Pudu deer, Pudu puda, are endemic to southern South America and strongly associated with temperate rainforest. Native forest loss and fragmentation are among the principal threats cited for the species, alongside predation by domestic dogs, competition with exotic species and poaching. The study focused on the provinces of Osorno, Llanquihue and Chiloé, where agricultural and forestry activity has contributed to increasingly fragmented native forest, particularly in the central valleys between the Andes and Coastal mountain ranges.

The researchers analyzed 20 georeferenced animals: five from Osorno, nine from Llanquihue and six from Chiloé. Most samples were skin and muscle from carcasses donated by institutions including the Museo de Historia Natural in Purranque, Parque Nacional Puyehue, the Sitio Paleontológico de Pilauco and the Centro de Reproducción del pudu in Osorno. Blood was also collected from captive animals at the Centro de Rehabilitación de Fauna Silvestre of the Universidad San Sebastián in Puerto Montt. Legal restrictions and the scarcity of carcasses with precise collection locations limited the sample size.

DNA was extracted from preserved tissue and individuals were genotyped at five polymorphic microsatellite loci: RT27, N, BM6506, BM203 and BBJ2. A sixth locus, Cervid14, was excluded because its amplification products could not be interpreted clearly. The researchers used the more polymorphic available markers because simulations cited in the study indicate that loci with greater allelic richness can monitor population genetic diversity more effectively when only a small number of loci is analyzed. Tests found no evidence of null alleles at the retained loci.

Mean numbers of alleles were 2.8 in Osorno, 3.2 in Chiloé and 4.2 in Llanquihue, while mean allelic richness was 2.5 in both Osorno and Chiloé and 3.1 in Llanquihue. Mean observed heterozygosity ranged from 0.423 in Chiloé to 0.547 in Llanquihue, with an overall mean of 0.473. All three populations showed significant heterozygote deficits, with mean inbreeding coefficients of 0.189 in Osorno, 0.131 in Chiloé and 0.091 in Llanquihue; the overall mean was 0.137, with P < 0.0001. The authors state that these measures indicate greater homozygosity than expected under Hardy–Weinberg equilibrium, although they do not by themselves establish the cause of the deficit.

The analysis did not detect significant differentiation among the three provincial samples. Mean F_ST was 0.0942, standardized F_ST was 0.2677 and the differentiation measure D_j was 0.3303; none showed a significant difference among populations. A STRUCTURE analysis favored two clusters under the ΔK criterion, but membership coefficients were nearly symmetric at 0.45–0.55 and the admixture parameter α ranged from 2.39 to 4.01. The authors therefore interpreted the results as showing no resolved population structure and as consistent with gene flow among the sampled populations. They cautioned that both the small sample and the small number of loci can affect STRUCTURE results.

Linkage-disequilibrium estimates gave an effective population size of 3 for Osorno under all three rare-allele thresholds, with a jackknife 95% confidence interval of 0.5 to infinity. For Chiloé and Llanquihue, the method found no evidence that genetic drift attributable to a finite number of parents explained the observations; the corresponding estimates were reported as infinite, with lower confidence limits of 3.0 and 0.6, respectively. The Osorno estimate was below the theoretical threshold of 50 cited by the authors, but it may be biased by the small sample and should be interpreted cautiously.

Fragmentation was measured within a 6.1 km radius around each sampling site, represented by a 12.2 × 12.2 km landscape rectangle. Land-cover data published in 2013 were derived from Landsat 8 imagery with a minimum mappable area of 0.24 hectares. FRAGSTATS was used to calculate class and patch metrics, including the proportion of landscape covered by native forest, patch density, division, splitting, patch number, patch area and patch proximity. Stepwise regression found that patch density and the proportion of forest cover were negatively associated with both the number of alleles per locus and observed heterozygosity. The adjusted R² was 0.3222, meaning that the model accounted for 32.22% of the variation in the response variables.

For the number of alleles per locus, the standardized coefficient was −0.6594 for patch density (P = 0.0123; bootstrap-corrected P = 0.028) and −0.8740 for forest cover (P = 0.0151; bootstrap-corrected P = 0.034). Similar associations were reported for observed heterozygosity. These cross-sectional relationships support an association between fragmentation and lower measured genetic variation, but they do not establish that contemporary forest loss caused the differences or that genetic variation is continuing to decline. The authors considered the possibility that small relict populations may have experienced variation loss over generations through drift, inbreeding or restricted gene flow, and proposed maintaining native-forest continuity, targeted reforestation and possible corridors as conservation strategies.

Subject of Research: Associations between native-forest fragmentation and microsatellite genetic variation in southern Chile pudu deer

Article Title: Genetic structure and microsatellite-based genetic variation influenced by habitat fragmentation in pudu deer ( Pudu puda ) from southern Chile

Article References: Colihueque, N., & Gantz, A. (2025). Genetic structure and microsatellite-based genetic variation influenced by habitat fragmentation in pudu deer (Pudu puda) from southern Chile. Neotropical Biology and Conservation, 20(3), 165-169. https://doi.org/10.3897/neotropical.20.e151162

Image Credits: AI Generated

DOI: 10.3897/neotropical.20.e151162

Keywords: pudu deer, landscape genetics, habitat fragmentation, microsatellites, genetic diversity, heterozygosity, effective population size, southern Chile, temperate rainforest, Genetic, structure, microsatellite-based

The Austrian populations are remnants of a species historically recorded across several eastern Austrian floodplains and wetlands. The Fadenbach population, rediscovered in 1992 after the last Danube-floodplain record in 1975, and the Jesuitenbach population near Moosbrunn are now the only two presumed natural sites in the country. European mudminnow is classified as Vulnerable across Europe and Critically Endangered in Austria.

Researchers sampled the Fadenbach across 15 sections covering 3.3 km in October 2024, when sufficiently high water produced continuous flow, and revisited areas where fish had been detected in August 2025, when the system consisted of isolated pools and sampling was conducted by wading. Electrofishing at the Jesuitenbach was conducted mainly from boats in October 2024 and November 2025. The study also sampled four ex situ populations maintained in garden ponds and at the Vienna Zoo.

Overall, 640 fish were captured, and 191 fin-clip DNA samples were collected between October 2024 and November 2025. Samples included 50 Fadenbach fish, 61 Jesuitenbach fish and 80 fish from the four ex situ populations. Eight microsatellite loci were analyzed, and data of sufficient quality were obtained for 189 samples. The markers had low to moderate polymorphism, with two to 15 alleles per locus across all populations. After correction for multiple testing, no population showed significant deviations from Hardy–Weinberg expectations, linkage disequilibrium between loci, or a significant inbreeding coefficient.

All six populations were significantly differentiated in pairwise comparisons, with the highest FST values consistently involving Jesuitenbach. Bayesian clustering identified two principal groups: Jesuitenbach formed a distinct cluster, while Fadenbach and all four ex situ populations formed another. Excluding Jesuitenbach from the analysis, each captive population was largely distinct, although Fadenbach fish showed assignment to all four ex situ clusters. Principal component and discriminant analyses also separated Jesuitenbach consistently from the other populations.

The linkage-disequilibrium method estimated contemporary effective population size at 36.9 for Fadenbach, with a 95% confidence interval of 24.1 to 77.6. The corresponding Jesuitenbach point estimate was infinite, with a 95% confidence interval of 220.0 to infinity. The researchers cautioned that the infinite estimate reflects a limitation of the method and available marker resolution when effective population size exceeds what can be estimated, rather than evidence of an exceptionally large population. Neither wild population showed significant heterozygote excess in bottleneck testing, so the analysis did not provide evidence of a very recent severe reduction in effective population size.

A comparison with Fadenbach data collected in 2011–2015 found broadly similar neutral diversity about a decade later. Rarefied allelic richness standardized to 20 individuals was 4.25 in the present study, compared with 4.37 previously, while observed heterozygosity was 0.538 and 0.523, respectively, and expected heterozygosity was 0.549 and 0.500. The authors said this apparent stability should not be interpreted as demographic security: neutral genetic measures can respond more slowly than census size to recent or gradual declines, and bottleneck tests have limited power with a modest number of loci and samples.

