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Results for “Admixed ancestry”

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At least 19 recordsLinked to original sources

PubMed2006

Reconstructing genetic ancestry blocks in admixed individuals.

A chromosome in an individual of recently admixed ancestry resembles a mosaic of chromosomal segments, or ancestry blocks, each derived from a particular ancestral population. We consider the problem of inferring ancestry along the chromosomes in an admixed individual and thereby delineating the ancestry blocks. Using a simple population model, we infer gene-flow history in each individual. Compared with existing methods, which are based on a hidden Markov model, the Markov-hidden Markov model (MHMM) we propose has the advantage of accounting for the background linkage disequilibrium (LD) that exists in ancestral populations. When there are more than two ancestral groups, we allow each ancestral population to admix at a different time in history. We use simulations to illustrate the accuracy of the inferred ancestry as well as the importance of modeling the background LD; not accounting for background LD between markers may mislead us to false inferences about mixed ancestry in an indigenous population. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application of our method is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Genetics, Medical↗

PubMed2025

A genealogy-based approach for revealing ancestry-specific structures in admixed populations.

Elucidating ancestry-specific structures in admixed populations is crucial for comprehending population history and mitigating confounding effects in genome-wide association studies. Existing methods to reveal the ancestry-specific structures generally rely on frequency-based estimates of genetic relationship matrix (GRM) among admixed individuals after masking segments from ancestry components not being targeted for investigation. However, these approaches disregard linkage information between markers, potentially limiting their resolution in revealing structure within an ancestry component. We introduce ancestry-specific expected GRM (as-eGRM), a novel framework for estimating the relatedness within ancestry components between admixed individuals. The key design of as-eGRM consists of defining ancestry-specific pairwise relatedness between individuals based on genealogical trees encoded in the ancestral recombination graph (ARG) and local ancestry calls and then computing the expectation of the ancestry-specific relatedness across the genome. Comprehensive evaluations using both simulated stepping-stone models of population structure and empirical datasets based on three-way admixed Latino cohorts showed that analysis based on as-eGRM robustly outperforms existing methods in revealing the structure in admixed populations with diverse demographic histories, which in turn improves the robustness against confounding due to population structure in association testing.

Humans↗

PubMed2026

Concordance and divergence between self-declared ancestry and genome-derived ancestry composition in 10 250 participants from the HostSeq cohort.

Accurate characterization of human genetic diversity is essential for robust genomic analyses. We compared self-declared and genome-derived ancestry composition in 10 250 participants from the pan-Canadian HostSeq cohort using whole-genome sequencing data. Global and local ancestry were inferred at the continental super-population level using the alignment-free ntRoot algorithm and evaluated through both hard-label concordance and multiclass Brier score analyses incorporating full ancestry fraction profiles. Strong agreement was observed among East Asian / Pacific Islander (mean Brier score ± SD: 0.012 ± 0.052), Black (0.013 ± 0.042), White (0.055 ± 0.022), and South Asian (0.057 ± 0.098) participants, whereas higher scores among Hispanic (0.083 ± 0.060) and Middle Eastern or Central Asian (0.122 ± 0.034) participants reflected broader and more admixed ancestry profiles. Principal component analysis of centered log-ratio-transformed ancestry fractions revealed overlapping ancestry gradients rather than discrete continental groupings. Entropy- and dominance margin-based analyses further indicated that many discordant cases reflected diffuse admixture rather than categorical mismatch. Together, these findings support representing ancestry as a continuous compositional spectrum rather than discrete categories. Genome-derived ancestry estimates describe patterns of genomic variation and should not be interpreted as proxies for race.

Humans↗

PubMed2001

The impact of population admixture on traditional linkage analysis.

