RAD-sequencing for estimating GRM-based heritability in the wild:a case study in roe deer

International audienceEstimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree‐free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long‐term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD‐sequencing for estimating heritability in a free‐ranging roe deer (Capreolous capreolus) population for which no prior genomic resources were available. We propose a step‐by‐step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the single nucleotide polymorphism (SNP) calling and filtering processes on the GRM structure and GRMbased heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7,000). Genomic relatedness matrix‐based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP data set. We also showed that quality filters, such as the removal of low‐frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD‐sequencing for estimating GRM‐based heritability in virtually any natural population

Population genomics applications for conservation: the case of the tropical dry forest dweller Peromyscus melanophrys

Recent advances in genomic sequencing have opened new horizons in the study of population genetics and evolution in non-model organisms. However, very few population genomic studies have been performed on wild mammals to understand how the landscape affects the genetic structure of populations, useful information for the conservation of biodiversity. Here, we applied a genomic approach to evaluate the relationship between habitat features and genetic patterns at spatial and temporal scales in an endangered ecosystem, the Tropical Dry Forest (TDF). We studied populations of the Plateau deer mouse Peromyscus melanophrys to analyse its genomic diversity and structure in a TDF protected area in the Huautla Mountain Range (HMR), Mexico based on 8,209 SNPs obtained through Genotyping-by-Sequencing. At a spatial scale, we found a significant signature of isolation-by-distance, few significant differences in genetic diversity indices among study sites, and no significant differences between habitats with different levels of human perturbation. At a temporal scale, while genetic diversity levels fluctuated significantly over time, neither seasonality nor disturbance levels had a significant effect. Also, outlier analysis revealed loci potentially under selection. Our results suggest that the population genetics of P. melanophrys may be little impacted by anthropogenic disturbances, or by natural spatial and temporal habitat heterogeneity in our study area. The genome-wide approach adopted here provides data of value for conservation planning, and a baseline to be used as a reference for future studies on the effects of habitat fragmentation and seasonality in the HMR and in TDF

Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region

International audienceThe impact of climate change and anthropogenic deforestation on biodiversity is of growing concern worldwide. Disentangling how past anthropogenic and natural factors contributed to current biome distribution is thus a crucial issue to understand their complex interactions on wider time scales and to improve predictions and conservation strategies. This is particularly important in biodiversity hotspots, such as Madagascar, dominated by large open habitats whose origins are increasingly debated. Although a dominant narrative argues that Madagascar was originally entirely covered by woodlands, which were destroyed by humans, a number of recent studies have suggested that past climatic fluctuations played a major role in shaping current biome distributions well before humans arrived. Here, we address the question of the origin of open habitats in the Daraina region in northern Madagascar, using a multiproxy approach combining population genetics modeling and remote-sensing analyses. We show that (i) contrary to most regions of Madagascar, the forest cover in Daraina remained remarkably stable over the past 60 y, and (ii) the golden-crowned sifaka (Propithecus tattersalli), a forest-dwelling lemur, underwent a strong population contraction before the arrival of the first humans, hence excluding an anthropogenic cause. Prehuman Holocene droughts may have led to a significant increase of grasslands and a reduction in the species' habitat. This contradicts the prevailing narrative that land cover changes are necessarily anthropogenic in Madagascar but does not preclude the later role played by humans in other regions in which recent lemur bottlenecks have been observed

Landscape genetics of an endangered primate species within its entire fragmented range

International audienc

Spatial variation in density and total size estimates in fragmented primate populations : the golden-crowned sifaka (Propithecus tattersalli)

International audienc

Pyrenean ptarmigans decline under climatic and human influences through the Holocene.

International audienceIn Europe, the Quaternary is characterized by climatic fluctuations known to have led to many cycles of contraction and expansion of species geographical ranges. In addition, during the Holocene, historical changes in human occupation such as colonization or abandonment of traditional land uses can also affect habitats. These climatically or anthropically induced geographic range changes are expected to produce considerable effective population size change, measurable in terms of genetic diversity and organization. The rock ptarmigan (Lagopus muta) is a small-bodied grouse occurring throughout Northern hemispheric arctic and alpine tundra. This species is not considered threatened at a continental scale, but the populations in the Pyrenees are of concern because of their small population size, geographical isolation and low genetic diversity. Here, we used 11 microsatellites to investigate genetic variations and differentiations and infer the overall demographic history of Pyrenean rock ptarmigan populations. The low genetic variability found in these populations has been previously thought to be the result of a bottleneck that occurred following the last glacial maximum (i.e., 10 000 years ago) or more recently (i.e., during the last 200 years). Our results clearly indicate a major bottleneck affecting the populations in the last tenth of the Holocene. We discuss how this decline can be explained by a combination of unfavorable and successive events that increased the degree of habitat fragmentation.Heredity advance online publication, 10 July 2013; doi:10.1038/hdy.2013.62

Bouquetins du Bargy et infection brucellique : que nous révèle la génétique ?

