Lethal gene defect in Swiss lynx traced to reintroduced founders

Every one of the 12 Swiss lynx found with a fatal organ disease carried two copies of the same faulty FGF23 gene variant, which arrived in the country’s newest lynx population with founder animals moved there from the Alps between 2001 and 2008.

Peer reviewed · Genetic study of one wild population · 12 affected animals · Cell-culture test of the protein

A single-letter change in one gene explains why young lynx in northeastern Switzerland have been dying with mineral deposits in their kidneys, lungs and stomachs, according to a study published in Nature Ecology & Evolution on 13 November 2026. Janna Niehaus and colleagues at the University of Bern, the KORA foundation and the WSL institute traced the variant to carrier lynx that conservationists moved from the Alps. The authors call it the first direct link between a reintroduction’s history and a lethal genetic disease in the wild. Whether the defect is holding back the small population’s growth is still unknown.

Evidence at a glance

Is this a big deal?

For conservation genetics, yes, in a specific way. Inbreeding has been blamed for problems in Florida panthers, Isle Royale wolves and California condors, but those links were mostly correlations between inbreeding and poor health. Here the team named the exact DNA change, showed what it does to the protein and followed it through 45 years of samples. It is one well-documented case, though, and its effect on the population as a whole is still unclear.

What scientists found

The disease looked the same in every case. Under the microscope, the kidneys, lungs and stomach lining of affected lynx were packed with mineral deposits, a pattern called metastatic mineralization. Pathologists judged the damage in each of the nine original cases severe enough to stop the organs working. Those nine were all young, juveniles or subadults, and males and females were affected equally.

The cause is a change at one position in the FGF23 gene (written c.38T>C). It swaps one building block of the protein, leucine at position 13, for proline. FGF23 is a hormone that helps control phosphate levels and stops minerals building up in soft tissue. In people, broken copies of FGF23 cause familial tumoral calcinosis, a rare inherited disease in which minerals build up in soft tissues. The lynx change is not the same as any of the known human variants.

The variant is recessive. A lynx with one copy stays healthy; a lynx with two copies develops the disease. When two carriers breed, each cub has a 1 in 4 chance of inheriting two copies, the same arithmetic that governs recessive diseases such as cystic fibrosis in people.

Show the maths: why two carriers have a 1 in 4 chance of a sick cub

Possible cubs from two healthy carrier parents (N = working copy, m = faulty FGF23 copy)

Copy from mother ↓ / father →	N	m
N	NN: healthy, not a carrier	Nm: healthy carrier
m	mN: healthy carrier	mm: fatal mineralization

Each box has the same chance: 1 in 4 cubs is expected to be sick, 2 in 4 to be healthy carriers and 1 in 4 to be free of the variant. These are averages per cub, not a guarantee for any one litter. Standard Mendelian inheritance; inheritance pattern from Niehaus et al. (2026).

How they found it

The story starts in a freezer and a database. Every lynx found dead in Switzerland, put down for illness or culled for repeatedly killing livestock goes to the Institute for Fish and Wildlife Health in Bern for a post-mortem, and tissue has been banked since the 1980s. Searching 421 records from 2000 to 2023, the team found 13 lynx with mineral deposits in several organs. Two reviewers, one a board-certified veterinary pathologist, re-examined the slides without knowing which animal was which. Nine shared the same severe pattern; all came from the northeast and died between 2012 and 2022. Six were found dead and three were found weak and emaciated; of those three, one was put down and two died soon after.

The researchers then sequenced the whole genomes of those 9 sick lynx and 41 healthy ones from all three Swiss populations. A genome-wide scan pointed to one spot (P = 4.88 × 10⁻⁸). On its own that signal fell just short of the study’s strict genome-wide threshold of 2.93 × 10⁻⁸, so the team checked it another way. Of more than 17 million raw variants, only one appeared as two copies in every sick lynx and in no healthy lynx, and it was the same FGF23 change.

Two further checks made the case. In cultured human cells, the normal lynx version of the protein’s signal sequence let FGF23 out of the cell, and the mutant version did not. And when the team genotyped 331 lynx sampled between 1981 and early 2026, the match was perfect: 241 animals with no copies and 78 with one copy were all healthy, and all 12 with two copies had the disease. Those 12 included the original 9, two new cases from 2024 and one lynx from the Alps found in 1999, whose archived tissue confirmed the diagnosis.

How the variant got there

Lynx were wiped out in central Europe and returned to Switzerland in the 1970s, when about 30 animals from the Carpathians were released in the Alps and the Jura Mountains. That small start left Swiss lynx with observed heterozygosity, a standard measure of genetic variety, about 30% lower than in the Carpathian source. The country now has roughly 360 lynx.

To link the two isolated groups, 12 lynx were captured between 2001 and 2008 and moved to northeastern Switzerland: 8 from the Alps and 4 from the Jura. Only 7 are confirmed to have founded the new population. Of the 10 translocated animals that could be genotyped, 3 were carriers, and family records suggest a fourth was too. All four came from the southwestern Alps.

