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PubMed2014

Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies.

Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs (Danaus plexippus) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel only short distances. Here, we used microsatellite markers to assess genetic differentiation among 18 monarch populations and to determine worldwide colonization routes. Our results indicate that North American monarch populations connected by land show limited differentiation, probably because of the monarch's ability to migrate long distances. Conversely, we found high genetic differentiation between populations separated by large bodies of water. Moreover, we show evidence for serial founder effects across the Pacific, suggesting stepwise dispersal from a North American origin. These findings demonstrate that genetic drift played a major role in shaping allele frequencies and created genetic differentiation among newly formed populations. Thus, range expansion can give rise to genetic differentiation and declines in genetic diversity, even in highly mobile species.

Animal Distribution↗
PubMed1978

Probability of founder effect in a tribal population.

When an unusually high frequency of an allele is encountered in a population, "founder effect" is often invoked as an explanation. As usually used, the term implies the disproportionate increase through chance (rather than selection) of an allele contributed to the population by a particular ancestor. While genetic theory leaves no doubt this is a possible explanation, problems arise when we try to determine how likely this explanation is for any specific finding in any specific, finite population, i.e., just how rare is this rare event? In this communication we consider the question in the context of Amerindian tribal populations, deriving specific probabilities under defined conditions. Our interest in the question has been whetted by the finding to date of some eight possible examples of a founder effect in studies of twelve different tribes.

Gene Frequency↗
PubMed2025

Combined Evidence Reveals the Origin of a Rapid Range Expansion Despite Retained Genetic Diversity and a Weak Founder Effect.

Many species are currently experiencing range shifts in response to changing environmental conditions with potentially serious genetic consequences. Repeated founder events and strong genetic drift are expected to erode genetic variation at the range front, reducing adaptive potential and slowing or even halting the expansion. However, the severity of these consequences for common and highly mobile species undergoing environment-driven range shifts (c.f. invasions) is less clear. Here, we combined historical observations and contemporary movement data of the common reed warbler (Acrocephalus scirpaceus) with genomic evidence from across its European breeding range to (1) infer the origin and (2) quantify the genetic consequences of a recent and rapid northward range expansion. Although there were no reductions in levels of nucleotide diversity or allelic richness, nor a signal of founder effect in the directionality index (ψ), our combined dataset approach was able to infer an expansion origin from the southwest. Furthermore, we found that private allelic richness retained a slight but significant linear decline along the colonisation route. These results suggest that high dispersal capabilities can allow even philopatric species to avoid the loss of genetic diversity during rapid range expansions. Nevertheless, if multiple lines of evidence enable identification of an expansion pathway, we may still detect genetic signals of expansion.

Founder Effect↗
PubMed1978

Founder effect and number of private polymorphisms observed in Amerindian tribes.

In studies extending over the past dozen years, we have observed eight examples of "private" genetic polymorphisms in 12 Amerindian tribes surveyed for electrophoretic variants of an average of 25 proteins. Each of these is presumed to trace to a single mutation. In a preceding communication [Thompson, E.A. & Neel, J.V. (1978) Proc. Natl. Acad. Sci. USA 75, 1442-1445] the statistical theory was developed for estimating the likelihood of such a founder effect in a tribal population of this type. In this paper that theory is applied to the distribution defined by these eight variants. It is demonstrated that on the assumption that the phenotypes in question are selectively neutral, such findings are most compatible with a mutation rate of 7 X 10(-6)/locus per generation. This figure applies only to variants that can be detected by the electrophoretic technique.

Alleles↗
PubMed2026

Genetic Ancestry and Carrier Variant Frequency Enrichment in a Colombian Andean Population: Insights From the Eje Cafetero.

