Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

A workshop recently held at the Ecole Polytechnique Federale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.

Elevation gradient of successful plant traits for colonizing alpine summits under climate change

Upward migration of plant species due to climate change has become evident in several European mountain ranges. It is still, however, unclear whether certain plant traits increase the probability that a species will colonize mountain summits or vanish, and whether these traits differ with elevation. Here, we used data from a repeat survey of the occurrence of plant species on 120 summits, ranging from 2449 to 3418 m asl, in south-eastern Switzerland to identify plant traits that increase the probability of colonization or extinction in the 20th century. Species numbers increased across all plant traits considered. With some traits, however, numbers increased proportionally more. The most successful colonizers seemed to prefer warmer temperatures and well-developed soils. They produced achene fruits and/or seeds with pappus appendages. Conversely, cushion plants and species with capsule fruits were less efficient as colonizers. Observed changes in traits along the elevation gradient mainly corresponded to the natural distribution of traits. Extinctions did not seem to be clearly related to any trait. Our study showed that plant traits varied along both temporal and elevational gradients. While seeds with pappus seemed to be advantageous for colonization, most of the trait changes also mirrored previous gradients of traits along elevation and hence illustrated the general upward migration of plant species. An understanding of the trait characteristics of colonizing species is crucial for predicting future changes in mountain vegetation under climate change.

Genetic diversity in caribou linked to past and future climate change

Climate-driven range fluctuations during the Pleistocene have continuously reshaped species distribution leading to populations of contrasting genetic diversity. Contemporary climate change is similarly influencing species distribution and population structure, with important consequences for patterns of genetic diversity and species' evolutionary potential1. Yet few studies assess the impacts of global climatic changes on intraspecific genetic variation2, 3, 4, 5. Here, combining analyses of molecular data with time series of predicted species distributions and a model of diffusion through time over the past 21 kyr, we unravel caribou response to past and future climate changes across its entire Holarctic distribution. We found that genetic diversity is geographically structured with two main caribou lineages, one originating from and confined to Northeastern America, the other originating from Euro-Beringia but also currently distributed in western North America. Regions that remained climatically stable over the past 21 kyr maintained a high genetic diversity and are also predicted to experience higher climatic stability under future climate change scenarios. Our interdisciplinary approach, combining genetic data and spatial analyses of climatic stability (applicable to virtually any taxon), represents a significant advance in inferring how climate shapes genetic diversity and impacts genetic structure.

Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics

Membrane-aerated biofilm reactors performing autotrophic nitrogen removal can be successfully applied to treat concentrated nitrogen streams. However, their process performance is seriously hampered by the growth of nitrite oxidizing bacteria (NOB). In this work we document how sequential aeration can bring the rapid and long-term suppression of NOB and the onset of the activity of anaerobic ammonium oxidizing bacteria (AnAOB). Real-time quantitative polymerase chain reaction analyses confirmed that such shift in performance was mirrored by a change in population densities, with a very drastic reduction of the NOB Nitrospira and Nitrobacter and a 10-fold increase in AnAOB numbers. The study of biofilm sections with relevant 16S rRNA fluorescent probes revealed strongly stratified biofilm structures fostering aerobic ammonium oxidizing bacteria (AOB) in biofilm areas close to the membrane surface (rich in oxygen) and AnAOB in regions neighbouring the liquid phase. Both communities were separated by a transition region potentially populated by denitrifying heterotrophic bacteria. AOB and AnAOB bacterial groups were more abundant and diverse than NOB, and dominated by the r-strategists Nitrosomonas europaea and Ca. Brocadia anammoxidans, respectively. Taken together, the present work presents tools to better engineer, monitor and control the microbial communities that support robust, sustainable and efficient nitrogen removal

Remote Sensing Change Analysis Methodology to Support Traffic Monitoring Programs, 2003

The Federal Highway Administration mandates that states collect traffic count information at specified intervals to meet the needs of the Highway Performance Monitoring System (HPMS). A manual land use change detection method was employed to determine the effects of land use change on traffic for Black Hawk County, Iowa, from 1994 to 2002. Results from land use change detection could enable redirecting traffic count activities and related data management resources to areas that are experiencing the greatest changes in land use and related traffic volume. Including a manual land use change detection process in the Iowa Department of Transportation’s traffic count program has the potential to improve efficiency by focusing monitoring activities in areas more likely to experience significant increase in traffic.

Remote Sensing Change Analysis Methodology to Support Traffic Monitoring Programs: Phase 2, 2004

The Center for Transportation Research and Education (CTRE) issued a report in July 2003, based on a sample study of the application of remote sensed image land use change detection to the methodology of traffic monitoring in Blackhawk County, Iowa. In summary, the results indicated a strong correlation and a statistically significant regression coefficient between the identification of built-up land use change areas from remote sensed data and corresponding changes in traffic patterns, expressed as vehicle miles traveled (VMT). Based on these results, the Iowa Department of Transportation (Iowa DOT) requested that CTRE expand the study area to five counties in the southwest quadrant of the state. These counties are scheduled for traffic counts in 2004, and the Iowa DOT desired the data to 1) evaluate the current methodology used to place the devices; 2) potentially influence the placement of traffic counting devices in areas of high built-up land use change; and 3) determine if opportunities exist to reduce the frequency and/or density of monitoring activity in lower trafficked rural areas of the state. This project is focused on the practical application of built-up land use change data for placement of traffic count data recording devices in five southwest Iowa counties.

