Evolutionary forces shaping genomic islands of population differentiation in humans

Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP) showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM). A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i) as much as 20% of islands are in non-genic regions ii) these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii) most loci are strongly differentiated between Africans and non-Africans, a result consistent with known human demographic history.

Dynamics of Shifting Cultivation Landscapes in Northern Lao PDR Between 2000 and 2009 Based on an Analysis of MODIS Time Series and Landsat Images

The rotational nature of shifting cultivation poses several challenges to its detection by remote sensing. Consequently, there is a lack of spatial data on the dynamics of shifting cultivation landscapes on a regional, i.e. sub-national, or national level. We present an approach based on a time series of Landsat and MODIS data and landscape metrics to delineate the dynamics of shifting cultivation landscapes. Our results reveal that shifting cultivation is a land use system still widely and dynamically utilized in northern Laos. While there is an overall reduction in the areas dominated by shifting cultivation, some regions also show an expansion. A review of relevant reports and articles indicates that policies tend to lead to a reduction while market forces can result in both expansion and reduction. For a better understanding of the different factors affecting shifting cultivation landscapes in Laos, further research should focus on spatially explicit analyses.

Effects of Landscape Segregation on Livelihood Vulnerability: Moving From Extensive Shifting Cultivation to Rotational Agriculture and Natural Forests in Northern Laos

This study investigates four decades of socio-economic and environmental change in a shifting cultivation landscape in the northern uplands of Laos. Historical changes in land cover and land use were analyzed using a chronological series of remote sensing data. Impacts of landscape change on local livelihoods were investigated in seven villages through interviews with various stakeholders. The study reveals that the complex mosaics of agriculture and forest patches observed in the study area have long constituted key assets for the resilience of local livelihood systems in the face of environmental and socio-economic risks. However, over the past 20 years, a process of segregating agricultural and forest spaces has increased the vulnerability of local land users. This process is a direct outcome of policies aimed at increasing national forest cover, eradicating shifting cultivation and fostering the emergence of more intensive and commercial agricultural practices. We argue that agriculture-forest segregation should be buffered in such a way that a diversity of livelihood opportunities and economic development pathways can be maintained.

Who Counts? Demography of Swidden Cultivators in Southeast Asia

Swidden cultivators are often found as a distinct category of farmers in the literature, but rarely appear in population censuses or other national and regional classifications. This has led to a worldwide confusion on how many people are dependent on this form of agriculture. The most often cited number of 200–300 million dates back to the early 1970s, but the source is obscure. We assess available, published data from nine countries in Southeast Asia and conclude that on this basis it is not possible to provide a firm estimate of the number of swidden cultivators in the region. A conservative range of 14–34 million people engaged in swidden cultivation in the region is suggested, however. We argue that along with improved knowledge of swidden livelihoods, there is an urgent need to develop techniques that will allow for better estimates of swidden populations in order to secure appropriate rural development and poverty reduction in swidden areas.

Finding Homogeneity in Heterogeneity - A New Approach to Quantifying Landscape Mosaics Developed for the Lao PDR

A key challenge for land change science in general and research on swidden agriculture in particular, is linking land cover information to human–environment interactions over larger spatial areas. In Lao PDR, a country facing rapid and multi-level land change processes, this hinders informed policy- and decision-making. Crucial information on land use types and people involved is still lacking. This article proposes an alternative approach for the description of landscape mosaics. Instead of analyzing local land use combinations, we studied land cover mosaics at a meso-level of spatial scale and interpreted these in terms of human–environmental interactions. These landscape mosaics were then overlaid with population census data. Results showed that swidden agricultural landscapes, involving 17% of the population, dominate 29% of the country, while permanent agricultural landscapes involve 74% of the population in 29% of the territory. Forests still form an important component of these landscape mosaics.

