Browsing by Author "Chikhi, L."
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- 2BAD: an application to estimate the parental contributions during two independent admixture eventsPublication . Bray, TC.; Sousa, VC.; Parreira, B.; Bruford, MW.; Chikhi, L.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.
- Daraina sportive lemur (Lepilemur milanoii) density and population size estimates in most of its distribution range: the Loky-Manambato region.Publication . Salmona, J.; Ralantoharijaona, T.; Thani, I.M.; Rakotonanahary, A.; Zaranaina, R.; Jan, F.; Rasolondraibe, E.; Barnavon, M.; Beck, A.; Wholhauser, S.; Ranirison, P.; Zaonarivelo, J.R.; Rabarivola, C.; Chikhi, L.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.).
- Estimation des densités et tailles de population du Microcèbe Roux du Nord de (Microcebus tavaratra) dans la région Loky-Manambato (Daraina)Publication . Salmona, J.; Rakotonanahary, A.; Thani, I.M.; Zaranaina, R.; Ralantoharijaona, T.; Jan, F.; Rasolondraibe, E.; Barnavon, M.; Beck, A.; Wholhauser, S.; Ranirison, P.; Zaonarivelo, J.R.; Rabarivola, C.; Chikhi, L.La région Loky-Manambato dans le Nord de Madagascar, est connue pour abriter le propithèque à couronne dorée (Propithecus tattersalli), un lémurien emblématique et endémique de la région. Néanmoins cette région composée d’une dizaine de fragments forestiers de taille moyenne et encore relativement peu étudiés, abrite aussi le microcèbe roux du nord (Microcebus tavaratra). Malgré la gestion des forêts de cette région par l’ONG Fanamby depuis 2005, aucune étude n’avait encore été menée dans chacun des fragments forestiers de la région pour déterminer la présence et quantifier la taille des populations de microcèbes de chacun d’entre eux. Lors de notre étude nous avons tenté d’estimer les densités et les tailles des populations de M. tavaratra dans neuf des dix principaux fragments forestiers de la région. Dans ce but nous avons utilisé la méthode de «line transect distance-sampling». Nos résultats montrent que les densités de microcèbes sont relativement élevées, et varient de 28 à 325 ind/km² entre fragments forestiers de la région. Desétudes plus approfondies des données collectées seront nécessaires pour déterminer les variables environnementales responsables des différences de densité observées.
- Landscape genetics of an endangered lemur (Propithecus tattersalli) within its entire fragmented rangePublication . Quemere, E.; Crouau-Roy, B.; Rabarivola, C.; Louis, EE.; Chikhi, L.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 observations
- Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus)Publication . Schneider, N.; Chikhi, L.; Currat, M.; Radespiel, U.Pleistocene events have shaped the phylogeography of many taxa worldwide. Their genetic signatures in tropical species have been much less explored than in those living in temperate regions. We analysed the genetic structure of a Malagasy primate species, a mouse lemur with a wide distribution (M. murinus), in order to investigate such phylogeographic processes on a large tropical island. We also evaluated the effects of anthropogenic pressures (fragmentation/deforestation) and natural features (geographic distance, rivers) on genetic structure in order to complement our understanding of past and present processes of genetic differentiation.
- Survey of the critically endangered Perrier’s sifaka (Propithecus Perrieri) across most if its distribution range.Publication . Salmona, J.; Jan, F.; Rasolondraibe, E.; Zaranaina, D.; Ousseni, D.S.; Mohamed-Thani, I.; Rakotonanahary, A.; Ralantoharijaona, T.; Kun-Rodrigues, C.; Carreira, M.; Wohlhauser, S.; Ranirison, P.; Zaonarivelo, J.R.; Rabarivola, C.; Chikhi, L.Propithecus perrieri (Perrier’s sifaka) is one of the most endangered lemur species due to its small and fragmented distribution range. Despite a Critically Endangered (CR) conservation and flagship species status, there are still many uncertainties regarding its actual distribution and its presence in some forests of its putative distribution range. We report the results of diurnal and nocturnal surveys carried out in 2012 across most forest fragments of its putative distribution range, namely the Ankarana National Park, the Analamerana Special Reserve and Andrafiamena-Andava-koera Protected Area. During our surveys the species was only observed in Andrafiamena and Analamerana protected areas.
- Taille de la population d’Avahi laniger dans la réserve d’Ambodiriana-Manompana, Nord-est de MadagascarPublication . Sabin, E.; Delarue, C.; Misandeau, C.; Besse, P.; Salmona, J.; Chikhi, L.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.
- The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical dataPublication . Paz-Vinas, I.; Quéméré, E.; Chikhi, L.; Loot, G.; Blanchet, S.Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.
- The scaling of genetic diversity in a changing and fragmented worldPublication . Arenas, M.; Mona, S.; Trochet, A.; Sramkova Hanulova, A.; Currat, M.; Ray, N.; Chikhi, L.; Rasteiro, R.; Schmeller, D.S.; Excoffier, L.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.
- The utility of existing passerine microsatellite markers for genetic studies in endangered species: as demonstrated for a critically endangered forest bird endemic to Réunion Island, the Réunion cuckooshrike (Coracina newtoni)Publication . Salmona, J.; Dawson, DA.; Fouillot, D.; Ghestemme, T.; Thebaud, C.; Chikhi, L.; Salamolard, M.Genetic data are increasingly recognized for their utility in conservation programs. However, many endangered species belong to families that have been understudied. Due to the urgency of their conservation status it is important to quickly identify polymorphic microsatellite loci from available resources. We show for the Re´union Cuckoo shrike Coracina newtoni, that this strategy can be very useful. Using 110 passerine microsatellite primer sets we identified eighteen polymorphic loci and tested them in 25 C. newtoni individuals. Following a Bonferroni correction one pair of loci displayed linkage disequilibrium