Colombia is one of the most genetically diverse populations in Latin America, and its demographic process has promoted the persistence and local enrichment of deleterious alleles, increasing the frequency of autosomal recessive disorders, particularly in semi-isolated Andean populations such as the Eje Cafetero. However, exome-based reference data from this region remain scarce, limiting ancestry-aware variant interpretation and carrier screening strategies. We aimed to characterize the ancestry proportions of this population using exome data, and to estimate the carrier frequency and distribution of pathogenic and likely pathogenic (P/LP) variants in clinically relevant recessive genes. We conducted a cross-sectional study with whole-exome sequencing (WES) in 316 unrelated individuals from the Colombian Eje Cafetero. P/LP variants were evaluated in 454 genes associated with autosomal recessive disorders. The global ancestry proportions were estimated using a validated panel of 250 exome-compatible ancestry-informative markers. Carrier frequencies were compared against Non-Finnish Europeans (NFE) and Admixed Americans (AMX) from gnomAD v4. The cohort showed predominant European ancestry (mean 51%), followed by Native American (36%) and African (13%) components. We identified 151 carriers of 89 distinct pathogenic variants across autosomal recessive genes. The most frequent variants were SERPINA1 c.863A>T (5.5%), CFTR c.1210-11T>G (3.5%), and PYGM c.1094C>T (1.5%). Also, recurrent variants were significantly enriched compared with both NFE and AMX populations, supporting regional founder effects. This study represents one of the most comprehensive exome-based genetic characterizations of the Colombian Eje Cafetero, revealing ancestry-specific enrichment of clinically relevant autosomal recessive variants driven by founder effects.

Female↗
PubMed2026

Analysis of APC promoter 1B deletions in Russian families with familial adenomatous polyposis.

OBJECTIVE: Familial adenomatous polyposis (FAP) is a severe autosomal dominant hereditary cancer syndrome. Patients develop hundreds of adenomatous polyps throughout the colon with the risk of colorectal cancer, if untreated, approaching 100%. FAP is caused by pathogenic germline variants in the APC gene. Deletions in the APC 1B promoter cause FAP in a small subgroup of patients. Previous studies suggested that the APC promoter deletions in unrelated FAP patients from the US and Italy are identical and may thus have spread from a single founder. The aim of this study was to investigate whether a similar founder effect can be detected in the Russian population. PATIENTS AND METHODS: We performed whole-genome sequencing on five unrelated patients (three males and two females) with extensive (over 100) colon polyps, family history of FAP, and germline APC 1B promoter deletions previously detected by the multiplex ligation-dependent probe amplification (MLPA) and detected precise deletion boundaries. RESULTS: The patients carried deletions in the APC 1B promoter ranging from ~3 to ~122 kbp. We found no association between the deletion size and either the age of the onset or severity of the disease. All deletions were unique and no identical deletion boundaries were observed. However, in four patients, the right deletion breakpoints fell into a 1 kbp region downstream of the 1B promoter. The right breakpoints of several deletions detected in FAP patients from other countries also fell into this narrow region. CONCLUSION: The APC 1B promoter deletions analyzed in this study had arisen independently and there is thus no evidence of a founder effect. Therefore, at least for the cohort of FAP patients with APC 1B promoter deletions studied here, WGS did not provide an added diagnostic benefit to MLPA aside from precisely determining the deletion breakpoints.

APC promoter 1B deletion↗
PubMed2026

Effect of founder breeds on genotype imputation accuracy in Canchim cattle.

UNLABELLED: Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP – single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson’s correlation between observed and imputed genotypes (R2). PERC values ranged from 66.52% to 97.39% and R² from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13353-026-01060-z.

Animal breeding↗
PubMedDate not supplied

Genetic considerations in human cancer incidence.

Analysis by the methods of genetic demography can offer plausible explanations for the unusual distribution of cancer in an area of high incidence. The important demographic characteristics include inbreeding, founder effect, and racial admixture. Inbreeding would elevate cancer incidence if autosomal recessive genes played a role in cancer etiology. Founder effect would limit this phenomenon to those recessive genes observed in the founding group and result in a cancer spectrum different from that of the surrounding populations. The preference of a racially admixed group for classification as white could result in an excess of cancer patients being classified as white. The population groups in southern Louisiana typify the kind of "human genetics laboratory" that inbred groups offer to investigators of the genetic aspects of cancer.

Adult↗
PubMed2025

Cancer spectrum in Mexican patients with the CHEK2 p.(Leu236Pro) variant: a retrospective study.