Field evidence indicates that the Fadenbach population remains in immediate hydrological difficulty. No fish were detected during Habitats Directive monitoring in summer 2023 after extensive desiccation in winter 2022 and spring 2023. Surveys in 2024 and 2025 captured 34 and 47 individuals, respectively, and the 47 fish captured in 2025 were moved to a dedicated conservation pond at the Donau-Auen National Park. Declining groundwater levels have been linked to drainage, intensive agriculture, Danube riverbed incision, and climate-driven changes in precipitation and evapotranspiration. Emergency supplementation with water from Danube side arms may improve connectivity temporarily but can also introduce fish, including pumpkinseed and topmouth gudgeon, and increase sediment inputs.

The four analyzed ex situ stocks all clustered with Fadenbach and were distinct from Jesuitenbach, supporting their documented Fadenbach origin and showing no detectable admixture from another source. They nevertheless differed significantly from one another and from the wild source, consistent with founder effects and subsequent drift. The original numbers were approximately 15–20 fish for pond Wanzenböck, about 12 for pond Engelhartszell, 50 for the Vienna Zoo, and unknown for pond Pekny. The authors recommend integrating individuals from all four lines in future breeding programs to maximize diversity and reduce inbreeding, together with continued genetic monitoring. For the wild populations, they emphasize hydrological restoration, drought refuges, separate management of the genetically distinct units and, for Fadenbach, avoidance of supportive stocking under current conditions. These conclusions are based on neutral microsatellite markers, which cannot assess adaptive diversity or fully resolve functional genetic differences.

Subject of Research: Genetic differentiation and effective population size of Austria’s remaining wild European mudminnow populations

Article Title: Small, isolated, and critically endangered: conservation genetics of the European mudminnow ( Umbra krameri ) in Austria

Article References: Donabaum, R., Jung, M., Ratschan, C., & Koblmüller, S. (2026). Small, isolated, and critically endangered: conservation genetics of the European mudminnow (Umbra krameri) in Austria. Nature Conservation, 65, 115-134. https://doi.org/10.3897/natureconservation.65.188874

Image Credits: AI Generated

DOI: 10.3897/natureconservation.65.188874

Keywords: European mudminnow, Umbra krameri, conservation genetics, microsatellite markers, effective population size, Fadenbach, Jesuitenbach, Austria, floodplain habitats, genetic differentiation, Small, isolated

The study, published in iScience, was led by Daniel García-Souto and Sofía Consuegra, with ancient DNA laboratory work carried out in the Harvard Medical School laboratory of David Reich, one of the leading figures in paleogenomics. The team extracted DNA from eight ancient vertebrae, most likely the remains of salmon consumed by humans at the cave. Endogenous DNA content varied considerably across samples, from 5.5 percent to 61.7 percent, and although nuclear genome coverage was extremely low, averaging between 0.0044-fold and 0.0339-fold, the mitochondrial genomes were recovered at usable depths for seven of the eight specimens. From the nuclear data, the researchers identified 58,341 reliable single nucleotide polymorphisms, of which 1,419 could be intersected with modern European SNP array datasets for population-level comparisons.

The mitochondrial results delivered the first surprise. All of the ancient individuals carried the AABBA haplotype, a maternal lineage that is now common in Northern Europe but was historically rare in Cantabrian rivers before the population crashes and stocking programs of the 1970s and 1980s. Phylogenetic analysis placed the ancient Iberian mitogenomes closest to modern salmon from southern England and western France, including haplotypes characteristic of rivers such as the Teign and the Allier, rather than with the lineages currently found in the river Asón. This pattern points to what the authors describe as a cryptic glacial refugium for Atlantic salmon during the Last Glacial Maximum, connecting the Iberian refuge to other putative refugial populations in Britain and France.

Nuclear genome data told the same story from an independent angle. When the ancient samples were projected onto a principal component space defined by modern European salmon, the first axis separated Baltic Sea populations from Atlantic European ones, while the second captured a well-known latitudinal gradient. The ancient Iberian fish did not cluster with modern Cantabrian salmon. Instead, they aligned with Northern European populations, particularly those from the British Isles, and admixture analyses showed that they share ancestry components with British and Norwegian populations that are absent or rare in today’s Iberian salmon. Even when the analysis was restricted to transversion SNPs alone, a strategy that guards against postmortem damage artifacts, the ancestry patterns held firm.

Because ancient DNA is notoriously prone to degradation and data loss, the team went to unusual lengths to rule out methodological artifacts. They simulated increasing levels of missing data, from 40 to 90 percent, and postmortem cytosine deamination damage, from 1 to 10 percent, in modern pseudohaploid genotypes before projecting them onto the same principal component space. Even under the most extreme missingness scenario, the 95th percentile of simulated displacement was roughly twelve times smaller than the observed separation between ancient and modern Cantabrian samples, and damage simulations produced displacements 31 to 52 times smaller. The genetic discontinuity, in other words, is far too large to be an artifact of damaged, incomplete ancient DNA.

What could explain an eighteen-thousand-year break in genetic continuity? The authors are careful to frame the finding as a difference in broad-scale allele-frequency structure rather than proof of direct ancestry or complete population replacement, given the vast temporal gap between the samples. Several non-mutually exclusive processes could be at work: demographic declines, genetic drift, selection, and the effects of historical stocking with a limited number of breeders, all of which have reshaped contemporary Iberian populations. Local population replacement cannot be entirely excluded, yet the continuous presence of salmon remains at El Mirón before and after the Last Glacial Maximum, together with historical records, suggests that a salmon population has persisted in the river Asón without interruption. The most likely interpretation is that thousands of years of natural and human-driven change have progressively overwritten the original genomic signature.

The ancient genomes also preserved traces of adaptation. Among the variants shared with modern salmon, the team identified eleven SNPs showing evidence of selection in contemporary populations, linked to roughly 140 candidate genes. One high-impact mutation in the hspe1 gene, which encodes a major heat shock protein involved in mitochondrial stress response, showed a marked allele frequency difference between southern and northern modern populations. Another, in the immune-related ifi44L gene, introduces a premature stop codon and also displays a significant north-south frequency shift. Although the key mutations at vgll3 and mMEP-2, the two loci best known for controlling age at sexual maturity in Atlantic salmon, could not be directly genotyped in the ancient samples, linked variation in half of the ancient individuals suggests that early-maturation haplotypes may already have been present in post-glacial Iberian salmon. A nonsynonymous substitution in the mitochondrial ND4 gene, previously identified as being under positive selection, was carried by seven of the eight ancient specimens.

Diversity estimates added a sobering dimension. Corrected mitochondrial nucleotide diversity in the ancient population was about twice that of the contemporary river Asón population, and the estimated female effective population size, at a mean of 1,548 individuals, was significantly higher than the modern estimate of 731. The ancient value fell in the lower-to-intermediate range compared with other European rivers, well below giants like the Rynda in Russia and the Teno in Norway, which exceed 3,000, but far above the collapsed southern populations of today. This pattern mirrors the more stable Northern European populations and contrasts sharply with the low current nuclear effective population sizes documented across Southern Europe, underscoring how severely recent bottlenecks have eroded Iberian salmon diversity.

The broader lesson extends well beyond salmon. Contemporary genomes are routinely used as proxies for a species’ evolutionary history, but this study demonstrates that they can be profoundly misleading, especially in species that have suffered declines, bottlenecks, and intensive management. Modern Iberian salmon are not living fossils of the post-glacial refuge; they are the product of millennia of drift, selection, migration, and, most recently, overexploitation, habitat fragmentation, climate change, and stocking. Without the ancient baseline, the deep history of the Iberian refuge would have been invisible, and the roles of natural post-glacial processes versus anthropogenic impacts would have remained hopelessly entangled.