Predictive Value of Readiness, Importance, and Confidence in Ability to Change Drinking and Smoking

Background: Visual analog scales (VAS) are used to assess readiness to changeconstructs, which are often considered critical for change.Objective: We studied whether 3 constructs -readiness to change, importance of changing and confidence inability to change- predict risk status 6 months later in 20 year-old men with either orboth of two behaviors: risky drinking and smoking. Methods: 577 participants in abrief intervention randomized trial were assessed at baseline and 6 months later onalcohol and tobacco consumption and with three 1-10 VAS (readiness, importance,confidence) for each behavior. For each behavior, we used one regression model foreach constructs. Models controlled for receipt of a brief intervention and used thelowest level (1-4) in each construct as the reference group (vs medium (5-7) and high(8-10) levels).Results: Among the 475 risky drinkers, mean (SD) readiness, importance and confidence to change drinking were 4.0 (3.1), 2.8 (2.2) and 7.2 (3.0).Readiness was not associated with being alcohol-risk free 6 months later (OR 1.3[0.7; 2.2] and 1.4 [0.8; 2.6] for medium and high readiness). High importance andhigh confidence were associated with being risk free (OR 0.9 [0.5; 1.8] and 2.9 [1.2;7.5] for medium and high importance; 2.1 [1.0;4.8] and 2.8 [1.5;5.6] for medium andhigh confidence). Among the 320 smokers, mean readiness, importance andconfidence to change smoking were 4.6 (2.6), 5.3 (2.6) and 5.9 (2.6). Neitherreadiness nor importance were associated with being smoking free (OR 2.1 [0.9; 4.7]and 2.1 [0.8; 5.8] for medium and high readiness; 1.4 [0.6; 3.4] and 2.1 [0.8; 5.4] formedium and high importance). High confidence was associated with being smokingfree (OR 2.2 [0.8;6.6] and 3.4 [1.2;9.8] for medium and high confidence).Conclusions: For drinking and smoking, high confidence in ability to change wasassociated -with similar magnitude- with a favorable outcome. This points to thevalue of confidence as an important predictor of successful change.

The global welfare impact of China: Trade integration and technological change

This paper evaluates the global welfare impact of China's trade integration and technological change in a multi-country quantitative Ricardian-Heckscher-Ohlin model.We simulate two alternative growth scenarios: a "balanced" one in which China's productivity grows at the same rate in each sector, and an "unbalanced" one in whichChina's comparative disadvantage sectors catch up disproportionately faster to theworld productivity frontier. Contrary to a well-known conjecture (Samuelson 2004),the large majority of countries experience significantly larger welfare gains whenChina's productivity growth is biased towards its comparative disadvantage sectors.This finding is driven by the inherently multilateral nature of world trade.

Do geographic distribution, niche property and life form explain plants' vulnerability to global change?

We modelled the future distribution in 2050 of 975 endemic plant species in southern Africa distributed among seven life forms, including new methodological insights improving the accuracy and ecological realism of predictions of global changes studies by: (i) using only endemic species as a way to capture the full realized niche of species, (ii) considering the direct impact of human pressure on landscape and biodiversity jointly with climate, and (iii) taking species' migration into account. Our analysis shows important promises for predicting the impacts of climate change in conjunction with land transformation. We have shown that the endemic flora of Southern Africa on average decreases with 41% in species richness among habitats and with 39% on species distribution range for the most optimistic scenario. We also compared the patterns of species' sensitivity with global change across life forms, using ecological and geographic characteristics of species. We demonstrate here that species and life form vulnerability to global changes can be partly explained according to species' (i) geographical distribution along climatic and biogeographic gradients, like climate anomalies, (ii) niche breadth or (iii) proximity to barrier preventing migration. Our results confirm that the sensitivity of a given species to global environmental changes depends upon its geographical distribution and ecological proprieties, and makes it possible to estimate a priori its potential sensitivity to these changes.

Demand-based structural change and balanced economic growth

[eng] We analyze the equilibrium of a multi-sector exogenous growth model where the introduction of minimum consumption requirements drives structural change. We show that equilibrium dynamics simultaneously exhibt structural change and balanced growth of aggregate variables as is observed in US when the initial intensity of minimum consumption requirements is sufficiently small. This intensity is measured by the ratio between the aggregate value of the minimum consumption requirements and GDP and, therefore, it is inversely related with the level of economic development. Initially rich economies benefit from an initially low intensity of the minimum consumption requirements and, as a consequence, these economies end up exhibiting balanced growth of aggregate variables, while there is structural change. In contrast, initially poor economies suffer from an initially large intensity of the minimum consumption requirements, which makes the growth of the aggregate variables unbalanced during a very large period. These economies may never exhibit simultaneously balanced growth of aggregate variables and structural change.

Maize leaf development under climate change scenarios

The objective of this work was to simulate maize leaf development in climate change scenarios at Santa Maria, RS, Brazil, considering symmetric and asymmetric increases in air temperature. The model of Wang & Engel for leaf appearance rate (LAR), with genotype-specific coefficients for the maize variety BRS Missões, was used to simulate tip and expanded leaf accumulated number from emergence to flag leaf appearance and expansion, for nine emergence dates from August 15 to April 15. LAR model was run for each emergence date in 100-year climate scenarios: current climate, and +1, +2, +3, +4 and +5°C increase in mean air temperature, with symmetric and asymmetric increase in daily minimum and maximum air temperature. Maize crop failure due to frost decreased in elevated temperature scenarios, in the very early and very late emergence dates, indicating a lengthening in the maize growing season in warmer climates. The leaf development period in maize was shorter in elevated temperature scenarios, with greater shortening in asymmetric temperature increases, indicating that warmer nights accelerate vegetative development in maize.