Characterizing fitness mutations – the elusive raw material of evolution – from population samples taken in real time

Philip Gerrish

Le vendredi 20 mars 2015 - Grande salle de réunion du CEFE - 11h30

 

Mutations that change fitness have been described as the “raw material” of evolution, because they are the ultimate source of heritable fitness variation upon which natural selection acts. Despite their central role in evolution, however, little is known about them. This fundamental deficiency in evolutionary biology is primarily due to the notorious difficulty of inferring the fitness effects of newly-arising mutations, a difficulty that derives from the unavoidable confounding effects of natural selection. Natural selection imposes a strong sampling bias in favor of higher-fitness genotypes, and as a further complication, this biasing effect itself depends on the dynamic composition of the population. We derive a novel framework for robust inference of fitness effects of mutations – a hierarchy of statistical relations that result from a cumulant expansion of PDE models of evolutionary dynamics. We assess the accuracy with which this framework is able to reconstruct the distribution of fitness effects of newly- arising mutations, using samples taken from simulated evolving populations as well as evolving populations of Escherichia coli. I will discuss our work in the context of other, more mechanistic but perhaps less accurate, attempts to re- construct this fundamental distribution; I will also mention how these methods might be used to decipher general features of fitness landscapes and perhaps even to forecast the near-future evolutionary trajectory or fate of a population.

The rise and demise of biodiversity hotspots. A geologist's perspective

Frank P. Wesselingh

Le vendredi 13 mars 2015 - Grande salle de réunion du CEFE - 11h30

Biodiversity in aquatic ecosystems is facing severe losses world-wide. But in order to understand the se-verity of the anthropogenic impact we must understand the resilience of faunas and processes that drive faunal turnover. Fossil lake systems are an ideal model system to study drivers of biodiversity change in the geological record. Not only to assess the development of biodiversity in such lake systems itself but also the landscape context of such change. In this talk we will look at the origin of the Amazonian megadiversity with a major role of a huge Miocene megalake Pebas. Furthermore we will explore the rise and demise of the unique endemic brackish water biota of the Caspian-Black Sea biota in the past two million years. Finally we will look into a record of marginal marine biodiversity (North Sea Basin, 2-4 million years ago). Component processes of biodiversity change or turnover (immigration, evolution and extinction/extirpation) can be distinguished and provide insights into driving processes behind biodiversity change. The geological perspective shows that turnover is a process of all times, but that the current rates are unprecedented and should be of great concern.Recent publications:
Renema W, (…) Wesselingh FP et al. (2008). Hopping Hotspots: global shifts in marine biodiversity. Science 321: 654-657.
Hoorn C, Wesselingh FP et al. (2010). The development of the Amazonian mega-wetland (Miocene; Brazil, Colombia, Peru, Bolivia). In: Hoorn C & Wesselingh FP (eds.). Amazonia, landscape and species evolution. Wiley-Blackwell, Oxford, pp. 123-142.
Joordens JCA, D’Errico F, Wesselingh FP et al. (2014), Homo erectus at Trinil on Java used shells for tool pro-duction and engraving, Nature. doi:10.1038/nature13962.

Functional traits have globally consistent effects on plant competition

Le 27/02/2015.

Georges Kunstler.

Grande salle de réunion du CEFE - 11h30 1e étage, aile C.

Competition is a very important type of ecological interaction, especially in terrestrial vegetation where plants greatly modify the local environment for each other. Competitive interactions influence the growth and survival of individuals, and thereby change community composition over time into the future. However firm generalizations have yet to be established about outcomes of competition among species. Here we show that key species’ traits have consistent influences on growth and competition. Our analysis synthesize individuals tree growth data for more than 3-millions trees across a global set of forest-monitoring plots. Some traits have a strong effect on the growth rate of the species. Then traits in part determine the tolerance to competition and the impact of competitor’s on a focal tree. A notable generalization is that trait values that favour tolerance to competition also render species slow growing in absence of competition. There is also a small but detectable benefit in reducing competition from trait-dissimilarity between a focal plant and its competitors. The trait-based picture that emerges is
much simpler and more general than a quantification of competition coefficients between each pair of species, which is intractable at the global scale. Our results demonstrate that traits may be used to pre-dict competitive interactions in forests at a large scale.

