Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies

The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high‐throughput next‐generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341 045 sequence reads from 12 populations that we were able to assemble into 15 262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non‐model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome‐level φ_ST while appropriately modelling uncertainty in locus‐specific φ_ST. We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome‐level φ_ST were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post‐Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome‐level data to better understand the phylogeographic history of populations.     

Places Of Transformation: Building Monuments From Water And Stone In The Neolithic Of The Irish Sea

Using the Irish Sea area as a case-study, we argue that both sites and landscapes can be understood as containing a series of components procured from the landscape and from human, animal, and object bodies. These components were organized in a way that commented on and related to specific cultural relationships between these different locations and through the substances found within them. This idea is explored by examining Neolithic monuments, material culture, and natural materials in southwest Wales, northwest Wales, the Isle of Man, and southwest Scotland. We trace some metaphorical schemes which were integral to Neolithic activity in this part of the Irish Sea. In particular, we highlight the metaphorical connections between water and stone in places associated with transformation, particularly the repeated transformation of human bodies. We suggest that the series of associations present in the Neolithic were not invested with a uniform meaning but, instead, were polyvalent, subject to conflicting interpretations, contextually specific and variable through both space and time. The relationship between these elements was therefore dependent on the contexts of their association. Nevertheless, the association of water and stone can be found repeatedly throughout the Neolithic world and may have been the medium of a powerful trope within broader conceptions of the world. This article is intended as a preliminary consideration of these issues (particularly the links between stone, mountains, water, quartz, shell, and human remains) and is offered as a thinking-point for ongoing research in this area.     

Rocky shore zonation in the Ranee tidal power basin

Data from a series of rocky shore transects, within the enclosed basin of the Ranee estuary and immediately outside the barrage, describe the distribution and zonation patterns of the intertidal biota, after more than a decade of its regular operation as a tidal power station. In the absence of quantitative pre-barrage information, the distribution of species has been compared with published information on their former extent of penetration into the estuary.     

The effect of sample duration on the quantification of stream drift

1. We performed computer simulations and a field experiment to determine the effect that sample duration and, thus, sample volume had on estimates of drift density and sample variance. 2. In computer simulations, when the spatial arrangement of individuals in the water column approximated a random and a contagious-random distribution, estimated mean drift density was not significantly affected by sample duration, but sample variance decreased curvilinearly as sample duration increased. 3. Similar results were obtained in field experiments in habitats of high and low water velocity. 4. Our findings from an Albertan stream indicate that the relationship between sample variance (i.e. coefficient of variation) and duration of drift samples is curvilinear. This relationship affected the number of samples required to achieve a specific level of precision (i.e. a standard error within 10% of the mean). For estimates in low and high current velocities, sample variation was halved by increasing the duration of sample collections from 10 to 20 min. The increased precision obtained with samples of 20 min duration reduced the amount of drift material that needed to be processed by approximately 50% compared with an equivalent 10% level of precision for samples of 10 min duration. This reduction in the number of samples required to obtain a given level of precision has important consequences to the cost of processing drift samples. 5. Thus to optimize studies of stream invertebrate drift, both in terms of sample precision and processing effort, researchers must consider the effect that sample volume has on the variance of drift density estimates. Because researchers generally use drift nets with similar-sized apertures (>300cm²), the problem for specific field applications becomes one of optimizing sample duration relative to variance estimates for drift density.     

Contrasting responses of Peromyscus mice of Yosemite National Park to recent climate change

Accurately predicting the response of species to climate change is crucial for the preservation of contemporary species diversity. In the current study, we analyze the response of two congeneric small mammal species (Peromyscus maniculatus and Peromyscus truei) to recent climate change in the region of Yosemite National Park (California, USA). The generalist P. maniculatus did not change its distribution in response to climate change while the specialist P. truei substantially changed its geographic and elevational distribution in the region, expanding into Yosemite. Using molecular genetic techniques we found that a cryptic geographic shift in genetic variation may have occurred within the geographically stable P. maniculatus distribution. Using a combination of morphometric and molecular genetic techniques we confirmed that a P. truei subspecies previously identified as a habitat specialist expanded into new habitat types, suggesting that this subspecies is not in fact a habitat specialist. Instead, we propose that the range of this subspecies is instead limited by climatic variables currently varying in response to contemporary climate change. These results underscore the importance of verifying the natural‐history‐based assumptions used to develop predictive models of species' response to climate change.