An Assessment of Trends in the Extent of Swidden in Southeast Asia

Swidden systems consisting of temporarily cultivated land and associated fallows often do not appear on land use maps or in statistical records. This is partly due to the fact that swidden is a diverse and dynamic land use system that is difficult to map and partly because of the practice of grouping land covers associated with swidden systems into land use or land cover categories that are not self-evidently linked to swiddening. Additionally, in many parts of Southeast Asia swidden systems have changed or are in the process of changing into other land use systems. This paper assesses the extent of swidden on the basis of regional and national sources for nine countries, and determines the pattern of changes of swidden on the basis of 151 cases culled from 67 articles. Findings include (1) a majority of the cases document swidden being replaced by other forms of agriculture or by other livelihood systems; (2) in cases where swiddening is still practiced, fallow lengths are usually, but not always, shorter; and (3) shortened fallow length does not necessarily indicate a trend away from swidden since it is observed that short fallow swidden is sometimes maintained along with other more intensive farming practices and not completely abandoned. The paper concludes that there is a surprising lack of conclusive data on the extent of swidden in Southeast Asia. In order to remedy this, methods are reviewed that may lead to more precise future assessments.

Social Learning Processes in Swiss Soil Protection? The 'From Farmer - To Farmer' Project

Social learning approaches have become a prominent focus in studies related to sustainable agriculture. In order to better understand the potential of social learning for more sustainable development, the present study assessed the processes, effects and facilitating elements of interaction related to social learning in the context of Swiss soil protection and the innovative ‘From Farmer - To Farmer’ project. The study reveals that social learning contributes to fundamental transformations of patterns of interactions. However, the study also demonstrates that a learning-oriented understanding of sustainable development implies including analysis of the institutional environments in which the organizations of the individual representatives of face-to-face-based social learning processes are operating. This has shown to be a decisive element when face-to-face-based learning processes of the organisations’ representatives are translated into organisational learning. Moreover, the study revealed that this was achieved not directly through formalisation of new lines of institutionalised cooperation but by establishing links in a ‘boundary space’ trying out new forms of collaboration, aiming at social learning and co-production of knowledge. It is argued that further research on social learning processes should give greater emphasis to this intermediary level of ‘boundary spaces’.

Socio-Economic Perspectives on Shifting Cultivation Landscapes in Northern Laos

Despite the rapid agricultural transition that has occurred in the past decade, shifting cultivation remains a widespread agricultural practice in the northern uplands of Lao PDR. Little information is available on the basic socio-economic situation and respective possible patterns in shifting cultivation landscapes on a regional level. On the basis of a recent approximation of the extent of shifting cultivation landscapes for two time periods and disaggregated village level census data, this paper characterizes these landscapes in terms of key socioeconomic parameters for the whole of northern Laos. Results showed that over 550,000 people live in shifting cultivation regions. The poverty rate of this population of 46.5 % is considerably higher than the national rural rate. Most shifting cultivation landscapes are located in remote locations and a high share of the population comprises ethnic minorities, pointing to multi-dimensional marginality of these areas. We discuss whether economic growth and increased market accessibility are sufficient to lift these landscapes out of poverty.

Life history, ecology and the biogeography of strong genetic breaks among 15 species of PaciWc rockWsh, Sebastes

Strong genetic change over short spatial scales is surprising among marine species with high dispersal potential. Concordant breaks among several species signals a role for geographic barriers to dispersal. Along the coast of California, such breaks have not been seen across the biogeographic barrier of Point Conception, but other potential geographic boundaries have been surveyed less often.;We tested for strong-population structure in 11 species of Sebastes sampled across two regions containing potential dispersal barriers, and conducted a meta-analysis including four additional species. We show two strong breaks north of Monterey Bay, spanning an oceanographic gradient and an upwelling jet. Moderate genetic structure is just as common in the north as it is in the south, across the biogeographic break at Point Conception. Gene Xow is generally higher among deep-water species, but these conclusions are confounded by phylogeny. Species in the subgenus Sebastosomus have higher structure than those in the subgenus;Pteropodus, despite having larvae with longer pelagic phases. DiVerences in settlement behavior in the face of ocean currents might help explain these diVerences. Across similar species across the same coastal environment, we document a wide variety of patterns in gene Xow, suggesting that interaction of individual species traits such as settlement behavior with environmental factors such as;oceanography can strongly impact population structure