INTRODUCTION: Families of admixed ancestry are routinely excluded from traditional (Log of the Odds [LOD] score) linkage analysis or are analyzed as being derived from a homogeneous population using the proband's ethnicity. Using traditional linkage analysis with these families can cause complications due to the mixing of different disease rates and allele frequencies that occurs. The presence of admixture violates the key assumptions of Hardy-Weinberg Equilibrium (HWE) and Linkage Equilibrium (LE) invoked in the current methods of linkage analysis. If one or more of these assumptions are violated, incorrect inference for linkage could result. DESIGN AND METHODS: Through simulation, we investigated the effect of admixture of two populations on the LOD score under various conditions, using prostate cancer as our underlying disease model. Four-generation homogeneous and admixed families were simulated with 27 markers and two linked, bi-allelic disease loci. Two different types of admixture were tested: admixture within a family unit and a mixture of homogeneous families within a data set. All mixing was done at the founder level in three different proportions: 30/70, 50/50 and 70/30. RESULTS AND CONCLUSIONS: We observed that the LOD scores under both models of admixture were closest to the homogeneous family scores of the population having the highest mixing proportion. Random sampling of families or ascertainment of families with disease affection status did not affect this observation, nor did the mode of inheritance (dominant/recessive) or sample size. Thus, the presence of families of mixed population ancestry impacts linkage analysis in terms of the LOD score and the estimate of the recombination fraction.

Alleles↗

PubMed2005

The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages.

Linguistic and archaeological evidence about the origins of the Malagasy, the indigenous peoples of Madagascar, points to mixed African and Indonesian ancestry. By contrast, genetic evidence about the origins of the Malagasy has hitherto remained partial and imprecise. We defined 26 Y-chromosomal lineages by typing 44 Y-chromosomal polymorphisms in 362 males from four different ethnic groups from Madagascar and 10 potential ancestral populations in Island Southeast Asia and the Pacific. We also compared mitochondrial sequence diversity in the Malagasy with a manually curated database of 19,371 hypervariable segment I sequences, incorporating both published and unpublished data. We could attribute every maternal and paternal lineage found in the Malagasy to a likely geographic origin. Here, we demonstrate approximately equal African and Indonesian contributions to both paternal and maternal Malagasy lineages. The most likely origin of the Asia-derived paternal lineages found in the Malagasy is Borneo. This agrees strikingly with the linguistic evidence that the languages spoken around the Barito River in southern Borneo are the closest extant relatives of Malagasy languages. As a result of their equally balanced admixed ancestry, the Malagasy may represent an ideal population in which to identify loci underlying complex traits of both anthropological and medical interest.

Africa↗

PubMedDate not supplied

Admixture estimates for Churuguara, a Venezuelan town in the State of Falcón.

BACKGROUND: The present Venezuelan population is the admixture product of Amerindians, Europeans and Africans, a process which was not homogeneous over the country. Blood groups, STRs and VNTRs, specifically D1S80, have been used successfully in admixture studies, but few have been made in Venezuela. AIM: This study aims to estimate the admixture components of Churuguara, Venezuela, and to evaluate the genetic relationship of this population with other Venezuelan as well as worldwide populations through principal component analysis and the study of dendrograms based on genetic distances. SUBJECTS AND METHODS: Gene frequencies of blood groups ABO and Rh (only anti D), of STRs VWA, F13A01, FES/FPS and VNTR D1S80 were studied in a sample of 60 individuals born in Churuguara, a Venezuelan town of admixed ancestry in the State of Falc6n. Admixture was estimated with Chakraborty's gene identity method, and Nei's standard genetic distance was used to build two dendrograms with the neighbour-joining approach, one based on the three STRs and the other based only on D1S80. Principal component analyses with the gene frequencies of these markers were also performed. RESULTS: The frequency of allele ABO*O was 0.788, of ABO*A was 0.187 and of RH*D was 0.74. D1S80 showed 16 different alleles with a heterozygosity of 0.880, whilst the three STRs showed only eight different alleles and heterozygosities between 0.733 and 0.797. The estimates of admixture obtained in this analysis were 52.5% for the Spanish parental group, 27.6% for the African and 19.9% for the Amerindian. Comparison of Churuguara with other Latin American populations shows that its African component is not as high as that observed in Colombian Choco, but it is higher than that observed in other samples from Colombia, Chile and Maracaibo (Venezuela). CONCLUSIONS: Results of the admixture analysis are consistent with those obtained with two dendrograms and principal component analyses, suggesting that the strong initial Amerindian component of 500 years ago has been diluted by the continuous flow of European genes, mainly Spanish, to this region.

ABO Blood-Group System↗

PubMed2026

Genome-wide association studies reveal genetic variants associated with antineoplastic monoterpenoid indole alkaloid accumulation in Catharanthus roseus.

