Using Ancient Samples in Projection Analysis.

Projection analysis is a tool that extracts information from the joint allele frequency spectrum to better understand the relationship between two populations. In projection analysis, a test genome is compared to a set of genomes from a reference population. The projection's shape depends on the historical relationship of the test genome's population to the reference population. Here, we explore in greater depth the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model), or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model). We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present-day population or not. Second, we compute projections for several published ancient genomes. We compare two Neanderthals and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these five ancient genomes to assess how well the observed projections are recovered

The development of a robotic endoscope

This paper describes the development of a prototype robotic endoscope for gastrointestinal diagnosis and therapy. The goal of this device is to access, in a minimally invasive fashion, the portions of the small intestine that cannot be accessed by conventional endoscopes. This paper describes the macroscopic design and function of the device, and the results of preliminary experiments that validate the concept

Understanding the evolution of native pinewoods in Scotland will benefit their future management and conservation

Scots pine (Pinus sylvestris L.) is a foundation species in Scottish highland forests and a national icon. Due to heavy exploitation, the current native pinewood coverage represents a small fraction of the postglacial maximum. To reverse this decline, various schemes have been initiated to promote planting of new and expansion of old pinewoods. This includes the designation of seed zones for control of the remaining genetic resources. The zoning was based mainly on biochemical similarity among pinewoods but, by definition, neutral molecular markers do not reflect local phenotypic adaptation. Environmental variation within Scotland is substantial and it is not yet clear to what extent this has shaped patterns of adaptive differentiation among Scottish populations. Systematic, rangewide common-environment trials can provide insights into the evolution of the native pinewoods, indicating how environment has influenced phenotypic variation and how variation is maintained. Careful design of such experiments can also provide data on the history and connectivity among populations, by molecular marker analysis. Together, phenotypic and molecular datasets from such trials can provide a robust basis for refining seed transfer guidelines for Scots pine in Scotland and should form the scientific basis for conservation action on this nationally important habitat

The Interpersonal Style and Complementarity Between Crisis Negotiators and Forensic Inpatients

Previous negotiation research has explored the interaction and communication between crisis negotiators and perpetrators. A crisis negotiator attempts to resolve a critical incident through negotiation with an individual, or group of persons in crisis. The purpose of this study was to establish the interpersonal style of crisis negotiators and complementarity of the interpersonal interaction between them and forensic inpatients. Crisis negotiators, clinical workers and students (n = 90) used the Check List of Interpersonal Transactions-Revised (CLOIT-R) to identify interpersonal style, along with eight vignettes detailing interpersonal styles. Crisis negotiators were most likely to have a friendly interpersonal style compared to the other non-trained groups. Complementarity theory was not exclusively supported as submissive individuals did not show optimistic judgments in working with dominant forensic inpatients and vice versa. Exploratory analysis revealed that dominant crisis negotiators were optimistic in working with forensic inpatients with a dominant interpersonal style. This study provides insight into the area of interpersonal complementarity of crisis negotiators and forensic inpatients. Whilst further research is required, a potential new finding was established, with significant ‘similarity’ found when dominant crisis negotiators are asked to work with dominant forensic inpatients

Gene-history correlation and population structure

Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.Comment: Revised and extended version: 26 pages, 5 figures, 1 tabl

Monte carlo simulations of parapatric speciation

Parapatric speciation is studied using an individual--based model with sexual reproduction. We combine the theory of mutation accumulation for biological ageing with an environmental selection pressure that varies according to the individuals geographical positions and phenotypic traits. Fluctuations and genetic diversity of large populations are crucial ingredients to model the features of evolutionary branching and are intrinsic properties of the model. Its implementation on a spatial lattice gives interesting insights into the population dynamics of speciation on a geographical landscape and the disruptive selection that leads to the divergence of phenotypes. Our results suggest that assortative mating is not an obligatory ingredient to obtain speciation in large populations at low gene flow.Comment: submitted to Phys.Rev.

Secondary contact and admixture between independently invading populations of the Western corn rootworm, diabrotica virgifera virgifera in Europe

The western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is one of the most destructive pests of corn in North America and is currently invading Europe. The two major invasive outbreaks of rootworm in Europe have occurred, in North-West Italy and in Central and South-Eastern Europe. These two outbreaks originated from independent introductions from North America. Secondary contact probably occurred in North Italy between these two outbreaks, in 2008. We used 13 microsatellite markers to conduct a population genetics study, to demonstrate that this geographic contact resulted in a zone of admixture in the Italian region of Veneto. We show that i) genetic variation is greater in the contact zone than in the parental outbreaks; ii) several signs of admixture were detected in some Venetian samples, in a Bayesian analysis of the population structure and in an approximate Bayesian computation analysis of historical scenarios and, finally, iii) allelic frequency clines were observed at microsatellite loci. The contact between the invasive outbreaks in North-West Italy and Central and South-Eastern Europe resulted in a zone of admixture, with particular characteristics. The evolutionary implications of the existence of a zone of admixture in Northern Italy and their possible impact on the invasion success of the western corn rootworm are discussed

Non-L\'evy mobility patterns of Mexican Me'Phaa peasants searching for fuelwood

We measured mobility patterns that describe walking trajectories of individual Me'Phaa peasants searching and collecting fuelwood in the forests of "La Monta\~na de Guerrero" in Mexico. These one-day excursions typically follow a mixed pattern of nearly-constant steps when individuals displace from their homes towards potential collecting sites and a mixed pattern of steps of different lengths when actually searching for fallen wood in the forest. Displacements in the searching phase seem not to be compatible with L\'evy flights described by power-laws with optimal scaling exponents. These findings however can be interpreted in the light of deterministic searching on heavily degraded landscapes where the interaction of the individuals with their scarce environment produces alternative searching strategies than the expected L\'evy flights. These results have important implications for future management and restoration of degraded forests and the improvement of the ecological services they may provide to their inhabitants.Comment: 15 pages, 4 figures. First version submitted to Human Ecology. The final publication will be available at http://www.springerlink.co

The geography of recent genetic ancestry across Europe

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.Comment: Full size figures available from http://www.eve.ucdavis.edu/~plralph/research.html; or html version at http://ralphlab.usc.edu/ibd/ibd-paper/ibd-writeup.xhtm