For conservation, the implications are immediate. Southern European salmon populations are critically endangered, and reintroduction and stocking decisions are often made using contemporary genetic data alone. An ancient DNA baseline offers an evolutionary yardstick against which present-day diversity can be measured, helping managers distinguish what has been lost recently from what was never there. The authors acknowledge the limitations of their dataset, including the small sample size, low nuclear coverage, and the fact that all ancient individuals came from a single archaeological site, and they call for broader sampling of ancient salmon with higher-coverage genomes. Even so, the message from El Mirón Cave is clear: the past is a different country, and its salmon were not the salmon we know. To understand and save what remains, scientists must read the genetic record written in bones eighteen millennia old.

Subject of Research: Ancient DNA analysis of Upper Paleolithic Atlantic salmon from Iberia and its implications for post-glacial phylogeography and conservation

Article Title: What modern genomes overlook: Ancient DNA rewrites the phylogeography of European atlantic salmon ( Salmo salar )

Article References: García-Souto, D., Mallick, S., Barreiro-Docío, E., Rohland, N., Kearns, A. B., Saura, M., Garcia de Leaniz, C., Straus, L. G., González Morales, M. R., Reich, D., & Consuegra, S. (2026). What modern genomes overlook: Ancient DNA rewrites the phylogeography of European atlantic salmon (Salmo salar). iScience, 29(11), Article 117875. https://doi.org/10.1016/j.isci.2026.117875

Image Credits: AI Generated

DOI: 10.1016/j.isci.2026.117875

Keywords: ancient DNA, Atlantic salmon, Salmo salar, phylogeography, glacial refugium, Iberian Peninsula, El Mirón Cave, population genetics, mitochondrial genomes, conservation, Last Glacial Maximum, effective population size

The research team, led by Marina Brasó-Vives and Diego A. Hartasánchez and including colleagues working in France and Switzerland, set out to resolve a puzzle that had been building in the literature for years. Earlier genomic surveys of amphioxus species had hinted at extraordinarily high diversity, but such estimates are notoriously sensitive to methodological choices. Assembling and reading the genome of an organism with so many heterozygous positions is technically challenging, because the two haplotypes inherited from an individual’s parents can differ so much that standard assembly pipelines may confuse them or collapse variants. The new work therefore aimed not only to measure diversity but to do so with an accuracy that could withstand scrutiny, and to explain the biological processes that could generate and maintain such extreme variation in a natural population.

To achieve this, the researchers leveraged whole-genome sequencing data from multiple individuals sampled at two geographically distant locations, one in the Atlantic and one in the Mediterranean Sea. This sampling design was deliberate. Adult amphioxus are sedentary burrowers that live partially buried in sandy substrates, filter-feeding in the water column only briefly, and they form localized settlements with very limited mobility as adults. If genetic diversity were shaped primarily by local processes, populations separated by hundreds of kilometers of coastline and an entire sea basin should show measurable differences. Instead, the team found that population differentiation between the Atlantic and Mediterranean samples was minimal, a result that immediately pointed to extensive gene flow connecting even the most distant adult settlements.

The measurement of heterozygosity itself deserves technical attention, because it is the central quantity of the study. Heterozygosity describes the proportion of positions in the genome where the two copies carried by an individual differ. An average of 2.73 percent means that tens of millions of single nucleotide differences exist between the maternal and paternal haplotypes of a single amphioxus. Such values rival or exceed those reported for many celebrated hyper-diverse organisms, including certain marine fishes and invertebrates with enormous census sizes. The authors confirmed that their estimates were consistent with previous measurements in other amphioxus species, suggesting that extreme diversity is a shared property of the lineage rather than a peculiarity of one population or one sequencing effort.

Explaining this diversity required distinguishing between two broad classes of evolutionary explanation. High heterozygosity can arise when two deeply diverged lineages hybridize, a scenario in which an individual inherits chromosomes from ancestral populations that separated long ago, producing a mosaic genome with ancient differences locked into every cell. Alternatively, high diversity can simply reflect a very large effective population size, the number of breeding individuals that governs how quickly genetic variation is lost through random drift. In small populations, drift purges variation; in vast ones, mutations accumulate over millions of generations and persist, inflating heterozygosity without any need for admixture between diverged lineages.

To separate these hypotheses, the team combined phylogenetic analyses with population genetic simulations. The phylogenetic approach examined the relationships among genome sequences to determine whether amphioxus genomes show the signatures expected from past population structure or admixture, while forward and backward simulations modeled how heterozygosity, differentiation, and genealogical patterns would evolve under different demographic scenarios. The verdict was clear: the elevated genomic diversity of the European amphioxus is primarily driven by a large effective population size. In other words, this is not a hybrid swarm or a relic of ancient population splits but the natural consequence of an enormous number of reproducing individuals maintaining variation across the species’ broad ecological range.

This conclusion raises an obvious question. If adults barely move, how does genetic variation stay evenly distributed across a range spanning the Atlantic and the Mediterranean? The answer lies in the animal’s early life history. Amphioxus reproduce by releasing gametes into the water, and the resulting larvae are planktonic, drifting with ocean currents for extended periods before settling into the sediment as juveniles. The study’s findings indicate that this long-distance larval dispersal is sufficient to generate a near-panmictic population structure, a term describing a population in which mating occurs essentially at random across the entire range, with no meaningful genetic barriers between distant localities. The ocean itself, in effect, functions as the amphioxus’s long-distance transport system, mixing genes on a scale that the sedentary adults never could.

The phrase in the study’s title, at the edge of panmixia, captures the nuance of the result. The population is not perfectly panmictic, and subtle structure may exist, but differentiation is so low that the species across its sampled range behaves, for most population genetic purposes, as a single interbreeding unit. This has practical implications for how the species should be studied and managed. Conservation assessments that treat Atlantic and Mediterranean settlements as separate units would misread the biology, since the larvae continuously homogenize the gene pool. It also matters for laboratory science: amphioxus has become an important model organism for evolutionary developmental biology, and knowing that wild individuals carry extraordinarily diverse genomes informs how researchers should interpret crosses, assemblies, and comparisons between laboratory strains and wild populations.

Beyond amphioxus itself, the study speaks to a broader theme in modern evolutionary genetics: the growing recognition that effective population size, sustained over deep time, is one of the most powerful determinants of genomic diversity. Species with vast, stable marine populations can accumulate and retain levels of variation that land-based animals with smaller or fluctuating populations rarely approach. The amphioxus result also demonstrates the value of pairing empirical sequencing with simulation-based inference, because raw measurements of heterozygosity alone cannot distinguish a large stable population from an admixed one. By combining both approaches, the authors converted a striking number, 2.73 percent, into a coherent biological story about larvae, currents, and drift.

There is also an evolutionary irony worth savoring. Amphioxus are often described as living fossils, conservative in body plan and seemingly unchanged for hundreds of millions of years, yet their genomes reveal a dynamic, well-mixed, and enormously variable population architecture. Morphological stasis and genomic exuberance are not contradictory; a species can look the same while its gene pool churns with variation. As sequencing costs fall and accurate haplotype-aware analyses become routine, researchers expect more animals to join amphioxus in the hyper-diverse club, forcing a rethinking of what typical animal genomes look like. For now, the European amphioxus stands as a reminder that some of the richest genetic libraries on the planet are hidden in plain sand, stirred every generation by the patient mixing of the sea.

Subject of Research: Genomic diversity and population structure of the European amphioxus Branchiostoma lanceolatum

Article Title: The highly heterozygous European amphioxus ( Branchiostoma lanceolatum ) at the edge of panmixia

Article References: Brasó-Vives, M., Hartasánchez, D. A., Pulido, A., Bertrand, S., Escriva, H., & Robinson-Rechavi, M. (2026). The highly heterozygous European amphioxus (Branchiostoma lanceolatum) at the edge of panmixia. PLOS Genetics, 22(9), e1012293. https://doi.org/10.1371/journal.pgen.1012293

Image Credits: AI Generated

DOI: 10.1371/journal.pgen.1012293

Keywords: amphioxus, Branchiostoma lanceolatum, genetic diversity, heterozygosity, population genetics, panmixia, larval dispersal, effective population size, whole-genome sequencing, marine invertebrates, gene flow, PLOS Genetics

The research team, led by Alma Račkauskaitė of the Department of Animal Breeding and Reproduction, combined two very different kinds of data. The first was a pedigree dataset covering 22,666 horses drawn from the studbooks of all five populations, provided by the Lithuanian Agricultural Data Center. The second was a genetic dataset of 1,293 horses based on parentage verification tests using blood group and blood protein markers, a technology introduced in Lithuania in 1985 and applied for decades in breeding control. Although blood typing has been replaced in many countries by DNA-based methods, the standardized long-term dataset it produced allowed the researchers to evaluate genetic relationships within and between populations with a consistency that few national archives can match.