Catharanthus roseus produces pharmacologically important monoterpenoid indole alkaloids (MIAs), yet their natural accumulation is low, limiting therapeutic exploitation. To dissect the genetic basis of natural variation in MIA accumulation, we integrated phenotypic, chemotypic, and genomic analyses of 93 C. roseus accessions sampled from six locations across India, including New Delhi, Lucknow, Jodhpur, Bangalore, and two locations in Gujarat: Navsari and Bardoli. Morphological characterization showed limited differentiation among locations, whereas accessions from Gujarat tended to be taller compared to other locations and more frequently white-flowered. Quantitative HPLC profiling revealed substantial accession- and location-dependent variation in total indole alkaloid levels, with Gujarat accessions showing the highest accumulation, largely driven by vindoline and catharanthine. Genotyping-by-sequencing generated 10,801 high-quality variants comprising 10,087 SNPs and 714 InDels corresponding to an average density of 19.34 variants per Mbp of the genome, revealing three genetic subgroups with overall admixed ancestry and weak geographic stratification. Genome-wide association study (GWAS) using five benchmark models identified 47 variants potentially associated with catharanthine, vindoline, and vinblastine content. These putative candidate loci were located near genes implicated in hormone signaling, mitochondrial function, nitrogen metabolism, and RNA processing, suggesting complex regulatory control of MIA biosynthesis. Notably, two missense variants in a carboxylesterase-like gene were associated with vindoline accumulation, and highly significant intergenic SNP clusters suggested putative regulatory hotspots for vinblastine biosynthesis. These results provide GWAS-based insights into the genetic architecture of MIA metabolism in C. roseus and nominate candidate variants for precision breeding and metabolic engineering to enhance pharmaceutical alkaloid production.

Catharanthus roseus↗

PubMed2001

Racial variation in the proximal and distal femur: heritability and forensic utility.

The femur has been studied successfully by physical anthropologists for many years. Such traits as femoral head diameter and bicondylar width have been examined extensively and are of great value to forensic anthropologists and other skeletal biologists in sex identification. A number of studies over the past decade by the author and his former students have shown marked racial differences in the shape of the proximal femur and in at least one trait of the distal femur--intercondylar notch height. Anterior-posterior (AP) diameter of the proximal femur is much greater among Whites and Blacks than among East Asians and American Indians. Blacks have slightly greater intercondylar notch height than Whites. Other features, such as torsion, also differ between the major geographic racial populations. Current analysis suggests that the East Polynesians fall close to the American Indians and East Asians in the degree of flatness of the proximal femur. One study has tracked the degree of change in flatness during individual development, and finds little change within major populations from the youngest to the oldest individuals. Temporal changes within populations are likewise minimal. Two studies have examined sex differences within populations, which are also found to be very slight. Racial differences, on the other hand, are quite significant, and individuals of admixed ancestry fall intermediate between the two parental populations. Such suggestions of high heritability in the shape of the proximal and distal femur make these traits very useful in assessing ancestry in forensic contexts.

Adult↗

PubMed2002

Admixture effects in the traditional linkage analysis of admixed families.

INTRODUCTION: Families of admixed ancestry are routinely excluded from traditional linkage analysis (LOD score) or are analyzed as deriving from a homogeneous population of the proband's ethnicity. Using traditional linkage analysis methods to analyze these families is complicated due to the admixture of different disease rates and allele frequencies that occurs. The presence of admixture violates the key assumptions of Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) invoked in the current methods of linkage analysis. If one or both of these assumptions are violated, incorrect inference for linkage could result. DESIGN AND METHODS: We propose a pooling procedure to correct for inflated estimates of the recombination fraction that can result from admixture when performing traditional linkage analysis. Data were simulated with 30 families per each of 200 replications for a dominant, highly selective, linked disease locus model in order to conduct further testing for allelic LE and HWE, while using an allele pooling procedure to account for allele frequency differences between the 2 populations. The differences in allele frequencies between the populations for the polymorphic loci were 0.05, 0.10 and 0.14. RESULTS AND CONCLUSIONS: Our pooling procedure does not eradicate all disequilibrium, because those replicates in which the disequilibrium exists are no longer affected by the disequilibrium in terms of maximization for linkage. Furthermore, our pooling procedure was able to exclude uninformative families or families far removed from HWE and/or LE that their LOD scores were unreliable.

