Population genomics
Where do the lapwings wintering in France come from?
A genomic study of 438 northern lapwings for the French national hunters’ federation, as part of the VanConnect project.
In brief
- Client
- Fédération nationale des chasseurs (French national hunters’ federation)
- Project
- VanConnect, Écocontribution no. 1274, action 1
- Species
- Northern lapwing, Vanellus vanellus
- Approach
- Genotyping by sequencing (3D-GBS), 40,746 SNPs
- Period
- 2024-2025
The context
A huntable migratory species listed in Annex II of the EU Birds Directive, the northern lapwing is declining, mainly because of low productivity. Birds wintering in France are thought to come from the United Kingdom, Scandinavia or Eastern Europe, but their origin and population structure were poorly known.
The question
Where do the lapwings wintering in France come from, and are their populations genetically structured?
The approach
Analysis of 479 muscle samples collected from 2018 to 2023 in nine French regions, genotyped by 3D-GBS. After quality control, 438 birds and 40,746 SNPs were analysed: genetic diversity, ADMIXTURE, principal component analysis, identity by state and by descent.
What we learn
The analyses reveal no marked genetic structure among the birds sampled in France and show high genetic diversity. These results are consistent with a weakly structured population; they do not assign each bird to a breeding region.
The birds analysed, by region
Number of samples per region (table 1 of the report). Three birds have no region recorded. The distribution reflects winter bird density and sampling effort.
From samples to data
- 479muscle samples, collected from 2018 to 2023
- 471birds sequenced with enough reads
- 930,912SNPs detected on the lapwing reference genome
- 438birds kept after filtering missing data
- 40,746independent SNPs for the structure analyses
What the analyses show
- ADMIXTURE: the most likely number of genetic groups is K = 1.
- Fis close to 0 in every region: no marked heterozygote deficit in the groups analysed.
- Principal component analysis: no grouping by region, sex, age, year or month of sampling; three groups stand out very subtly on the first axis.
- Identity by state: most pairs of birds between 0.75 and 0.85, as expected in a weakly structured natural population.
- Identity by descent: only five pairs of birds appear related.
Going further
Adding birds sampled at their breeding sites, in the United Kingdom, Scandinavia and Eastern Europe, would identify the origin of the lapwings wintering in France.
Who did what
- Report: Maeva Leitwein and Emilie Delpuech (LDgenX), Carole Bodin and Pascal Lapébie (French national hunters’ federation).
- Samples: carcasses collected by the Ardennes departmental hunters’ federation, thanks to hunters who volunteered.
- DNA extraction, library preparation and sequencing: IBIS platform, Université Laval (Quebec), on an AVITI sequencer.
The related service
Population genomics
Understanding diversity, connectivity and adaptation.
Explore this serviceThe other studies
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