The pedigree analysis revealed a sharp divide between closed and open breeding systems. Pedigree completeness six generations deep was highest in the closed Zemaitukai population at 96.9 percent, followed by the Trakehner at 82.0 percent and the Arabian at 72.4 percent. The open Baltic Warmblood and Lithuanian Warmblood populations showed far lower completeness, at 39.9 percent and 54.5 percent respectively, reflecting the frequent use of imported animals whose pedigrees extend back only a few generations in national records. The number of founders told the same story from the opposite direction: just eight in the Arabian and 23 in the Zemaitukai, against 431 and 592 in the Baltic and Lithuanian Warmbloods, consistent with their open, internationally connected breeding programs.

Perhaps the most technically interesting result concerns the effective population size, a key measure of how fast a population is losing genetic variation. The researchers calculated it in two ways: from the numbers of breeding males and females, and from the rate of inbreeding per generation. For the Trakehner, with 78 reproductive mares and 21 stallions, the effective population size came out at 211, with moderate inbreeding of 0.0373 and a very low rate of inbreeding per generation of 0.0033, indicating controlled mating strategies. The open populations showed far higher effective sizes based on breeding animal counts, 851 for the Baltic Warmblood and 758 for the Lithuanian Warmblood, but these figures collapsed when calculated from the inbreeding rate, dropping to 311 and 216. That gap of more than 60 percent signals hidden relatedness and unbalanced parental contributions that a simple headcount of breeders conceals.

The endangered Zemaitukai showed the most dramatic discrepancy of all. Its effective population size based on breeding animals was 223, but based on the rate of inbreeding it fell to just 19, reflecting strong inbreeding pressure, with an inbreeding coefficient of 0.234. This pattern echoes findings in other endangered horse breeds, such as the Hucul and Cleveland Bay, where estimates based on inbreeding rates revealed far more severe inbreeding than counts of breeding animals suggested. The lesson, the authors argue, is that effective population size estimates are highly sensitive to the method used, to pedigree completeness, and to mating patterns, and that conservation decisions should never rest on a single metric or on basic thresholds alone.

On the molecular side, the blood typing data covered 49 alleles at 12 blood group loci, plus five blood protein systems including albumin, transferrin, and serum esterase. Across all horses, the average observed heterozygosity was 0.475 and the expected heterozygosity 0.395, indicating moderate diversity. The most polymorphic locus, EAD, carried 12 alleles with an expected heterozygosity of 0.864. Within the Trakehner population specifically, the mean number of alleles per locus was 3.833 across all animals and 3.417 in the reference group of currently breeding animals. Crucially, observed heterozygosity in the Trakehner rose from 0.460 in the full dataset to 0.488 in the reference population, while expected heterozygosity increased from 0.375 to 0.392, evidence that recent breeding efforts are successfully preserving, and perhaps even improving, genetic diversity despite the constraints of a partly closed studbook.

The open populations showed the highest heterozygosity overall, as expected from their constant crossbreeding with imported stallions, but the Baltic Warmblood reference group showed a slight decline in effective allele numbers, hinting at potential erosion of rare alleles under stabilized selection. The Arabian population, by contrast, exhibited the lowest genetic variability of all, with observed heterozygosity of 0.441 in the total population and 0.444 in the reference group, confirming a narrow genetic base. Although the Arabian carried a relatively high total allele count, it also had the highest proportion of rare alleles and lacked several variants found in the other breeds, a signature of long-term breeding within a closed population.

The relationships among the populations emerged clearly from genetic distances, assignment tests, and multivariate analyses. The Trakehner was most closely related to the Baltic Warmblood and Lithuanian Warmblood, with Nei’s genetic distances of just 0.008 and 0.009 in the full dataset, reflecting historical and ongoing gene flow from Trakehner stallions into these open sport horse populations. In the assignment test, only 57.9 percent of all Trakehner horses were correctly assigned to their own population, with the remainder assigned mainly to the Lithuanian Warmblood and the Arabian, the latter reflecting the breed’s permitted Thoroughbred and Arabian ancestry. In the reference group, however, correct assignment rose to 62.1 percent, suggesting that the actively bred Trakehner subpopulation is becoming more genetically homogeneous and internally consistent.

The Arabian and Zemaitukai, by contrast, formed clear, isolated clusters in every analysis, from principal component plots to hierarchical clustering heatmaps. Fully 89 percent of Zemaitukai and 83 percent of Arabian individuals were assigned to their own populations, indicating strong genetic integrity and minimal external introgression. The principal component analysis explained 36.2 percent and 22.3 percent of total variation on its first two axes, with no single dominant marker driving the separation. The heatmap analysis also revealed that reference populations of the Baltic and Lithuanian Warmbloods clustered separately from the full historical gene pools of their own breeds, evidence of recent shifts in allele composition driven by selection, drift, or targeted breeding strategies. The moderate but rising differentiation between the Trakehner and Arabian, with the fixation index increasing from 0.015 to 0.021 in the reference dataset, suggests that structured breeding in recent years is strengthening boundaries between breeds.

The authors conclude that population structure, historical gene flow, and management practices jointly shape genetic variability, and their results point to concrete management actions: optimizing mating plans by balancing sire and dam contributions, monitoring inbreeding and effective population size trends, managing gene flow among the related Trakehner, Baltic Warmblood, and Lithuanian Warmblood populations, and developing targeted conservation strategies for the genetically distinct Zemaitukai and Arabian. The Trakehner’s relatively long generation interval of 12 years, typical of sport horse breeding, may itself help stabilize diversity by slowing genetic turnover. Encouragingly, from 2025 Lithuania has introduced national support for genetic testing and parentage verification of breeding horses, a move expected to open the door to microsatellite- and SNP-based analyses that will build on this blood-group legacy. For a breed whose numbers are falling but whose genes remain resilient, that combination of historical depth and modern tools may be exactly what sustainable breeding requires.

Subject of Research: Genetic diversity and population structure of Trakehner and other horse breeds in Lithuania

Article Title: Genetic variability and associations of Trakehner and other horse populations in Lithuania

Article References: Račkauskaitė, A., Šveistienė, R., Razmaitė, V., Jatkauskienė, V., & Marašinskienė, Š. (2026). Genetic variability and associations of Trakehner and other horse populations in Lithuania. Archives Animal Breeding, 69(2), 323-336. https://doi.org/10.5194/aab-69-323-2026

Image Credits: AI Generated

DOI: 10.5194/aab-69-323-2026

Keywords: Trakehner, Zemaitukai, Lithuania, genetic diversity, inbreeding, effective population size, pedigree analysis, blood group markers, horse breeding, conservation genetics, heterozygosity, studbooks

The research team, led by scientists at the University of Wollongong in Australia, combined systematic field surveys, population genomics and species distribution modelling to assess the conservation status of Fiji’s endemic Hylaeus bees. These tiny insects, averaging just 3.9 millimetres in body length, belong to a radiation of six canopy-specialist species found nowhere else on Earth. Unlike most bees, they carry pollen internally in their crops rather than on external hairs, and they appear to specialise on red-flowered canopy plants, a preference that challenges the long-standing assumption that bees cannot see red. Their small size likely limits their foraging ranges, making them particularly vulnerable to habitat fragmentation and forest disturbance.