Alleles↗

PubMed2026

Genome-Wide and Rare Variant Association Studies of Amblyopia in Admixed American and African Ancestry Groups.

OBJECTIVE: To identify genetic variants associated with amblyopia in African (AFR) and Admixed American (AMR) ancestry groups, expanding on previous studies conducted in European ancestry. DESIGN: Retrospective ancestry-stratified genome-wide association study (GWAS) and gene-level rare variant association study (RVAS). PARTICIPANTS: Participants in the All of Us Research Program from AFR and AMR ancestry groups who had whole-genome sequencing available. Cases and controls were distinguished based on the presence of International Classification of Diseases 9/10/SNOMED diagnosis codes for amblyopia in electronic health records. This yielded ancestry-stratified subsets of 269 cases and 71 585 controls of AMR ancestry and 366 cases and 79 460 controls of AFR ancestry. METHODS: Stratified logistic regression models were adjusted for age, biological sex, and the top 10 principal components of genomic ancestry. GWAS was limited to common variants (minor allele frequency ≥1%), and RVAS was limited to rare variants with coding sequence-altering effects (minor allele frequency >1%, exonic only, excluding synonymous variants) aggregated at the gene level using the SKAT algorithm. Downstream analyses of the significant variants were performed using KEGG and GO pathway analysis and STRING database queries for protein-protein interactions and gene-gene interactions. MAIN OUTCOME MEASURES: Single-nucleotide polymorphisms were determined to have genome-wide significance if P < 5e-8 in the GWAS, and genes were determined to have significant association with amblyopia in the RVAS if P < 8.0 × 10-4. RESULTS: In the AMR GWAS, 245 unique single-nucleotide polymorphisms mapping to 97 distinct loci were identified, notably within neurodevelopmental and axonal guidance genes, including ROBO1, SEMA4B, PTPRD, NRXN1, and CAMK2D. The AFR GWAS identified 11 significant variants corresponding to 6 loci mapping primarily to long noncoding RNAs and pseudogenes. The AMR RVAS identified 15 genes, including axonal transport genes (KIF1B and KIF7) and growth factor signaling genes (EGF, ERBIN, and AKAP17A). The AFR RVAS identified a single gene, DLG2, which encodes the postsynaptic protein PSD-93, which promotes the closure of the sensitive period of neuroplasticity for vision in early childhood. CONCLUSIONS: Genetic risk architectures for amblyopia differ across ancestries but fundamentally converge on neurodevelopmental signaling, cortical synapse assembly, and sensitive period plasticity rather than ocular structural dynamics. FINANCIAL DISCLOSURE(S): The authors have no proprietary or commercial interest in any materials discussed in this article.

Amblyopia↗

PubMed2025

DiscoDivas: Leveraging genetic ancestry continuum information to interpolate PRS for admixed populations.

The relatively low representation of admixed populations in both discovery and fine-tuning individual-level datasets limits polygenic risk score (PRS) development and equitable clinical translation for admixed populations. Under the assumption that the most informative PRS model for a genetically homogeneous sample varies linearly in an ancestry continuum space, we introduce a Genetic Distance-assisted PRS Combination Pipeline for Diverse Genetic Ancestries (DiscoDivas) to interpolate a harmonized PRS for diverse, especially admixed, genetic ancestries, leveraging multiple PRS models fine-tuned within existing samples, which are mostly of single ancestry, and genetic distance. DiscoDivas treats genetic ancestry as a continuous variable and does not require shifting between different models when calculating PRS for different ancestries. We generated PRS with DiscoDivas and the current conventional method, i.e. fine-tuning multiple GWAS PRS using the matched or similar genetic ancestry samples. DiscoDivas generated a harmonized PRS of the accuracy comparable to or higher than the conventional approach, with the greatest advantage exhibited in admixed individuals.

PRS harmonization↗

PubMed2005

Genetic admixture and asthma-related phenotypes in Mexican American and Puerto Rican asthmatics.

