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Sixteen New DNA Markers Produced Genotypes From Red Squirrel Hair in Southern France

Eurasian red squirrel feeding on the ground in Talence, France
Research · Genetics & genomics

Researchers developed 16 new microsatellite markers for Eurasian red squirrels (Sciurus vulgaris) and tested them with non-invasive hair samples from four populations in southern France. The aim was to expand the genetic toolkit available for monitoring populations without having to capture the animals.

Using Illumina sequencing and tissue samples from seven squirrels, the team screened 48 candidate microsatellite regions and selected 16 for further testing. Those markers were then evaluated in hair samples from 120 squirrels.

Most hair samples produced usable genotypes

The marker set produced usable genotypes from 104 of the 120 hair samples, about 87%. The markers were polymorphic, averaging 6.1 alleles per locus, so they captured enough genetic variation to help distinguish individuals and compare genetic diversity and population structure.

Only one marker showed the same warning across all four populations: evidence of a likely null allele. A null allele is a genetic variant that is present in the DNA but may fail to be detected during genotyping, which can distort some population-genetic analyses. The authors therefore recommend caution when using that marker in analyses where undetected alleles would matter.

The markers are designed for non-invasive population genetics

Microsatellites are short, variable DNA sequences that can be used with lower-quality DNA such as hair samples. The 16 new markers give researchers more genetic information for distinguishing individuals and comparing red-squirrel populations across continental Europe.

The authors developed the set in response to the need for better population-genetic monitoring as red squirrels face habitat-related pressures and, in parts of Europe, competition and disease risks associated with introduced squirrel species.

Sources and image credit

  1. Isolation and characterization of 16 new microsatellite loci markers for the European red squirrel (Sciurus vulgaris)Open-access peer-reviewed primary study published 14 January 2026. Seven tissue samples were used to screen 48 candidate microsatellite inserts; 16 loci were then evaluated in hair samples from 120 squirrels across four southern French populations, with successful amplification in 104 samples.

Image: Eurasian red squirrel feeding on the ground in Talence, France. Photo: Murielle Desrois / Wikimedia Commons. Representative image for this story; not presented as an animal or scene from the reported study or event. · CC0 1.0 · Source

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