Sampling these bees posed a formidable challenge. The team designed a stratified, randomised survey across Viti Levu, dividing the island into elevational bands and land-use categories, and generating 36 primary sampling sites along the road network, with 36 auxiliary sites as backups. At each site, crews of three to five people worked in parallel: one person always sweep-netting low vegetation with a standard net, and at least one person always deploying a specialised canopy net extending nine to fourteen metres into the treetops. This dual approach was essential, because traditional ground-level surveys systematically miss entire pollinator communities living in the canopy. Between April 14 and May 11, 2025, the team visited 54 locations and collected 101 Hylaeus specimens, dominated by the species Geissois superba and Metrosideros collina as floral hosts.

The elevational patterns were immediately striking. Hylaeus navai and H. veli were found only between 875 and 1,334 metres, while H. derectus ranged from 371 to 900 metres and H. albaeus from 3 to 923 metres. Critically, of the 26 randomly generated sites below 600 metres, the team collected only a single Hylaeus specimen, despite nearly an hour of average sampling effort per site. This near-total absence from lowlands, where historical records from 1970 to 2016 show these bees were once present, is deeply concerning and points to possible extirpations across Fiji’s lowland forests, which make up 78 percent of the country’s forested area.

To read the demographic history written into the bees’ genomes, the researchers sequenced genome-wide single nucleotide polymorphisms from 94 specimens using Diversity Arrays Technology, filtering the raw data down to 4,839 high-quality loci for the focal species H. navai. They supplemented this with mitochondrial COI barcoding from 16 pinned representatives, sequenced rapidly using Oxford Nanopore technology at the Australian National University. The nuclear data revealed a single, panmictic population of H. navai across the highland forests: principal component analyses, discriminant analyses and ancestry coefficient estimates all pointed to one interbreeding population, with no significant isolation by distance. This genetic uniformity likely reflects ongoing gene flow through the contiguous highland forest, though the COI phylogeny revealed clear divergence between island populations on Viti Levu and Taveuni, hinting that structure emerges at larger geographic scales.

The most dramatic results came from coalescent-based demographic reconstruction using Stairway Plot 2, which infers past effective population size from the site frequency spectrum. Calibrated with a honey bee mutation rate and an estimated six generations per year, based on the life history of the related Hawaiian species Hylaeus anthracinus, the reconstruction revealed a staggering trajectory. A modest decline of about 7 percent began around 1550, plausibly linked to the spread of slash-and-burn agriculture, first evidenced in Fiji around 2,000 years ago. Then, from roughly 1874, coinciding with European colonisation, the declines accelerated sharply. Three separate ten-year windows each saw losses that would individually justify IUCN Red List categories: a 61 percent drop between 1933 and 1942, a 76 percent drop between 2002 and 2011, and an 82 percent drop between 2016 and 2025. Taken together, the effective population size fell by approximately 99 percent over 150 years, with even the most conservative confidence intervals indicating a decline of at least 81.6 percent.

The timing of these crashes aligns with known ecological upheavals. Fiji’s closed natural forests declined by 21 percent between 1991 and 2007, largely through urban and agricultural expansion. The invasive African tulip tree, introduced as an ornamental in the 1930s, produces nectar toxic to honey bees and stingless bees, and as a red-flowering canopy tree it may act as an ecological trap for the red-flower-specialist Hylaeus. Species distribution models built with MaxEnt showed strong predictive performance, with suitable habitat for H. navai confined to just 1.4 to 2.4 percent of Fiji’s terrestrial area, concentrated at mid-to-high elevations, while the African tulip tree’s suitable habitat, covering 13.4 percent of the study area, was largely inverse to the bee’s, concentrated in the lowlands the bees appear to have abandoned.

Cyclones add another layer of threat. The 2020 population crash coincides with Tropical Cyclone Harold, a category four storm that struck in April of that year. The team also noted that a 2015 specimen of H. albaeus from Rakiraki could not be recollected after Tropical Cyclone Winston devastated the area in 2016, despite repeated targeted efforts in subsequent years. Cyclones destroy canopy cover, fell nest-bearing stems and create disturbed habitat that favours African tulip tree establishment, and projected increases in cyclone intensity under climate change could accelerate these declines further. Warming temperatures, rising by 0.018 to 0.024 degrees Celsius per year in daily maxima across Fiji, may also be narrowing the bees’ suitable elevational niche, as experimental work on related megachilid bees has shown reduced emergence rates at warmer, lower elevations.

Contemporary effective population size estimates from linkage disequilibrium methods were inconsistent across allele frequency thresholds, ranging from 121 to 418, and the researchers chose the most conservative estimate of 121 as the most reliable. Either way, the numbers are extraordinarily small for a species that appears to be the most commonly encountered Hylaeus in Fiji. The authors argue that these findings should form the basis of a Critically Endangered listing for H. navai under IUCN criterion A2b, and they emphasise that the declines show no sign of abating. As populations shrink, proportional losses can accelerate, creating a demographic ratchet that becomes progressively harder to reverse.

Beyond the immediate conservation implications for Fiji, the study offers a transferable framework for detecting cryptic declines in understudied ecosystems worldwide. Canopy-specialist Hylaeus bees are expected to be widespread across the Pacific, linking Australian and French Polynesian taxa, and the threats documented here are likely to affect relatives throughout the region. Only 2.6 percent of the world’s 21,000 described bee species have been assessed with sufficient data for the IUCN Red List, and research remains heavily skewed toward North America and Western Europe. The authors argue that systematic, multi-strata sampling paired with molecular techniques provides a roadmap for uncovering hidden biodiversity losses, particularly for forest pollinators that traditional ecological surveys never encounter. Without such integrative approaches, entire radiations of specialist pollinators could collapse before anyone knows they exist.

Subject of Research: Population genomics and conservation status of endemic canopy-specialist Hylaeus bees in Fiji

Article Title: Genomics Reveal Population Crash and Range Contraction in Elusive Fijian Hylaeus Bees

Article References: Edwards, T. A., Esquerré, D., Johnston, N. P., Galvin, S., Maxwell, N. L., Encinas‐Viso, F., & Dorey, J. B. (2026). Genomics Reveal Population Crash and Range Contraction in Elusive Fijian Hylaeus Bees. Ecology and Evolution, 16(10), Article e74366. https://doi.org/10.1002/ece3.74366

Image Credits: AI Generated

DOI: 10.1002/ece3.74366

Keywords: Hylaeus bees, Fiji, population genomics, pollinator decline, canopy ecology, effective population size, species distribution modelling, invasive species, African tulip tree, IUCN Red List, tropical forest, conservation

The study focused on the Late Iron Age and Early Medieval period, an era that Finnish archaeologists have traditionally called the “Crusade Period,” reflecting the long-held assumption that Swedish kings launched violent military campaigns to convert the local population to Christianity. Modern scholars largely regard these so-called crusades as later literary constructions, and the researchers instead use the term Early Medieval Period to describe the gradual emergence of Christian institutions and Swedish political influence. During this time, Finland was not a unified state but a patchwork of culturally distinct regions, including a coastal zone with strong Scandinavian ties and an inland zone known as Häme, whose material culture blended western and eastern traditions.

Recovering ancient DNA from Finland is notoriously difficult. The country’s acidic soil rapidly destroys unburnt human remains, and before this study only 26 ancient genomes with sufficient genome-wide coverage had ever been published from the entire country. The team, led by researchers at the University of Turku and the Max Planck Institute for Evolutionary Anthropology, generated new target-capture data from 38 individuals buried at 17 archaeological sites, carefully screening each genome for contamination and excluding four that could not be reliably authenticated. The resulting dataset, analysed alongside biobank genomes from thousands of present-day Finns, provides the most detailed genomic portrait of pre-modern Finland ever assembled.

The first major finding concerns the relationship between the coastal and inland zones. Despite their documented differences in economy, burial practice, and material culture, the ancient populations of the two zones were genetically indistinguishable. Statistical analyses of allele frequencies showed that the coastal and inland groups formed a single genetic clade, excluding both modern and other ancient comparison populations. Proximal ancestry modelling revealed that both groups could be described as a three-way mixture of Scandinavian, Baltic Iron Age, and Sámi-related ancestry, with the inland group showing a slight, though not statistically significant, tilt toward the Siberian-associated component that characterises Uralic-speaking populations further east.

