of S. alterniflora, suggesting that enhanced invasive ability of S. alterniflora may have depressed the growth of the native species. There was no significant difference in most measures of performance among six genotypes, but we observed a transgressive over performance in four measures in multiple‐genotype patches. At the end of the experiment, there were significant nonadditive effects of genotypic diversity according to Monte Carlo permutations, in six‐genotype, but not three‐genotype plots. Our results indicated that both additive and nonadditive effects played roles in the positive relationship between genetic diversity and invasion success, and nonadditive effects were stronger as duration increased.     

Sex, drugs and recombination: the wild life of Aspergillus

Throughout the eukaryotes, sexual reproduction is an almost universal phenomenon. However, within the Kingdom Fungi, this relationship is not so clear‐cut. Fungi exhibit a spectrum of reproductive modes and life‐cycles; amongst the better known species, sexual reproduction is often facultative, can be rare, and in over half of the known Ascomycota (the moulds) is unknown ( Taylor et al. 1999 ). However, over the last decade, it has become apparent that many of these asexual mitosporic taxa undergo cryptic recombination via unobserved mechanisms and that wholly asexual fungi are, in fact, a rarity ( Taylor et al. 1999, 2001 ; Heitman 2010 ). This revolution in our understanding of fungal sexuality has come about in two ways: Firstly, sexual reproduction leaves an imprint on fungal genomes by maintaining genes required for mating and by generating patterns of mutation and recombination restricted to meiotic processes. Secondly, scientists have become better at catching fungi in flagrante delicto. The genus Aspergillus is one such fungus where a combination of population genetics, genomics and taxonomy has been able to intuit the existence of sex, then to catch the fungus in the act and formally describe their sexual stages. So, why are sexy moulds exciting? One species in particular, Aspergillus flavus, is notorious for its ability to produce a diverse array of secondary metabolites, of which the polyketide aflatoxins (AF) are carcinogenic and others (such as cyclopiazonic acid) are toxigenic. Because of the predilection of A. flavus to grow on crops, such as peanuts, corn and cotton, biocontrol is widely used to mitigate infection by pre‐applying nonaflatoxigenic (AF?) strains to competitively exclude the wild‐type AF+ strains. However, the eventual fate in nature of these biocontrol strains is not known. In this issue of Molecular Ecology, Olarte et al. (2012) make an important contribution by using laboratory crosses of A. flavus to show that not only is AF highly heritable, but AF? strains can become AF+ via crossing over during meiosis. This observation has raised the spectre of cross‐breeding and non‐mendelian inheritance of AF between native and biocontrol strains of the fungus, leading to an increase in the natural diversity of the fungus with perhaps unanticipated consequences.     

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small‐scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine‐scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F_ST = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite‐based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ_ST = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine‐scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter‐related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine‐scale population structure among bottlenose dolphins in Moreton Bay.     

A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae: Colias behrii)

Spatial and environmental heterogeneity are major factors in structuring species distributions in alpine landscapes. These landscapes have also been affected by glacial advances and retreats, causing alpine taxa to undergo range shifts and demographic changes. These nonequilibrium population dynamics have the potential to obscure the effects of environmental factors on the distribution of genetic variation. Here, we investigate how demographic change and environmental factors influence genetic variation in the alpine butterfly Colias behrii. Data from 14 microsatellite loci provide evidence of bottlenecks in all population samples. We test several alternative models of demography using approximate Bayesian computation (ABC), with the results favouring a model in which a recent bottleneck precedes rapid population growth. Applying independent calibrations to microsatellite loci and a nuclear gene, we estimate that this bottleneck affected both northern and southern populations 531–281 years ago, coinciding with a period of global cooling. Using regression approaches, we attempt to separate the effects of population structure, geographical distance and landscape on patterns of population genetic differentiation. Only 40% of the variation in F_ST is explained by these models, with geographical distance and least‐cost distance among meadow patches selected as the best predictors. Various measures of genetic diversity within populations are also decoupled from estimates of local abundance and habitat patch characteristics. Our results demonstrate that demographic change can have a disproportionate influence on genetic diversity in alpine species, contrasting with other studies that suggest landscape features control contemporary demographic processes in high‐elevation environments.