Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia.
Molecular Biology and Evolution 33(4):946 (2016)
Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the last glacial maximum (LGM) affected the demography ...
Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback.
PLoS Genetics 12(2):e1005887 (2016)
Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproduct...
Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.
PNAS 113(4):E440 (2016)
The Out-of-Africa (OOA) dispersal ∼ 50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test...
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.
Nature Communications 7:11693 (2016)
Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstructi...
Inference of Evolutionary Forces Acting on Human Biological Pathways.
Genome Biology and Evolution 7(6):1546 (2015)
Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger se...
Expansion load: recessive mutations and the role of standing genetic variation.
Molecular Ecology 24(9):2084 (2015)
Expanding populations incur a mutation burden - the so-called expansion load. Previous studies of expansion load have focused on codominant mutations. An important consequence of this assumption is that expansion load stems exclusively from the accumulation of new mutations occurring in individu...
Expansion load and the evolutionary dynamics of a species range.
American Naturalist 185(4):E81 (2015)
Expanding populations incur a mutation burden, the so-called expansion load. Using a mixture of individual-based simulations and analytical modeling, we study the expansion load process in models where population growth depends on the population's fitness (i.e., hard selection). We show that exp...
Detection of convergent genome-wide signals of adaptation to tropical forests in humans.
PLoS ONE 10(4):e0121557 (2015)
Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments without external resources. It is therefore possible that humans have developed recent biological adaptations in response to specific sel...
Prehistoric genomes reveal the genetic foundation and cost of horse domestication.
PNAS 111(52):E5661 (2014)
The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced tw...
Impact of range expansions on current human genomic diversity.
Current Opinion in Genetics & Development 29:22 (2014)
The patterns of population genetic diversity depend to a large extent on past demographic history. Most human populations are known to have gone recently through a series of range expansions within and out of Africa, but these spatial expansions are rarely taken into account when interpreting ob...
Widespread Signals of Convergent Adaptation to High Altitude in Asia and America
The American Journal of Human Genetics 95(4):394 (2014)
Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of conve...
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers.
PNAS 111(35):E3596 (2014)
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the...
Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of microtus voles.
Molecular Biology and Evolution 31(4):817 (2014)
Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough...
Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis).
PLoS ONE 9(11):e112332 (2014)
Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scal...
Robust demographic inference from genomic and SNP data.
PLoS Genetics 9(10):e1003905 (2013)
We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be...
Divergent evolutionary processes associated with colonization of offshore islands.
Molecular Ecology 22(20):5205 (2013)
Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morpho...
Evidence for polygenic adaptation to pathogens in the human genome.
Molecular Biology and Evolution 30(7):1544 (2013)
Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of individually "significant" genes with strong effects. However, a collection of small effect mutations could have a large effect on a given biologi...
Influence of admixture and paleolithic range contractions on current European diversity gradients.
Molecular Biology and Evolution 30(1):57 (2013)
Cavalli-Sforza and Edwards (Analysis of human evolution. 1963. In: Geerts SJ, editor. Genetics today: Proceedings of the 11th International Congress of Genetics, The Hague, The Netherlands. New York: Pergamon. p. 923-993.) initiated the representation of genetic relationships among human populat...
European phylogeography of the epiphytic lichen fungus Lobaria pulmonaria and its green algal symbiont.
Molecular Ecology 21(23):5827 (2012)
In lichen symbiosis, fungal and algal partners form close associations, often codispersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts...
Similarity in recombination rate and linkage disequilibrium at CYP2C and CYP2D cytochrome P450 gene regions among Europeans indicates signs of selection and no advantage of using tagSNPs in population isolates.
Pharmacogenetics and Genomics 22(12):846 (2012)
Linkage disequilibrium (LD) and recombination rate variations are known to vary considerably between human genome regions and populations mostly because of the combined effects of mutation, recombination, and demographic history. Thus, the pattern of LD is a key issue to disentangle variants ass...