That genetic unity, however, did not last. When the researchers compared the ancient genomes with modern inhabitants of the same regions, a striking asymmetry emerged. People living in the inland zone today are the direct descendants of their Early Medieval predecessors: rare identity-by-descent segments shared between ancient and modern genomes map onto a broad regional pattern of connectedness across the inland zone, demonstrating nearly a millennium of population continuity. This extends earlier work on medieval cemeteries in Pirkanmaa from a local phenomenon to a regional one, showing that the persistence is a feature of the whole inland gene pool rather than an artefact of a few closely related burial sites.

The coastal zone tells a completely different story. Present-day coastal Finns carry roughly 25 percentage points more Scandinavian-derived ancestry than their Early Medieval counterparts, and their Baltic-derived ancestry has all but vanished. Haplotype-based analyses found no discernible pattern of shared DNA segments between the ancient coastal population and modern residents of the same municipalities, indicating a genuine population turnover rather than gradual drift. The researchers attribute this shift primarily to large-scale emigration from Sweden, most likely concentrated in the late thirteenth and early fourteenth centuries, when the expanding Kingdom of Sweden consolidated its rule over what medieval documents called Österland, the eastern lands. Crucially, the genetic data show that this immigration was confined to the coast: Swedish settlement did not penetrate the hinterland, and the consolidation of Swedish authority inland appears to have proceeded through administrative and ecclesiastical structures rather than through mass movement of people.

The study also reconstructed the demographic trajectory of the region using a technique called time-transect effective population size estimation, which exploits shared DNA segments among individuals who lived at different times. The results show a population in rapid expansion: the effective population size of southwestern Finland grew from roughly 2,500 individuals around 800 CE to approximately 13,000 by 1250 CE, a fivefold increase in four and a half centuries. This boom coincides with the introduction of new plough technologies from Scandinavia and the Baltics, which allowed farmers to break the heavy clay soils that dominate the region, as well as with pollen and macrofossil evidence for expanding grasslands from the mid-1100s. Notably, the researchers found no evidence of consanguinity: while many individuals carried short runs of homozygosity consistent with distant parental relatedness in a small population, none showed the long stretches that would indicate mating between close relatives, suggesting that social mechanisms to avoid inbreeding were already in place.

Perhaps the most visually compelling result is a network map of shared DNA segments connecting 103 ancient individuals from around the Baltic Sea, from the Viking Age to the Early Modern period. The network resolves into three clusters, Scandinavian, Slavic, and Finnish, linked by a single Viking Age individual from Gotland whose ancestry was previously modelled as more than 90 percent Finnish-like. When adjusted for sample size, Finland shared its strongest connections with Gotland, Latvia, and Russia, mirroring the archaeological record of trade, diplomacy, and intermarriage that tied coastal Finland into the exchange systems of the medieval North. The Finnish word for money, raha, originally meant fur pelt, a linguistic fossil of the fur trade that likely drove much of this connectivity.

Some of the individual connections are remarkably specific. A genetically female individual buried at Laukskola on the Daugava river in Latvia, dated to 1031 to 1147 CE and likely a speaker of the nearly extinct Liv language, shares DNA segments with two individuals from Early Medieval Finland consistent with a relationship as close as sixth cousins. Because the three were largely contemporaneous, their shared ancestry points to a common forebear who moved between the regions within living memory of the burials. Even more striking, the researchers recovered IBD links between Early Medieval Finns and two crew members of the Kronan, a Swedish warship that sank at the Battle of Öland in 1675. Historical records attest that officers for the Kronan were recruited from Finland, and the genetic evidence corroborates that these sailors were either Finnish themselves or recent descendants of Finnish immigrants to Sweden.

The study does have limits. Because all the sampled burials predate the main wave of Swedish immigration, the analysis can only establish that the coastal shift occurred after roughly 1300 CE, and the researchers note that genomes from the fourteenth to sixteenth centuries, particularly from sites along the axis between the two zones, will be needed to trace the migration in finer detail. The Siberian ancestry cline that runs from northeast to southwest across Finland, likely reflecting ancient admixture with Sámi-related groups, also remains only partially resolved, since no ancient genomes from eastern Finland were available. Nevertheless, the big picture is clear. Early Medieval southwestern Finland was not a remote periphery waiting to be conquered, but a genetically homogeneous and rapidly growing population firmly embedded in the circum-Baltic world. When Swedish power arrived, it reshaped the coast through settlement while leaving the inland gene pool untouched, a dichotomy whose imprint is still visible in the DNA of Finns today, nearly eight centuries later.

Subject of Research: Population genomics and demographic history of Early Medieval southwestern Finland using ancient DNA

Article Title: Population genomics, demography, and circum-Baltic connectivity of Early Medieval southwestern Finland

Article References: O’Sullivan, R. J., Nordfors, U., Saari, N.-J., Majander, K., Taavitsainen, J.-P., Salo, K., Rohrlach, A. B., Salmela, E., Lamnidis, T. C., Traverso, L., Krause, J., Peltola, S., & Onkamo, P. (2026). Population genomics, demography, and circum-Baltic connectivity of Early Medieval southwestern Finland. Genome Biology, 27(1), Article 288. https://doi.org/10.1186/s13059-026-04277-7

Image Credits: AI Generated

DOI: 10.1186/s13059-026-04277-7

Keywords: ancient DNA, Finland, Early Medieval period, population genomics, identity-by-descent, Scandinavian ancestry, Viking Age, Baltic Sea, effective population size, Swedish migration, Sámi ancestry, archaeogenetics

The research team, led by Olivier Lepais of BIOGECO at the University of Bordeaux and INRAE, together with Maya Gonzalez of ISPA and Marie-Lise Benot, set out to answer a question that population geneticists have rarely tackled at the scale of an entire ecological community. Most studies of demographic history examine a single species at a time, inferring past population trajectories from patterns of genetic variation. But species that share a habitat are exposed to the same storms, the same shifting sands, and the same episodes of habitat loss. If past environmental changes were strong enough, the argument goes, they should leave comparable genetic fingerprints across many unrelated species at once. Testing that idea required a sampling effort of unusual breadth: the researchers developed species-specific microsatellite markers for eight dune plants and genotyped 3,116 individuals collected along the French Atlantic coast.

Microsatellites, also known as simple sequence repeats, are stretches of DNA in which a short motif of two to six base pairs is repeated over and over. Because the number of repeats changes relatively quickly through mutation, microsatellites are superb recorders of recent demographic events. Allelic richness, the number of distinct repeat-length variants circulating in a population, responds within generations to changes in effective population size, the genetically meaningful size of a population that determines how fast diversity is lost. The catch is that this fast mutation rate also means microsatellites saturate over longer timescales, blurring signals from the deeper past. To recover that deeper history, the team turned to the DNA sequences flanking each microsatellite, where point substitutions accumulate far more slowly. Heterozygosity at these flanking sites preserves a memory of ancient population sizes that the rapidly evolving repeat tracts have long since overwritten.

Combining the two marker types in a single inference framework is what gives the study its temporal reach. The researchers built a simple demographic model in which each population underwent a single change in size at some point in the past, and they used coalescent simulations to generate genetic data under a wide range of scenarios: different ancient and modern effective population sizes, different timings of the change, and different mutation rates. These simulated datasets were then compared with the observed genetic data using approximate Bayesian computation, or ABC, a family of methods that sidesteps the need for an analytical likelihood by simulating millions of datasets and retaining those that resemble the real one. In a further refinement, the team employed ABC random forests, a machine learning approach in which summary statistics computed from the genetic data act as predictors of the underlying demographic parameters, allowing the inference to weigh which combinations of statistics carry the most information.