Genetic association studies in admixed populations may be biased if individual ancestry varies within the population and the phenotype of interest is associated with ancestry. However, recently admixed populations also offer potential benefits in association studies since markers informative for ancestry may be in linkage disequilibrium across large distances. In particular, the enhanced LD in admixed populations may be used to identify alleles that underlie a genetically determined difference in a phenotype between two ancestral populations. Asthma is known to have different prevalence and severity among ancestrally distinct populations. We investigated several asthma-related phenotypes in two ancestrally admixed populations: Mexican Americans and Puerto Ricans. We used ancestry informative markers to estimate the individual ancestry of 181 Mexican American asthmatics and 181 Puerto Rican asthmatics and tested whether individual ancestry is associated with any of these phenotypes independently of known environmental factors. We found an association between higher European ancestry and more severe asthma as measured by both forced expiratory volume at 1 second (r=-0.21, p=0.005) and by a clinical assessment of severity among Mexican Americans (OR: 1.55; 95% CI 1.25 to 1.93). We found no significant associations between ancestry and severity or drug responsiveness among Puerto Ricans. These results suggest that asthma severity may be influenced by genetic factors differentiating Europeans and Native Americans in Mexican Americans, although differing results for Puerto Ricans require further investigation.

Adolescent↗

PubMed2004

Effects of birthplace and individual genetic admixture on lung volume and exercise phenotypes of Peruvian Quechua.

Forced vital capacity (FVC) and maximal exercise response were measured in two populations of Peruvian males (age, 18-35 years) at 4,338 m who differed by the environment in which they were born and raised, i.e., high altitude (Cerro de Pasco, Peru, BHA, n = 39) and sea level (Lima, Peru, BSL, n = 32). BSL subjects were transported from sea level to 4,338 m, and were evaluated within 24 hr of exposure to hypobaric hypoxia. Individual admixture level (ADMIX, % Spanish ancestry) was estimated for each subject, using 22 ancestry-informative genetic markers and also by skin reflectance measurement (MEL). Birthplace accounted for the approximately 10% larger FVC (P < 0.001), approximately 15% higher maximal oxygen consumption (VO(2)max, ml.min(-1).kg(-1)) (P < 0.001), and approximately 5% higher arterial oxygen saturation during exercise (SpO(2)) (P < 0.001) of BHA subjects. ADMIX was low in both study groups, averaging 9.5 +/- 2.6% and 2.1 +/- 0.3% in BSL and BHA subjects, respectively. Mean underarm MEL was significantly higher in the BSL group (P < 0.001), despite higher ADMIX. ADMIX was not associated with any study phenotype, but study power was not sufficient to evaluate hypotheses of genetic adaptation via the ADMIX variable. MEL and FVC were positively correlated in the BHA (P = 0.035) but not BSL (P = 0.335) subjects. However, MEL and ADMIX were not correlated across the entire study sample (P = 0.282). In summary, results from this study emphasize the importance of developmental adaptation to high altitude. While the MEL-FVC correlation may reflect genetic adaptation to high altitude, study results suggest that alternate (environmental) explanations be considered.

Acclimatization↗

PubMed2026

Quantitative trait loci mapping of gene expression and chromatin accessibility in primary fibroblasts reveals shared allelic effects between Latin American and European ancestries.

BACKGROUND: Quantitative Trait Locus (QTL) analysis of molecular data has identified genetic variants associated with traits such as gene expression, and colocalization of these functional QTL with GWAS risk loci has offered insights into the genetic basis of human disease. We employed gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) obtained from human primary fibroblasts to investigate quantitative trait loci (QTLs) in cohorts ascertained for bipolar disorder of European (n = 150) and Latin American (n = 96) ancestries. RESULTS: Leveraging data from three countries of origin (The Netherlands, Colombia, Costa Rica) within our cohort, we characterized differences among individuals at the SNP, gene, and accessible-chromatin levels to compute ancestry-specific expression (e)QTLs and chromatin-accessibility (ca)QTLs. Across ancestries, we observed R2 ≥ 0.93 for eQTL effect sizes and R2 ≥ 0.95 for caQTLs, indicating a high degree of concordance. Integrating chromatin data with expression and genotype information enabled precise fine-mapping of eQTLs, yielding 203 genes with high-confidence (posterior probability > 90%) candidate regulatory pathways. In downstream analyses, transcriptome-wide (TWAS) and chromatin-wide (CWAS) association studies with brain- and skin-related GWAS identified 36 TWAS-significant genes and 77 CWAS-significant open chromatin regions. CONCLUSIONS: These findings underscore the shared genetic regulatory mechanisms across European and Latin American ancestries, while demonstrating that ancestry-specific reference panels enhance the accuracy of TWAS and CWAS in diverse populations. More broadly, this study highlights the value of paired multi-omic datasets from diverse cohorts for interpreting disease-associated genetic variation.