National audiencePour comprendre les modalités d’infection d’une population naturelle par un agent pathogène et de transmission en son sein, il est nécessaire de connaître les caractéristiques génétiques et immunogénétiques de cette population. En effet, la diversité génétique est essentielle pour que les populations puissent s’adapter aux risques multi-parasitaires auxquels elles sont continuellement exposées. Or la diversité génétique d’une population est le reflet de son histoire démographique et évolutive. Lors de la réintroduction de bouquetins dans les Alpes, les populations ont subi plusieurs goulots d’étranglements successifs qui ont considérablement érodé leur variabilité génétique adaptative. Nous avons testé l’hypothèse que la sensibilité intrinsèque de la population de bouquetins (Capra ibex) du Bargy à la brucellose est liée à une forte consanguinité et une faible diversité génétique, notamment des gènes de l’immunité. Afin d’évaluer les risques de diffusion de l’agent pathogène, nous avons également mesuré les flux de gènes historiques et contemporains entre les différentes unités socio-spatiales du massif du Bargy et avec les populations des massifs alentours de Leschaux-Andey et des Aravis. Nos résultats suggèrent une très faible diversité génétique neutre et adaptative mais très comparable à celle observée dans un grand nombre de populations restaurées des Alpes et des populations sources. Par contre, sa taille efficace limitée (NE~50 individus) présage une forte diminution de la diversité génétique à moyen terme en l’absence de renforcement/migration. Dans l’ensemble, les gènes de l’immunité étudiés sont très peu polymorphes, mais certains variants rares dans la population (du gène SLC11A1 et dans une moindre mesure Tlr1) sont associés à une plus faible prévalence de brucellose, suggérant une résistance des animaux concernés. Enfin, les flux de gènes entre la population de Bargy et les populations voisines sont historiquement limités, mais nous avons détecté de nombreux mouvements contemporains entre Bargy et Aravis qui indiquent un risque de propagation de la maladie. Mot-clés : Brucella melitensis, diversité génétique, immunogénétique, SLC11A1

Bouquetins du Bargy et infection brucellique : que nous révèle la génétique ?

National audiencePour comprendre les modalités d’infection d’une population naturelle par un agent pathogène et de transmission en son sein, il est nécessaire de connaître les caractéristiques génétiques et immunogénétiques de cette population. En effet, la diversité génétique est essentielle pour que les populations puissent s’adapter aux risques multi-parasitaires auxquels elles sont continuellement exposées. Or la diversité génétique d’une population est le reflet de son histoire démographique et évolutive. Lors de la réintroduction de bouquetins dans les Alpes, les populations ont subi plusieurs goulots d’étranglements successifs qui ont considérablement érodé leur variabilité génétique adaptative. Nous avons testé l’hypothèse que la sensibilité intrinsèque de la population de bouquetins (Capra ibex) du Bargy à la brucellose est liée à une forte consanguinité et une faible diversité génétique, notamment des gènes de l’immunité. Afin d’évaluer les risques de diffusion de l’agent pathogène, nous avons également mesuré les flux de gènes historiques et contemporains entre les différentes unités socio-spatiales du massif du Bargy et avec les populations des massifs alentours de Leschaux-Andey et des Aravis. Nos résultats suggèrent une très faible diversité génétique neutre et adaptative mais très comparable à celle observée dans un grand nombre de populations restaurées des Alpes et des populations sources. Par contre, sa taille efficace limitée (NE~50 individus) présage une forte diminution de la diversité génétique à moyen terme en l’absence de renforcement/migration. Dans l’ensemble, les gènes de l’immunité étudiés sont très peu polymorphes, mais certains variants rares dans la population (du gène SLC11A1 et dans une moindre mesure Tlr1) sont associés à une plus faible prévalence de brucellose, suggérant une résistance des animaux concernés. Enfin, les flux de gènes entre la population de Bargy et les populations voisines sont historiquement limités, mais nous avons détecté de nombreux mouvements contemporains entre Bargy et Aravis qui indiquent un risque de propagation de la maladie. Mot-clés : Brucella melitensis, diversité génétique, immunogénétique, SLC11A1

ASreml code and Data from the study "Between-population differences in the genetic and maternal components of body mass in roe deer"

This repository contains the source code (ASremL input files) and the data used to perform the QG analyses (univariate, bivariate, random regression animal models) in the study "Between-population differences in the genetic and maternal components of body mass in roe deer". Quéméré E et al