This study aimed to characterize, for the first time, the cancer spectrum associated with the most frequent pathogenic CHEK2 variant-NM_007194.4(CHEK2):c.707T > C p.(Leu236Pro)-in Mexican individuals. Although this variant is frequently detected through multi-gene panel testing, limited data on its associated cancer risks complicates genetic counseling and surveillance strategies. We retrospectively analyzed 5,759 patients who underwent multi-gene panel testing between August 2015 and August 2024 due to suspected hereditary cancer syndromes. Among them, 58 CHEK2 p.(Leu236Pro) carriers with confirmed cancer diagnoses were identified. Geographical clustering was observed, with 81% of patients originating from central Mexico, suggesting a possible founder effect. Ten distinct clinical indications for genetic testing were identified, with hereditary breast and ovarian cancer (HBOC) syndrome being the most common (74.1%). The mean age at first diagnosis among carriers was 43.8 ± 12 years, and 61.1% of them reported a family history of cancer in first- or second-degree relatives. A second or third primary cancer occurred in 20.7% of cases. Tumors were identified in 12 anatomical sites. Breast cancer predominated (67.6%, including one male case), followed by ovarian (8.1%), prostate (6.7%), gastric (4.1%), thyroid (2.7%), and endometrial (2.7%) cancers. Lymphoma, lung, sacrococcygeal bone, colorectal, and non-melanoma skin cancers each occurred in a single patient. Significant risk association was identified only for breast, ovarian, and gastric cancers. These results highlight the need for personalized surveillance, especially for breast cancer. Incorporating CHEK2 p.(Leu236Pro) into clinical decision-making tools may enhance risk assessment in the Mexican population, but larger studies are needed to refine risk estimates and to clarify the possible founder effect.

Humans↗
PubMed2025

Conservation Arks: Genomic Erosion and Inbreeding in an Abundant Island Population of Koalas.

The persistence of many threatened species depends on isolated habitat patches such as conservation parks, fenced reserves, and islands. While these 'conservation arks' provide refuge from many contemporary threats, they can also pose risks of genetic diversity loss and inbreeding depression, further exacerbating extinction risk. A pertinent example is the Kangaroo Island koala population in South Australia that originated from a few translocated founding individuals in the 1920s but now sustains a large population with a low prevalence of infectious disease. We investigated the extent and consequences of founder effects on genomic diversity, inbreeding, and adaptive potential in Kangaroo Island koalas by comparing them with mainland Australian populations using high-coverage whole genomes. Our findings support sharp, recent declines in effective population sizes (Ne) in both mainland and Kangaroo Island populations. However, Kangaroo Island koalas had much lower individual and population-level diversity. Together with longer and more numerous runs of homozygosity and an increased proportion of homozygous genetic load, these results support the hypothesis that a severe bottleneck has contributed to inbreeding and maladaptation in Kangaroo Island koalas. While Kangaroo Island has the potential to conserve a viable population of koalas, we recommend genetic rescue to restore diversity and mitigate inbreeding depression in this isolated population. Our results emphasise the need for longitudinal genomic monitoring and genetic management to maintain long-term viability and resilience in potential conservation arks. Understanding the demographic history of such populations will help inform future conservation aimed at preventing genetic erosion and preserving biodiversity.

Animals↗
PubMed1976

Genetic and anthropological studies in the human adaptability section of the International Biological Programme.

In the U.K. contribution to the H.A. (Human Adaptibility) section of I.B.P., genetic and anthropological studies have focused on three concerns. First, attempts have been made in a number of investigation to gain additional descriptive information about the genetic compostition of the world's populations. Concentrating on blood groups, blood enzymes, serum proteins and other polmorphic markers important gaps have been filled in our knowledge of the geographical paterns of human variation and of the affinities of populations wig and characterizing populations which were being studied for other purposes. For example, it was of critical concern in interpreting results to know in the investigations of climatic physiology and nutrition in Ethiopia and Israel whether the various groups studied in different environments were genetically the same or not. Finally, attention was focused in a number of investigations, especially those in New Guinea, Tristan da Cunha, Tanzania, and the Orkneys, on the factors which determine the genetic structure of populations. In these the effects of such phenomena as inbreeding, genetic drift, founder effects, migration and gene flow and the relation between genetic variety and health were examined and much attention was given to the interaction between demographic forces and genetics.

