Beyond multiregional and simple out-of-Africa models of human evolution

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Beyond multiregional and simple out-of-Africa models of human evolution

The past half century has seen a move from a multiregionalist view of human origins to widespread acceptance that modern humans emerged in Africa. Here the authors argue that a simple out-of-Africa model is also outdated, and that the current state of the evidence favours a structured African metapopulation model of human origins

2BAD: an application to estimate the parental contributions during two independent admixture events

Several approaches have been developed to calculate the relative contributions of parental populations in single admixture event scenarios, including Bayesian methods. In many breeds and populations, it may be more realistic to consider multiple admixture events. However, no approach has been developed to date to estimate admixture in such cases. This report describes a program application, 2BAD (for 2-event Bayesian ADmixture), which allows the consideration of up to two independent admixture events involving two or three parental populations and a single admixed population, depending on the number of populations sampled. For each of these models, it is possible to estimate several parameters (admixture, effective sizes, etc.) using an approximate Bayesian computation approach. In addition, the program allows comparing pairs of admixture models, determining which is the most likely given data. The application was tested through simulations and was found to provide good estimates for the contribution of the populations at the two admixture events. We were also able to determine whether an admixture model was more likely than a simple split model

Landscape genetics of an endangered lemur (Propithecus tattersalli) within its entire fragmented range

Habitat fragmentation may strongly reduce individuals' dispersal among resource patches and hence influence population distribution and persistence. We studied the impact of landscape heterogeneity on the dispersal of the golden-crowned sifaka (Propithecus tattersalli), an endangered social lemur species living in a restricted and highly fragmented landscape. We combined spatial analysis and population genetics methods to describe population units and identify the environmental factors which best predict the rates and patterns of genetic differentiation within and between populations. We used non-invasive methods to genotype 230 individuals at 13 microsatellites in all the main forest fragments of its entire distribution area. Our analyses suggest that the Manankolana River and geographical distance are the primary structuring factors, while a national road crossing the region does not seem to impede gene flow. Altogether, our results are in agreement with a limited influence of forest habitat connectivity on gene flow patterns (except for North of the species' range), suggesting that dispersal is still possible today among most forest patches for this species. Within forest patches, we find that dispersal is mainly among neighbouring social groups, hence confirming previous behavioural observation

Taille de la population d’Avahi laniger dans la réserve d’Ambodiriana-Manompana, Nord-est de Madagascar

Avahi laniger est le seul lémurien nocturne appartenant à la famille des Indriidae qui habite les forêts humides de l’est de Madagascar (Mittermeier et. al., 2010) dont une partie disparaît chaque année (exploitation du bois, pratique du «tavy» ou culture sur brûlis) (Beaucent and Fayolle, 2011; Lehman and Wright, 2000). La fragmentation et la destruction de leur habitat ainsi que la chasse menacent la survie de nombreuses espèces de lémuriens incluant celle de A. laniger (Jenkins et. al., 2011; Rakotondravony and Rabenandrasana, 2011; Anderson, Rowcliffe and Cowlishaw, 2007). Nous avons réalisé, entre fin Avril et Mai 2012, une étude de densité de la population de A. laniger au sein de l’aire protégée de Manompana-Ambodiriana afin d’estimer la taille de la population totale et de déterminer l’impact du projet de conservation menée par l’Association de Défense de la Forêt d’Ambodiriana (ADEFA) qui recherche l’évolution démographique à moyen terme de cette espèce."LABEX" TULIP: (ANR-10-LABX-41), fct fellowship: (SFRH/BD/64875/2009)

The scaling of genetic diversity in a changing and fragmented world

Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions faced extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probability of extinction and expected patterns of diversity at different scales. Importantly, all these evolutionary processes may affect genetic diversity, which can affect the chance of populations to persist. In this chapter we provide an overview on the consequences of fragmentation, long-distance dispersal, range contractions and range shifts on genetic diversity. In addition, we describe new methods to detect and quantify underlying evolutionary processes from sampled genetic data.Laboratoire d’Excellence (LABEX) entitled TULIP: (ANR-10-LABX-41)

Genetic differentiation of draa indigenous breed and relationships with other goat populations assessed by microsatellite DNA markers