Humans↗

PubMed2025

Leveraging local ancestry and cross-ancestry genetic architecture to improve genetic prediction of complex traits in admixed populations.

The broader application of polygenic risk score (PRS) is hindered by the limited transferability of PRS developed in Europeans to non-European populations. While many statistical methods have been developed to improve the performance of PRS in non-European populations, most of them focused on discrete genetic ancestry clusters and did not consider admixed individuals. Admixed individuals pose a unique challenge for PRS calculation due to the complexity of local ancestry and cross-ancestry effect sizes. Here, we present a statistical method called SDPR_admix for calculating PRS in admixed individuals. SDPR_admix characterizes the joint distribution of the effect sizes of a genetic variant with two ancestries to be both zero, ancestry enriched, or shared with correlation. SDPR_admix outperformed other methods in simulations and improved the prediction of real traits in European-African admixed individuals in UK Biobank when trained on the Population Architecture using Genomics and Epidemiology (PAGE) dataset (N = 13,000). Deployment of SDPR_admix on All of Us (N = 52,000) further increased the prediction accuracy by approximately 5-fold on average compared with training on PAGE. This enhancement was achieved with manageable computational time and cost, demonstrating the feasibility of training PRS models on large-scale All of Us data. We provided several examples demonstrating that both ancestral-enriched and shared effects, as included in the SDPR_admix prediction model, are helpful for improving polygenic prediction in admixed populations. We also applied SDPR_admix to construct PRS for admixed Americans with mixture of European and Amerindigenous ancestries and showed that SDPR_admix overall outperformed other methods.

Humans↗

PubMed1998

Frequencies of the butyrylcholinesterase K mutation in Brazilian populations of European and African origin.

The frequency of the butyrylcholinesterase K mutation was calculated on the basis of data obtained by polymerase chain reaction primer-introduced restriction analysis (PCR-PIRA). The population sample was composed of 177 Brazilians: 95 whites of predominantly European ancestry and 82 admixed individuals (European and African origin). The frequencies--18.4 +/- 2.8% for whites and 17.1 +/- 2.9% for admixed--did not differ from those previously obtained in North America, Scotland, Japan, and Denmark. The occurrence of the K mutation in Europeans, East Asians, and Africans suggests a relatively old origin for this mutation, and the similar frequencies found in these populations may suggest the operation of selective forces.

Black People↗

PubMed2004

Design and analysis of admixture mapping studies.

Admixture between populations originating on different continents can be exploited to detect disease susceptibility loci at which risk alleles are distributed differentially between these populations. We first examine the statistical power and mapping resolution of this approach in the limiting situation in which gamete admixture and locus ancestry are measured without uncertainty. We show that, for a rare disease, the most efficient design is to study affected individuals only. In a typical African American population (two-way admixture proportions 0.8/0.2, ancestry crossover rate 2 per 100 cM), a study of 800 affected individuals has 90% power to detect at P values <10(-5) a locus that generates a risk ratio of 2 between populations, with an expected mapping resolution (size of 95% confidence region for the position of the locus) of 4 cM. In practice, to infer locus ancestry from marker data requires Bayesian computationally intensive methods, as implemented in the program ADMIXMAP. Affected-only study designs require strong prior information on the frequencies of each allele given locus ancestry. We show how data from unadmixed and admixed populations can be combined to estimate these ancestry-specific allele frequencies within the admixed population under study, allowing for variation between allele frequencies in unadmixed and admixed populations. Using simulated data based on the genetic structure of the African American population, we show that 60% of information can be extracted in a test for linkage using markers with an ancestry information content of 36% at 3-cM spacing. As in classic linkage studies, the most efficient strategy is to use markers at a moderate density for an initial genome search and then to saturate regions of putative linkage with additional markers, to extract nearly all information about locus ancestry.

Black People↗

PubMed2026

The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.

Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g. ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared with random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original, and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.

Animals↗