Adaptation, Physiological↗
PubMed2026

Genetic structure and selection signatures of Beijing-You chicken populations provide insight into breed conservation.

Preserving genetic diversity and maintaining population viability are critical yet challenging goals that demand rigorous evaluation of conservation strategies. Beijing-You chicken, as the sole indigenous chicken breed originating from Beijing, China, is currently maintained as four independent populations under distinct conservation programs. How different conservation regimes have shaped its genomic architecture remains largely unknown, limiting evidence-based evaluation. Here, we generated whole-genome resequencing data from 240 individuals representing four Beijing-You chicken populations to assess population structure, genetic diversity, and signatures of selection over decades of conservation. All four populations formed distinct clusters, reflecting measurable differentiation after decades of separate conservation. The differences in genetic diversity were broadly consistent with the variation in effective population size estimates. Runs of homozygosity and linkage disequilibrium decay patterns further characterized each population, with extended values indicating reduced effective population size and increased inbreeding under long-term conservation. We applied the fixation index (FST) and pairwise diversity ratio (θπ) methods to identify selection signatures. A total of 171 genes were identified as candidates. These genes were enriched in pathways related to reproduction, growth regulation, and environmental adaptation. These findings highlight patterns of reduced diversity and skewed relatedness, which could arise from management-related factors such as breeding preferences or mating strategies. Still, they are also compatible with neutral processes, including drift and founder effects. Regardless of the underlying cause, integrating scientifically informed conservation strategies with routine genomic monitoring across generations is essential for sustaining genetic diversity in Beijing-You chicken and other indigenous breeds.

Beijing-You chicken↗
PubMed1977

The genetic structure of natural populations of Drosophila melanogaster XIII. Further studies on linkage disequilibrium.

The Raleigh, North Carolina, population of Drosophila melanogaster was examined for linkage disequilibrium in 1974, several years after previous analyses in 1968, 1969, and 1970. alphaglycerol-3-phosphate dehydrogenase-1 (alphaGpdh-1), malate dehydrogenase-1 (Mdh-1), alcohol dehydrogenase (Adh), and hexokinase-C (Hex-C, tentative name, F. M. Johnson, unpublished; position determined by the present authors to be 2-74.5) were assayed for 617 second chromosomes, and esterase-C (Est-C) and octanol dehydrogenase (Odh) were assayed for 526 third chromosomes. In addition, two polymorphic inversions in the second chromosomes [In(2L)t and In(2R)NS] were examined, and the following findings were obtained: (1) No linkage disequilibrium between isozyme genes was detected. Significant linkage disequilibria were found only between the polymorphic inversions and isozyme genes [In(2L)t vs. Adh, and In(2R)NS vs. Hex-C]. Significant disequilibrium was not detected between In(2L)t and alphaGpdh-1, which is included in the inversion, but a tendency toward disequilibrium was consistently found from 1968 to 1974. The frequency of two-strand double crossovers within inversion In(2L)t involving a single crossover on each side of alphaGpdh-1 was estimated to be 0.00022. Thus, the consistent but not significant linkage disequilibrium between the two factors can be explained by recombination after the inversion occurred. (2) Previously existing linkage disequilibrium between Adh and In(2R)NS (the distance is about 30 cM, but the effective recombination value is about 1.75%) was found to have disappeared. (3) No higher-order linkage disequilibrium was detected. (4) Linkage disequilibrium between Odh and Est-C (the distance of which was estimated to be 0.0058 +/- 0.002) could not be detected (chi(2) (df=1) = 0.9).-From the above results, it was concluded that linkage disequilibria among isozyme genes are very rare in D. melanogaster, so that the Franklin-Lewontin model (Franklin and Lewontin 1970) is not applicable to these genes. The linkage disequilibria between some isozyme genes and polymorphic inversions may be explained by founder effect.

Alleles↗
PubMed1978

Alkaptonuria in the Trencín District of Czechoslovakia.

