Characterization of the genetic diversity of black bees in France and identification of adaptive pro

 Stage · Stage M2  · 6 mois    Bac+5 / Master   UMR7206 - Eco-anthropologie · Paris (France)  Gratification de stage

 Date de prise de poste : 8 janvier 2024


Genome analysis, Computational Statistics, population genomics


As pollinators, honeybees play a critical role in ecosystem functions and human food security1. Accordingly, the widespread bee decline observed over years threatens both biodiversity conservation and global food supplies. To preserve the existence and the genetic diversity of local honey bee populations, French black bee conservatories have maintained and developed apicultural practices that follow traditional observations on bee life cycle and respect their natural living conditions by prohibiting artificial selection, insemination and transhumance, notably2. However, the efficiency of the protective measures set-up in such conservatories on Apis mellifera diversity has not been fully investigated.

The aim of the internship will be to (i) characterize the genetic architecture at the genome- wide level of Apis mellifera populations sampled in different French black bee conservatories, (ii) highlight population structure and relatedness across honeybee populations, (iii) identify genes that have been selected for Apis mellifera survival and adaptation to changing environments and (iv) contrast the obtained population genetics metrics with those from honeybee populations collected in managed apiaries, for which genetic data is publicly available3. The student will be responsible for the development of the analysis pipeline, which includes the quality check and cleanup of the sequencing data, as well as the alignment of the reads to the Apis mellifera reference genome4. The student will also perform exploratory analyses using population genomics tools such as “selscan” and “AdeGenet” 5,6.

The investigation of the evolutionary history of native Apis mellifera in France is detrimentally missing in the literature, knowing that it informs on the genetic capacity of these bees to persist when facing habitat and climatic changes. Therefore, we expect from the resulting analyses to gain original insights into Apis mellifera genetics, based on which effective strategies can be developed for constructing future sustainable apiculture managements and favoring the conservation of honeybees.

1. Potts SG, Imperatriz-Fonseca V, Ngo HT et al. 2016; Safeguarding pollinators and their values to human well-being. Nature 540(7632): 220-9.
2. Requier F, Garnery L, Kohl PL et al. 2019; The Conservation of Native Honey Bees Is Crucial. Trends in Ecology & Evolution 34(9): 789-98.
3. Espregueira Themudo G, Rey-Iglesia A, Robles Tascón L et al. 2020; Declining genetic diversity of European honeybees along the twentieth century. Scientific Reports 10(1).
4. DePristo MA, Banks E, Poplin R et al. 2011; A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43(5): 491-8.
5. Szpiech ZA (2021) selscan 2.0: scanning for sweeps in unphased data. Biorxiv.
6. Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ. 2014; PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R. Molecular Biology and Evolution 31(7): 1929-36.


Procédure : Envoi de la candidature par mail

Date limite : 15 décembre 2023


Helene Quach

Offre publiée le 2 novembre 2023, affichage jusqu'au 15 décembre 2023