Moroccan goats are characterized by the presence of different populations identified only based on their phenotypes. The objectives of this study were to assess the genetic differentiation of the Draa goat breed and to analyze its genetic structure and its relationships with other local populations using 12 microsatellite markers. The screening was done in South Eastern and Southern Morocco on 192 animals form 5 popula-tions, including Draa, Atlas, Barcha, Ghazzalia breeds, and from a set of goats showing highly variable phenotypes grouped together into "undefined goats" population. Population structure was assessed by stan-dard diversity indices, multivariate statistics, analysis of molecular variance and bayesian clustering tech-niques. The mean allelic richness was 6.526, varying from 2.777 to 9.669. More than 88.4% of the total variance was distributed between individuals and only 1.85% was due to differences between populations. The Draa breed had the lowest observed heterozygosity (0.579), the highest inbreeding coefficient (0.161) and a higher number of deviations from Hardy-Weinberg equilibrium. Moreover, it had the highest genetic distances from the other populations. Bayesian clustering showed a high level of admixture between popu-lations, with a single well defined cluster identifiable within Draa breed. It was concluded that the studied Moroccan goat populations have a substantial but weakly structured genetic diversity, with the exception of Draa breed which shows a higher degree of differentiation and population substructure

The value of the spineless monkey orange tree (Strychnos madagascariensis) for conservation of northern sportive lemurs (Lepilemur milanoii and L. ankaranensis)

Tree hollows provide shelters for a large number of forest-dependent vertebrate species worldwide. In  Madagascar, where high historical and ongoing rates of deforestation and forest degradation are  responsible for a major environmental crisis, reduced availability of tree hollows may lead to declines in hollow-dwelling species such as sportive lemurs, one of the most species-rich groups of lemurs. The identification of native tree species used by hollow-dwelling lemurs may facilitate targeted management interventions to maintain or improve habitat quality for these lemurs. During an extensive survey of sportive lemurs in northern Madagascar, we identified one tree species, Strychnos madagascariensis (Loganiaceae), the spineless monkey orange tree, as a principal sleeping site of two species of northern sportive lemurs, Lepilemur ankaranensis and L. milanoii (Lepilemuridae). This tree species represented 32.5% (n=150) of the 458 sleeping sites recorded. This result suggests that S. madagascariensis may be valuable for the conservation of hollow-dwelling lemurs. De nombreux vertébrés forestiers à travers le monde trouvent refuge dans des cavités et des trous  d’arbres. À Madagascar, les taux de déforestation historiques et actuels sont responsables d’une crise environnementale majeure. Dans ce contexte, une disponibilité réduite d’arbres pourvus de cavités  pourrait entrainer le déclin des espèces dépendant de ces abris comme par exemple les lépilemurs, un des groupes de lémuriens les plus riches en espèces. L’identification des espèces d’arbres indigènes creusés de trous et utilisés par les lémuriens pourrait faciliter la mise en place d’actions de conservation ayant pour but de maintenir ou améliorer l’habitat de ces lémuriens. Au cours d’une étude réalisée dans le Nord de Madagascar, nous avons observé que Strychnos madagascariensis  (Loganiaceae) était   fréquemment utilisé comme site dortoir par les deux espèces de lépilemurs présentes, Lepilemur   ankaranensis and L. milanoii (Lepilemuridae). Cette espèce d’arbre concernait 32,5% (n = 150) des 458  sites dortoirs enregistrés. Ce résultat suggère que S. madagascariensis pourrait être important pour la  conservation des lémuriens dépendant de sites dortoirs

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Daraina sportive lemur (Lepilemur milanoii) density and population size estimates in most of its distribution range: the Loky-Manambato region.

The population of the Daraina sportive lemur (Lepilemur milanoii) is believed to be mostly confined to the Loky-Manambato region (Louis et al., 2006). Very little is known about L. milanoii and it is classified as “Data Deficient” by the IUCN (IUCN, 2013; Schwitzer et al., 2013). Despite the management of the area by the NGO Fanamby since 2005, no study had been conducted to determine the presence and the abundance of L. milanoii in the main forest fragments of the region. During the 2011 dry season we surveyed the ten main forest fragments of the Loky-Manambato region and estimated L. milanoii densities and population sizes using line transect distance sampling (Buckland, 2001) and the DISTANCE software (Thomas et al., 2010). The results suggest that sportive lemur densities are reasonably high in the region, but with important discrepancies between forest fragments, with densities ranging from 49.8 ind./km² in Antsaharaingy to 590.5 ind./km² in Ampondrabe. For the region Loky-Manambato we were able to estimate a population size of 52,000 individuals. This is the first estimate for the total population size and we argue that similar studies should be repeated to monitor environmental changes and anthropogenic pressures (hunting, deforestation, mining, etc.).FCT grant: (SFRH/BD/64875/2009); the Groupement de Recherche International (GDRI); "Laboratoire d’Excellence" (LABEX) entitled TULIP : (ANR-10-LABX-41); Rufford Small Grant Foundation grant: (10941-1)