For several years the Clinical Genetics Research Laboratory at Martin, Czechoslovakia, has been studying alkaptonuria (AU) in the northern part of the District of Trencín in Slovakia. These affected individuals are part of a group of 103 alkaptonurics originated mostly in the mountainous parts of Slovakia. We report results of pedigree analyses; population and affected-family biochemical urine screening; estimation of inbreeding coefficient, of exogamy rate and of average marital distance and of calculation of the frequency of the AU allele, and of homozygotes and heterozygotes in this portion of the Trencín District. Twelve homozygotes were found, but seven originated from a single hamlet in which a founder effect - genetic drift and inbreeding - are thought to account for the high prevalence of AU.

Alkaptonuria↗
PubMed2025

Insights into the heterogeneity of oculopharyngeal muscular dystrophy.

Oculopharyngeal muscular dystrophy (OPMD) is a rare, adult-onset, autosomal dominant myopathy characterized by variability in the age of onset and disease progression. However, its pathogenesis and phenotypic variability remain poorly understood. The disorder is caused by an expansion of a short polyalanine tract in the poly(A) binding protein nuclear 1 (PABPN1) gene. This study presents data from 23 patients across 19 Greek families with pathogenic PABPN1 expansions, including demographic and laboratory data, as well as molecular and electron microscopy findings. Eight distinct trinucleotide expansion genotypes were identified. Electron microscopy consistently demonstrated mitochondrial abnormalities, including swelling, disrupted cristae and atypical lipid inclusions. Clinical heterogeneity was observed at both inter- and intrafamilial levels, and milder phenotypes were generally linked to smaller alleles. Notably, maternally inherited expansions were associated with an earlier disease onset and more severe progression in affected offspring. Given the genetic variability observed in the cohort, the presence of a founder effect could not be supported. A significant degree of underdiagnosis or diagnostic delay was noted, largely attributable to the rarity and clinical heterogeneity of the disease. The observed intrafamilial heterogeneity - particularly in maternally inherited expansions - supports previous reports suggesting that mitochondrial dysfunction may contribute to transgenerational disease progression in the context of a dominant, causative nuclear variant.

Humans↗
PubMed2026

WWOX-related developmental and epileptic encephalopathy (WOREE): A case series of seven patients from Argentina.

PURPOSE: WWOX-related developmental and epileptic encephalopathy (WOREE) is a rare autosomal recessive disorder caused by biallelic pathogenic WWOX variants, characterized by very early-onset epilepsy, profound developmental delay, and progressive brain abnormalities. Detailed electroclinical descriptions remain limited. METHODS: We conducted a retrospective study of seven patients with pathogenic/likely pathogenic WWOX variants. Clinical features, seizure evolution, EEG findings, brain MRI, and genetic data were reviewed. Epilepsy syndromes were classified according to International League against Epilepsy (ILAE) criteria. Variants were identified through next-generation sequencing and interpreted following American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS: Median seizure onset was 3 months (range 2-6). Five patients presented with focal seizures evolving to infantile epileptic spasms syndrome (IESS), while two had IESS at onset. Epilepsy was drug-resistant in all. Developmental delay was evident from birth with generalized hypotonia, acquired microcephaly, and impaired visual attention. Four patients had dysmorphic features. During the IESS period, EEG showed hypsarrhythmia in six patients and a severely disorganized encephalopathic background that did not strictly fulfill the criteria for hypsarrhythmia in one. Brain MRI revealed abnormalities in all patients, including frontotemporal atrophy and corpus callosum hypoplasia; delayed myelination was observed in one case. Eight pathogenic/likely pathogenic WWOX variants were found; including one novel variant (NM_016373.4:c.571C>T, p.(Gln191*)). The recurrent splice-site variant NM_016373.4:c.107+1G>A was identified in five patients, suggesting a possible regional founder effect. CONCLUSION: WOREE shows a recognizable electroclinical and neuroimaging profile with early drug-resistant epilepsy and profound developmental delay. Recognition of this pattern may facilitate early diagnosis and targeted genetic testing, particularly in populations with recurrent variants.

Developmental and epileptic encephalopathy↗