Anne Duputié

The evolutionary ecology of clonally propagated domesticated plants.

While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

How do genetic correlations affect species range shifts in a changing environment

Species may be able to respond to changing environments by a combination of adaptation and migration. We study how adaptation affects range shifts when it involves multiple quantitative traits evolving in response to local selection pressures and gene flow. All traits develop clines shifting in space, some of which may be in a direction opposite to univariate predictions, and the species tracks its environmental optimum with a constant lag. We provide analytical expressions for the local density and average trait values. A species can sustain faster environmental shifts, develop a wider range and greater local adaptation when spatial environmental variation is low (generating low migration load) and multitrait adaptive potential is high. These conditions are favoured when nonlinear (stabilising) selection is weak in the phenotypic direction of the change in optimum, and genetic variation is high in the phenotypic direction of the selection gradient.

Phylogeography and the origin of cassava: New insights from the northern rim of the Amazonian basin

1. IntroductionThe origin of cassava (Manihot esculenta Crantz) is still unclear,although several recent studies have addressed this issue (Fregeneetal.,1994;Roaetal.,1997,2000;OlsenandSchaal,1999,2001;Eliaset al., 2000; Olsen, 2004). Rogers and Appan (1973) postulated thatcassava was a ‘‘compilo-species”, i.e., the result of hybridizationevents between several species, among them Manihot aesculifolia(Kunth) Pohl, a species endemic to Central America. On the otherhand,Allemhypothesizedthecroptobeissuedfromasinglespecies,Manihot esculenta, with two subspecies found only in the wild:Manihot esculenta ssp. flabellifolia (Pohl) Ciferri and Manihot escu-lenta ssp. peruviana (Muell. Arg.) Allem (Allem, 1994; Allem et al.,2001).Thesewildtaxatogetherhaveabroadecologicalrange,fromsouthwestern Amazonia to the savannas of the Guianas.Molecular studies have favored the latter scenario, generallyshowing that cassava was domesticated only once, in SouthAmerica,withnocontributionfromtheMesoamericanspeciespool,or at least not from M. aesculifolia (Roa et al., 1997, 2000; Olsen andSchaal, 1999, 2001; Olsen, 2004). Study of this and seven otherMesoamerican species (A. Duputie, unpublished data) show thatallareonlydistantlyrelatedtocassava,excludingthepossibilitythatcassava was domesticated in Central America. These studies,however,sufferseverallimitations.First,theyhaveconsideredonlya limited sample of domesticated cassava accessions. Second, theyoverlooked a part of the range of Manihot esculenta ssp. flabellifolia:whilethetaxonisdistributedonanarcpartiallycirclingtheAmazonbasin, from eastern Bolivia westwards to central Brazil eastwards,andintheGuianasandeasternVenezuelanorthwards,thesestudiesconsidered only samples from Brazil, thereby excluding any possi-bility of testing the hypothesis that cassava could have more thanone center of domestication. Yet, several other crops have beenshown to have been domesticated twice (e.g., the common bean,Gepts et al., 1986).The present study aims at filling some of these gaps. Olsen andSchaal (1999) sampled accessions of M. esculenta ssp. flabellifoliaand the closely related species M. pruinosa Pohl from Brazil and20 accessions of cultivated cassava from the CIAT core collection,a collection constituted with the goal of representing cassava’sgenetic and morphological diversity worldwide (Hershey et al.,1994). We combined their sample of wild Manihot with samplesof Manihot esculenta ssp. flabellifolia from the northern rim of theAmazonian basin, to cover most of the range of this taxon. Further-more, to test the hypothesis that cassava could have more than onecenter of domestication, we also broadened the sample of domes-ticated cassava to include landraces cultivated in the Guianas, thusfilling an acknowledged gap in earlier studies (Olsen and Schaal,2001). Even though these samples all come from the same region,

ASYMMETRIC PATCH SIZE DISTRIBUTION LEADS TO DISRUPTIVE SELECTION ON DISPERSAL

Numerous models have been designed to understand how dispersal ability evolves when organisms live in a fragmented landscape. Most of them predict a single dispersal rate at evolutionary equilibrium, and when diversification of dispersal rates has been predicted, it occurs as a response to perturbation or environmental fluctuation regimes. Yet abundant variation in dispersal ability is observed in natural populations and communities, even in relatively stable environments. We show that this diversification can operate in a simple island model without temporal variability: disruptive selection on dispersal occurs when the environment consists of many small and few large patches, a common feature in natural spatial systems. This heterogeneity in patch size results in a high variability in the number of related patch mates by individual, which, in turn, triggers disruptive selection through a high per capita variance of inclusive fitness. Our study provides a likely, parsimonious and testable explanation for the diversity of dispersal rates encountered in nature. It also suggests that biological conservation policies aiming at preserving ecological communities should strive to keep the distribution of patch size sufficiently asymmetric and variable.

H19 Antisense RNA Can Up-Regulate Igf2 Transcription by Activation of a Novel Promoter in Mouse Myoblasts

It was recently shown that a long non-coding RNA (lncRNA), that we named the 91H RNA (i.e. antisense H19 transcript), is overexpressed in human breast tumours and contributes in trans to the expression of the Insulin-like Growth Factor 2 (IGF2) gene on the paternal chromosome. Our preliminary experiments suggested that an H19 antisense transcript having a similar function may also be conserved in the mouse. In the present work, we further characterise the mouse 91H RNA and, using a genetic complementation approach in H19 KO myoblast cells, we show that ectopic expression of the mouse 91H RNA can up-regulate Igf2 expression in trans despite almost complete unmethylation of the Imprinting-Control Region (ICR). We then demonstrate that this activation occurs at the transcriptional level by activation of a previously unknown Igf2 promoter which displays, in mouse tissues, a preferential mesodermic expression (Pm promoter). Finally, our experiments indicate that a large excess of the H19 transcript can counteract 91H-mediated Igf2 activation. Our work contributes, in conjunction with other recent findings, to open new horizons to our understanding of Igf2 gene regulation and functions of the 91H/H19 RNAs in normal and pathological conditions.