The results were reassuringly clear on the quantities that matter most. Recent effective population sizes were well recovered, informed chiefly by allelic richness at the microsatellite repeats, while ancient effective population sizes were reliably estimated from heterozygosity in the flanking sequences. The timing of the demographic event proved harder to pin down for any single species, but the combined summary statistics, which mix microsatellite variation with flanking substitutions, sharpened the estimates considerably. This division of labor between fast and slowly mutating markers is the technical heart of the paper, and it demonstrates that sequencing-based microsatellite genotyping can do double duty: the same sequencing reads that yield repeat counts also yield the surrounding nucleotide variation needed to anchor the timeline.

What emerged from the analysis was a demographic signature shared across the community. Most of the eight species showed a strong and roughly synchronous decline in effective population size, with the timing of the crash estimated at between 135 and 450 years before the present. That window overlaps squarely with the Little Ice Age, the cold period lasting roughly from the fourteenth to the nineteenth century during which the North Atlantic storm belt intensified. For the Aquitaine coast, historical and geological records document exactly what intensified storminess means: waves of sand mobilization, known as sand drift, that buried vegetation and rolled inland across the coastal plain. Previous work on late Holocene sand invasion along this coast, including studies of the Médoc peninsula and the wider Aquitaine basin, has mapped these dune incursions and linked them to cold climate events. The genetic data now provide a biological mirror of that geomorphological story.

The mechanism the researchers propose is habitat loss. Open sand dune vegetation, the early-successional communities that colonize bare, mobile sand, depends on exactly the disturbance regime that storms once provided. But when storm-driven sand drift became too intense, it likely wiped out most of the open dune habitat rather than creating it, squeezing the specialist plants into a narrow strip along the shoreline where they remain today. A community-level contraction of habitat translates into a community-level contraction of effective population size, and that is precisely the synchronous decline the genomes record. Because the eight species are ecologically distinct, with different life histories and dispersal strategies, their shared demographic trajectory is best explained by a shared external driver rather than by any species-specific process.

The study also carries a cautionary note for conservation. Effective population size, not census count, determines a population’s capacity to maintain genetic diversity and adapt to changing conditions, and the classic 50/500 benchmarks for short- and long-term viability are measured in these terms. A historical crash that reduced effective population sizes across an entire community constrains the evolutionary options of every member species, even those that appear locally abundant today. The authors argue that this legacy of past habitat loss will limit how sand dune plants respond to future environmental change, including the ongoing transformation of European dunes by stabilization, afforestation, and development. Restoration efforts, other researchers have argued, must specifically consider species that require open and early-successional dune habitats, and the new genetic evidence underscores why: these species may already be running on reduced genetic capital accumulated through centuries of contraction.

Methodologically, the paper joins a growing movement in population genetics toward joint analysis of different mutation classes at the same loci. Earlier work on rear-edge oak populations by members of the same team showed that combining microsatellite repeat variation with flanking sequence substitutions could illuminate complex demographic histories involving gene flow and vicariance. The present study extends that approach from a single species to a whole community, and from a proof of concept to a comparative framework. The researchers also made their raw data available, depositing low-coverage whole genome sequences used for marker development in the European Nucleotide Archive, alongside extensive supplementary analyses that test how marker number, sample size, and mutation rate estimates affect the reliability of the demographic inference.

For ecologists and conservation biologists, the broader message is that genomes can serve as community-level archives. When multiple species sharing a landscape tell the same demographic story, with the same timing and the same direction of change, the case for a common environmental cause becomes compelling in a way that single-species studies cannot achieve. The dune plants of southwest France, it turns out, all recorded the same stormy centuries in their DNA. Reading that record required 3,116 genotyped individuals, hundreds of newly developed markers, and a simulation framework capable of extracting timing from a mixture of fast and slow mutations, but the payoff is a demonstration that past climate-driven habitat loss left a coherent, measurable signature across an entire plant community, one that continues to shape its capacity to face the changes still to come.

Subject of Research: Shared demographic history of coastal sand dune plant communities inferred from microsatellites and flanking sequence variation

Article Title: Joint analysis of microsatellites and flanking sequences shows shared demographic response of coastal sand dune plant communities to past environmental changes

Article References: Lepais, O., Gonzalez, M., & Benot, M.-L. (2026). Joint analysis of microsatellites and flanking sequences shows shared demographic response of coastal sand dune plant communities to past environmental changes. Heredity. https://doi.org/10.1038/s41437-026-00881-2

Image Credits: AI Generated

DOI: 10.1038/s41437-026-00881-2

Keywords: population genetics, microsatellites, flanking sequences, approximate Bayesian computation, effective population size, coastal sand dunes, Little Ice Age, habitat loss, community ecology, Aquitaine coast, plant conservation, demographic history

The timing of the study could hardly be more consequential. Managing authorities in Norway and Sweden have decided to reduce the Scandinavian wolf population to approximately 170 individuals, a census size they consider sustainable. That decision rests in part on recent population viability analyses commissioned by the same authorities, which concluded that a population of this magnitude could maintain its genetic viability. The new pedigree-based analysis directly challenges those conclusions, questioning whether the scientific foundation for the cull quotas is sound.

At the heart of the study is a concept that conservation biologists regard as perhaps the single most important number in population genetics: the effective population size, abbreviated Ne. Unlike the census count of animals, the effective size captures how many individuals would be needed in an idealized population to produce the same rate of genetic drift, inbreeding, and loss of diversity as the real population actually experiences. In practice, Ne is almost always far smaller than the raw headcount, because not every animal breeds, sex ratios are rarely balanced, and reproductive success is unevenly distributed. The effective size determines the pace at which genetic diversity erodes and inbreeding accumulates, and it therefore governs both short-term extinction risk through inbreeding depression and long-term viability through the loss of adaptive potential.

What makes the new analysis unusually powerful is the quality of the underlying data. Since the Scandinavian wolf population was re-established by a handful of founders, researchers have meticulously reconstructed its complete pedigree, drawing on decades of field monitoring, DNA sampling, and individual identification. Raw source data drawn from the pedigree compilation published by Åkesson and colleagues in 2023 allowed the team to calculate Ne precisely for every year since the population’s founding, using four-year cohorts along a one-year moving window. Rather than inferring genetic health from statistical snapshots of DNA samples, the researchers could trace the actual reproductive paths of every known animal, an approach that removes much of the uncertainty that plagues conventional genetic estimates.

The results reveal a population whose effective size has remained persistently and critically low throughout its history. The Scandinavian population was founded by only a few individuals and, despite growing to several hundred animals in census terms, has never achieved an effective size compatible with widely accepted conservation genetic benchmarks. The population’s history includes a well-documented severe inbreeding depression episode in the late 1990s and early 2000s, when pups from closely related pairs suffered dramatically reduced survival, and a partial genetic rescue delivered by a single immigrant male from the Finnish-Russian population. Subsequent work has documented the genomic consequences of this intensive inbreeding, including elevated levels of harmful homozygosity across the genome.

The study also scrutinizes the assumptions of the recent simulation studies that inform current management, including minimum viable population analyses prepared for the Swedish Environmental Protection Agency. According to Mergeay and colleagues, those simulations greatly overestimate the effective size of the Scandinavian wolf population, likely because they fail to adequately account for the population’s peculiar and well-documented reproductive structure. Wolves live in territorial packs in which typically only the dominant pair breeds, a social system that dramatically inflates the gap between census numbers and effective size. When this mating structure is properly represented, the same census count translates into a far smaller effective population than the commissioned analyses assumed, and the projected timelines for inbreeding and diversity loss become correspondingly more alarming.

The implications reach beyond Scandinavia. Conservation genetics has long relied on rules of thumb, notably the 50/500 rule, which suggests that an effective size of at least 50 is needed to avoid short-term inbreeding depression and 500 to retain long-term evolutionary potential, with revised recommendations pushing the long-term figure considerably higher. A population managed at a census size of roughly 170 animals, with a pack structure that suppresses Ne far below the census count, falls short of these benchmarks by a wide margin. The findings echo warnings issued in 2022 in the journal Science, when prominent conservation geneticists argued that planned culls would endanger the Swedish wolf population, and they align with a growing body of evidence from other inbred wolf populations, including the famously inbred wolves of Isle Royale, where genetic erosion contributed to a population crash.