Recent publications:
Kunstler, G., Courbaud, B., Lavergne, S., Thuiller, W., Vieilledent, G., Zimmerman, N.E., Kattage, J.;
Coomes, D.A. (2012) Competitive interactions between forest trees are driven by species’ trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly. Ecology Letters, 15, 831-840.

Semaines du vendredi 13 février au vendredi 20 février 2015

Les séminaires, colloques et soutenances

 

13 et 20/02 : Pas de séminaire (vacances scolaires)

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

Kateryna Makova

Le 6 mars 2015 - Grande salle de réunion du CEFE - 11h30

 

The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis. For deleterious heteroplasmies, a severe bottleneck may abruptly transform a benign (low) frequency in a mother into a disease-causing (high) frequency in her child. Here we present a high-resolution study of heteroplasmy transmission conducted on blood and buccal mtDNA of 39 healthy mother-child pairs of European ancestry (a total of 156 samples, each sequenced at 20,000× per site). On average, each individual carried one heteroplasmy, and one in eight individuals carried a disease-associated heteroplasmy, with minor allele frequency ≥1%. We observed frequent drastic heteroplasmy frequency shifts between generations and estimated the effective size of the germ-line mtDNA bottleneck at only 30-35 (interquartile range from 9 to 141). Accounting for heteroplasmies, we estimated the mtDNA germ-line mutation rate at 1.3 × 10(-8) (interquartile range from 4.2 × 10(-9) to 4.1 × 10(-8)) mutations per site per year, an order of magnitude higher than for nuclear DNA. Notably, we found a positive association between the number of heteroplasmies in a child and maternal age at fertilization, likely attributable to oocyte aging. This study also took advantage of droplet digital PCR (ddPCR) to validate heteroplasmies and confirm a de novo mutation. Our results can be used to predict the transmission of disease-causing mtDNA variants and illuminate evolutionary dynamics of the mitochondrial genome.

Recent Publications:

Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen T, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. (2014) Maternal Age Effect and Severe Germline Bottleneck in the Inheritance of Human Mitochondrial DNA. PNAS 2014 111 (43) 15474-15479

Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD. 2013. Segmenting the human genome based on states of neutral genetic divergence. Proceedings of the National Academy of Sciences USA 110

(36): 14699-14704

Consequences of spatial expansions on population functional diversity

Le 06/02/2015.

Laurent Excoffier (Institut d’Ecologie et d’Evolution, Université de Berne, Suisse).

Grande salle de réunion du CEFE, 1e étage, aile C.

It is known that spatial expansions have had a major influence on population genetic diversity: some neutral variants can increase in frequency and spread over large areas in newly occupied territories.
This is the phenomenon of gene surfing. However, selected variants can also surf and thus modify the fitness of expanding populations. We have studied this phenomenon by simulations and by analytical derivations in relatively simple models of expansions in homogeneous environments. Very generally, we find that the fitness of populations located on the expansion front decreases as a function of their distance from the origin of the expansion. The creation of this expansion load happens in 1D or 2D expansions, in case of hard or soft selection, in presence or absence of recombination and for different distribution of fitness effects. However, the evolutionary dynamics of the expansion load differs between cases, and also depends on the level of dominance between variants. All these cases will be briefly presented, and we will conclude by showing some evidence that this phenomenon also occurred in human populations.

Mille Milliards de Fourmis

Appli-Phone-Com

A l’occasion de son exposition Mille milliards de fourmis, le Palais de la découverte propose une application gratuite sur mobiles et tablettes pour entrer dans le monde extraordinaire des fourmis.

Découvrez la grande biodiversité des espèces vivant en France avec des fiches descriptives captivantes accompagnées de magnifiques photos.

Utilisez la grille d’identification pour reconnaître à l’œil nu la plupart des fourmis que vous pourrez rencontrer et prenez connaissance de leurs modes de vie particuliers.

Géolocalisez vos observations et collectionnez vos photos.

Posez des questions à nos spécialistes et participez à une communauté de passionnés de myrmécologie (l’étude des fourmis).

[Universcience : Etablissement public du Palais de la découverte et de la Cité des sciences et de l'industrie]