The variant was already common there. Among 47 lynx sampled in the southwestern Alps between 1981 and 2000, 24 carried one copy and 1 carried two. By 2012 to 2025 the picture had split. In the Alps, 16 of 158 animals were carriers. In the northeast, 23 of 47 healthy lynx carried one copy, and all 11 sick lynx from that period came from there. No carriers or cases have turned up in the Jura.

The authors propose a mix of causes for the falling share in the Alps: two-copy animals dying before they could breed, carriers being moved away, chance, and lynx moving in from neighbouring regions. In the northeast, a few carrier founders, some of whom left more offspring than others, plus close inbreeding, made two-copy cubs far more likely. The northeastern population had about 21 independent lynx in winter 2024/25 (95% confidence interval 21 to 29), with growth stalled since 2016.

Why it matters to you

This won’t change anything in your daily life. It matters if you care about how lost species are brought back, because moving animals to restore populations is a standard conservation tool, and this study shows one of its hidden costs. The study gives managers a concrete reason to start new populations from more, and less related, animals, and to screen them genetically before release. It also has an awkward sequel: four female carriers from the northeastern population were later moved to another European population in a cross-border project, before anyone knew about the variant.

What the evidence does not show

• Population decline: The study does not show that the variant caused the northeastern population to stop growing. The authors say the variant and inbreeding may have contributed, but other factors could play a role.
• How many die: Twelve confirmed cases is a minimum. Dead lynx are easier to find in the gentler northeastern terrain than in the high Alps, so cases there were probably missed, especially under the lighter monitoring of the 1990s.
• Other species: One variant in one reintroduced cat population is a case study. It shows a risk is real, not how common it is.
• Inside the lynx: The protein test used human cells and human FGF23 fused to the lynx signal sequence, not lynx tissue.

How this fits what we already knew

Swiss lynx were already known to be highly inbred. In this study, the inbreeding coefficient based on long runs of identical DNA was above 0.35 in all three populations, which the authors compare with Isle Royale’s wolves before new wolves were brought in to save them. Effects of inbreeding are visible in other animals too, from captive white tigers to wild killer whales, and genetic warning signs are increasingly measured directly, as in a recent study of deep-sea Gulf species.

The new twist concerns where founders come from. Recent debate has focused on the risk of importing harmful variants from large, genetically diverse source populations. This paper describes the opposite: a source that had itself been through a bottleneck, carrying a lethal variant at high frequency without obvious harm, until a handful of its animals started a new population.

Independent perspective

SciQuest has not yet obtained comment from a scientist outside the study. The paper names two of its peer reviewers, Diana Aguilar-Gomez and Rebecca Taylor, alongside others who were anonymous; their reports are listed as available from the journal. We will add independent comment if we receive it.

How other headlines framed it

We found no credible outlet reporting the peer-reviewed paper at the time of writing. When the preprint appeared in November 2025, SRF framed it as a solved mystery: unexplained deaths of young lynx traced to a genetic defect caused by inbreeding, with the wider message that inbreeding threatens Swiss lynx. The published paper is more specific about origin. It puts the weight on where the founders came from, a bottlenecked Alpine source, and is careful not to blame the defect for the population’s stalled growth.

What happens next

The authors argue for larger and more diverse founder groups, better links between populations, continued health and population monitoring, and genetic screening before animals are moved. They also call for careful genetic screening of populations that receive animals, which now includes the population that took in the four carrier females.

In one sentence

A recessive FGF23 variant, carried into northeastern Switzerland by a few lynx from an already depleted Alpine population, became common through inbreeding and now explains every known case of a fatal organ disease in young Swiss lynx.

Quick check: did it click?

1. Why do lynx with one copy of the variant stay healthy? The variant is recessive: one working copy of FGF23 is enough, and only lynx with two faulty copies get sick.
2. Where did the variant come from? Carrier lynx from the southwestern Swiss Alps, moved to the northeast between 2001 and 2008.
3. Does the study prove the variant stopped the population growing? No. The authors say it may have contributed, but other factors could be involved.

Read next

• Deep-sea Gulf species show genetic signs of extinction risk: how small effective population sizes are measured.
• Why are killer whales going extinct?: another small population where inbreeding is in the picture.

Sources and disclosure

1. Niehaus, J. et al. Lynx reintroduction from a bottlenecked source exposes a lethal genetic defect. Nature Ecology & Evolution (2026), published 13 November 2026. Code: Zenodo.
2. Niehaus, J. et al. Evolutionary dynamics of a lethal recessive allele in reintroduced fragmented lynx populations. bioRxiv preprint, 7 November 2025.
3. SRF Wissen, Inzucht gefährdet Luchse: Genetischer Defekt entdeckt, 7 November 2025 (in German).

Disclosure: This article was drafted with AI assistance and checked against the sources above. Carrier percentages in the graphic are SciQuest calculations from counts in the paper; the 1-in-4 figure is standard Mendelian inheritance. The study authors declare no competing interests. Spotted an error? See our corrections policy.