The study arrives amid a charged political and legal debate over wolf management in Europe. Wolf culling policies in both Norway and Sweden have drawn formal complaints under the Bern Convention on the conservation of European wildlife and natural habitats, and the European Court of Justice has recently clarified the legal yardstick of favourable conservation status in a wave of wolf-related cases. Under the EU Habitats Directive, member states must maintain populations at a status where they can thrive long term without being dependent on continued conservation measures, a standard that inherently involves genetic considerations. If the effective size of the Scandinavian population is genuinely too small for long-term persistence, the legal and scientific case for reducing it further becomes considerably harder to defend.

The authors emphasize that their findings do not merely refine an academic parameter; they strike at the usefulness of the very models being used to set quotas. If simulation studies overestimate Ne, they will systematically underestimate the rate of inbreeding and the speed of diversity loss, producing optimistic projections of viability that the real population cannot match. The researchers suggest that management informed by these flawed models risks steering the population into an extinction vortex, in which shrinking numbers accelerate inbreeding, inbreeding depresses survival and reproduction, and the resulting decline further shrinks the population. Recent theoretical work suggests such vortices can be driven as much by a shortage of beneficial mutations as by the accumulation of harmful ones, underscoring how difficult a genetically impoverished population is to rescue once diversity is gone.

For the Scandinavian wolf, the path forward suggested by the genetics is clear even if politically difficult: either the population must be allowed to grow substantially, or gene flow from the larger Finnish-Russian wolf population must be facilitated at a rate sufficient to counteract drift and inbreeding. The one-migrant-per-generation rule, long a staple of conservation genetics, may need to be exceeded in this case given the population’s extreme isolation and skewed reproductive structure. What the new study makes unmistakable is that the current management trajectory, a population capped at 170 animals justified by models that overestimate its genetic buffer, is incompatible with the population’s own pedigree. As the authorities finalize their reduction plans, they will have to reckon with a complete, individual-level record of every wolf that has lived in Scandinavia, and that record tells a story of a population living dangerously close to its genetic limits.

Subject of Research: Effective population size and genetic viability of the Scandinavian wolf population

Article Title: The effective size of the Scandinavian wolf population is too small for both short- and long-term conservation

Article References: Mergeay, J., Flagstad, Ø., & Waples, R. S. (2026). The effective size of the Scandinavian wolf population is too small for both short- and long-term conservation. Heredity. https://doi.org/10.1038/s41437-026-00877-y

Image Credits: AI Generated

DOI: 10.1038/s41437-026-00877-y

Keywords: Scandinavian wolf population, effective population size, inbreeding, conservation genetics, population viability analysis, genetic drift, wolf culling, pedigree analysis, Heredity, large carnivore management, genetic rescue, extinction risk

An international research team led by Arne Bielke and Elmira Mohandesan of the University of Vienna, working with colleagues in Sweden, Wales, the United States and New Zealand, generated genome-wide single nucleotide polymorphism data from Kaimanawa Horses and integrated these results with previously generated mitochondrial and Y-chromosome markers. The comparison set comprised 22 domestic breeds, allowing the researchers to place the feral population within the broader landscape of global horse genetic diversity. The study was conducted in collaboration with the Kaimanawa Heritage Horse society and with the informed consent of horse owners who provided hair samples, photographs and background information on individual animals.

The genetic story that emerged is one of multiple founding contributions layered on top of one another. Admixture analyses showed that Kaimanawa Horses share genetic components mainly associated with British pony lineages, Thoroughbreds, Arabians and draft breeds, a pattern consistent with historical records describing the varied stock that contributed to the population during the colonial era and afterwards. Rather than descending from a single narrow source, the herd represents a living archive of the mixed breeding practices of nineteenth and twentieth century New Zealand, when working horses of many types were moved across pastoral land and often left to fend for themselves.

Yet the same analyses also documented the genetic costs of isolation. The population exhibits reduced heterozygosity, elevated inbreeding and an effective population size estimated at fewer than 50 individuals, a threshold widely regarded by conservation geneticists as dangerously low for long-term viability. The researchers traced this erosion of diversity to the population’s isolation and to recent demographic contraction, driven in part by management interventions. Kaimanawa Horses are subject to periodic musters, in which animals are rounded up and removed from the ranges to keep the population within an officially mandated ceiling, a practice that inevitably influences which genes persist in the free-ranging herd.

One of the most technically revealing aspects of the study involved runs of homozygosity, the long stretches of the genome where an individual inherits identical DNA segments from both parents, signaling recent or ancient inbreeding. By measuring the inbreeding coefficient derived from these runs and stratifying them by length class, the team could distinguish between older inbreeding events and more recent mating among relatives. The results confirmed that Kaimanawa Horses carry a substantial burden of homozygous segments relative to many domestic breeds, underscoring how founder effects, small population size and restricted gene flow have combined to shape the population’s genomic landscape.

Population structure analyses identified two distinct genetic subgroups within the herd, suggesting that geography and management history have produced detectable internal differentiation. Horses captured in different zones of the Kaimanawa Ranges, including the Argo Valley, southern zones and a designated capture zone, showed patterns consistent with limited movement between groups. Linkage disequilibrium decay, a measure of how quickly genetic variants lose their statistical association with physical distance along chromosomes, provided further evidence of the population’s demographic trajectory, while historical estimates of effective population size reconstructed over roughly the last seventeen generations revealed a declining trend that has accelerated in recent generations.

Perhaps the most striking discovery came from the paternal line. Analysis of the male-specific region of the Y-chromosome in 26 stallions revealed private paternal haplotypes that are absent from modern breed reference panels, indicating that the Kaimanawa population has retained unique paternal diversity that has disappeared, or was never present, in the registered breeds used for comparison. Mitochondrial DNA analysis of the maternal side complemented this picture, placing Kaimanawa maternal lineages within the broader spectrum of global horse diversity while highlighting the population’s distinctiveness. Together, these uniparental markers demonstrate that feral populations can serve as reservoirs of genetic variation lost from managed breeding programs.

The implications for conservation and management are considerable. An effective population size below 50 places the herd in a category where loss of genetic variation and inbreeding depression, including reduced fertility and foal survival, become realistic concerns. The authors argue that genomic approaches of the kind used in this study can directly inform management strategies, for example by guiding which animals are retained or relocated during musters to preserve the two genetic subgroups and maximize the retention of the population’s rare alleles and unique haplotypes. Without such informed intervention, the very management practices designed to control the population’s ecological footprint could inadvertently erode the genetic legacy that makes it scientifically and culturally valuable.

Beyond New Zealand, the study offers a template for understanding how founder history, demographic processes and human management jointly shape the genomes of free-ranging animal populations around the world. Feral horses occupy a contested space between pest and heritage icon, and their management is often decided in the absence of genetic data. By demonstrating that a feral population can harbor both documented vulnerability and irreplaceable diversity, the Kaimanawa work makes a compelling case that conservation genomics belongs at the center of such debates. As the researchers conclude, these findings not only illuminate the past of one of New Zealand’s most iconic wild animals but also support future research and evidence-based stewardship of feral horse populations wherever they roam.

Subject of Research: Genomic analysis of demographic history and genetic diversity in New Zealand's feral Kaimanawa Horses

Article Title: Demographic history and management practices shape the genomic landscape of New Zealand’s feral Kaimanawa Horses

Article References: Bielke, A., Ardestani, S. S., Sharif, B., Orozco-ter Wengel, P., Fitak, R. R., Wallner, B., Wilson, K., & Mohandesan, E. (2026). Demographic history and management practices shape the genomic landscape of New Zealand’s feral Kaimanawa Horses. BMC Genomics. https://doi.org/10.1186/s12864-026-13345-y

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13345-y

Keywords: Kaimanawa Horses, feral horses, population genomics, conservation genomics, inbreeding, New Zealand, genetic diversity, Y-chromosome, effective population size, runs of homozygosity, horse breeds, population structure