Traditional Amerindian cultivators combine directional and ideotypic selection for sustainable management of cassava genetic diversity

Plant domestication provides striking examples of rapid evolution. Yet, it involves more complex processes than plain directional selection. Understanding the dynamics of diversity in traditional agroecosystems is both a fundamental goal in evolutionary biology and a practical goal in conservation. We studied how Amerindian cultivators maintain dynamically evolving gene pools in cassava. Farmers purposely maintain diversity in the form of phenotypically distinct, clonally propagated landraces. Landrace gene pools are continuously renewed by incorporating seedlings issued from spontaneous sexual reproduction. This poses two problems: agronomic quality may decrease because some seedlings are inbred, and landrace identity may be progressively lost through the incorporation of unrelated seedlings. Using a large microsatellite dataset, we show that farmers solve these problems by applying two kinds of selection: directional selection against inbred genotypes, and counter‐selection of off‐type phenotypes, which maintains high intra‐landrace relatedness. Thus, cultural elements such as ideotypes (a representation of the ideal phenotype of a landrace) can shape genetic diversity.

How climate, migration ability and habitat fragmentation affect the projected future distribution of European beech

Recent efforts to incorporate migration processes into species distribution models (SDMs) are allowing assessments of whether species are likely to be able to track their future climate optimum and the possible causes of failing to do so. Here, we projected the range shift of European beech over the 21st century using a process-based SDM coupled to a phenomenological migration model accounting for population dynamics, according to two climate change scenarios and one land use change scenario. Our model predicts that the climatically suitable habitat for European beech will shift north-eastward and upward mainly because (i) higher temperature and precipitation, at the northern range margins, will increase survival and fruit maturation success, while (ii) lower precipitations and higher winter temperature, at the southern range margins, will increase drought mortality and prevent bud dormancy breaking. Beech colonization rate of newly climatically suitable habitats in 2100 is projected to be very low (1-2% of the newly suitable habitats colonised). Unexpectedly, the projected realized contraction rate was higher than the projected potential contraction rate. As a result, the realized distribution of beech is projected to strongly contract by 2100 (by 36-61%) mainly due to a substantial increase in climate variability after 2050, which generates local extinctions, even at the core of the distribution, the frequency of which prevents beech recolonization during more favourable years. Although European beech will be able to persist in some parts of the trailing edge of its distribution, the combined effects of climate and land use changes, limited migration ability, and a slow life-history are likely to increase its threat status in the near future.

Estimating consensus and associated uncertainty between inherently different species distribution models

Summary 1. Forecasting shifts in biome and species distribution is crucially needed in the current context of global change. So far, most projections of vegetation distribution rely on correlative species distribution models (SDMs). Yet, process-based or hybrid models based on explicit physiological description may be more robust to extrapolation under future climatic conditions. Differences between model projections may be wide, leading to scepticism among environmental stakeholders. 2. Here, we propose to combine outputs of several distribution models based on physiological responses, to produce both consensual maps of occurrences and maps of associated uncertainty. The consensus map relies on the conditional projections of each SDM. Because the models used are based on processes, their errors are likely to vary consistently with climate as some processes not implemented in a model might be important under a given set of climatic conditions. Uncertainty of the consensus model is thus assessed through multimodel regression of deviance maps with respect to current climatic conditions, and can be extrapolated to forecast climates. 3. We illustrate this approach using three SDMs, on three widely distributed European trees (Fagus sylvatica L., Quercus robur L. and Pinus sylvestris L.), and project their distributions under two scenarios. The conditional consensus outperforms classical methods of model consensus (i.e. to use the mean, the median or a weighted average of individual SDM outputs) in projecting current occurrences. 4. Consistently, with the results of individual SDMs, the conditional consensus projects that the suitable areas for F. sylvatica and Q. robur will expand towards north-eastern Europe, while that of P. sylvestris will contract. Projections of future occurrence are most uncertain towards the margins of the distribution (particularly the trailing edge). 5. Our approach can help modellers identify the limitations of each SDM and stakeholders pinpoint the regions of models agreement and highest certainty.

Population genetics of Manihot esculenta ssp. flabellifolia gives insight into past distribution of xeric vegetation in a postulated forest refugium area in northern Amazonia

The Guianas have often been proposed as a forest refugium; however, this view has received little testing. Studies of population genetics of forest taxa suggest that the central part of French Guiana remained forested, while the southern part (currently forested) may have harboured more open vegetation. Insights into the population structure of species restricted to non‐forested habitats can help test this hypothesis. Using six microsatellite loci, we investigated the population genetics of French Guianan accessions of Manihot esculenta ssp. flabellifolia, a taxon restricted to coastal savannas and to rocky outcrops in the densely forested inland. Coastal populations were highly differentiated from one another, and our data suggest a recent colonization of these savannas by M. esculenta ssp. flabellifolia in a west‐to‐east process. Coastal populations were strongly differentiated from inselberg populations, consistent with an ancient separation of these two groups, with no or low subsequent gene flow. This supports the hypothesis that the central part of the region may have remained forested since the Last Glacial Maximum, impeding the establishment of Manihot. Contrary to coastal populations, inselberg Manihot populations were strikingly homogeneous at a broad spatial scale. This suggests they were connected until recently, either by a large continuous savanna area or by smaller, temporary disturbed areas shifting in space.