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CABALLERO, ARMANDO, and MIGUEL A. TORO. "Interrelations between effective population size and other pedigree tools for the management of conserved populations." Genetical Research 75, no. 3 (2000): 331–43. http://dx.doi.org/10.1017/s0016672399004449.
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Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.
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Sölkner, J., L. Filipcic, and N. Hampshire. "Genetic variability of populations and similarity of subpopulations in Austrian cattle breeds determined by analysis of pedigrees." Animal Science 67, no. 2 (1998): 249–56. http://dx.doi.org/10.1017/s1357729800010006.
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AbstractParameters based on probabilities of gene origin were used to evaluate the genetic variability of four Austrian cattle breeds. Effective numbers of founders, ancestors and remaining founder genomes showed that all four populations investigated are rather small genetically. Effective numbers of remaining founder genomes were 94 for Simmental, 41 for Braunvieh (Brown Swiss), 32 for Pinzgauer and 21 for Grauvieh (Grey cattle, a small mountain breed). As the value of 94 for Simmental was rather large in comparison with estimates from other populations in previous studies, the effect of population structure was investigated. A cosine measure of similarity based on differences in individual founder contributions to different subpopulations was defined and used for analysis. Subpopulations defined by regions were clearly more distinct for Simmental than for Braunvieh. The size of the cosine values depended on the method of calculating founder contributions and was overestimated when choosing the method not accounting for drift and bottlenecks (effective number of founders).
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Montero-Pau, Javier, Africa Gómez, and Manuel Serra. "Founder effects drive the genetic structure of passively dispersed aquatic invertebrates." PeerJ 6 (December 11, 2018): e6094. http://dx.doi.org/10.7717/peerj.6094.
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Populations of passively dispersed organisms in continental aquatic habitats typically show high levels of neutral genetic differentiation despite their high dispersal capabilities. Several evolutionary factors, including founder events, local adaptation, and life cycle features such as high population growth rates and the presence of propagule banks, have been proposed to be responsible for this paradox. Here, we have modeled the colonization process to assess the impact of migration rate, population growth rate, population size, local adaptation and life-cycle features on the population genetic structure in these organisms. Our simulations show that the strongest effect on population structure are persistent founder effects, resulting from the interaction of a few population founders, high population growth rates, large population sizes and the presence of diapausing egg banks. In contrast, the role of local adaptation, genetic hitchhiking and migration is limited to small populations in these organisms. Our results indicate that local adaptation could have different impact on genetic structure in different groups of zooplankters.
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Gruber, Stephen B. "Population stratification in epidemiologic studies of founder populations." Cancer Biomarkers 3, no. 3 (2007): 123–28. http://dx.doi.org/10.3233/cbm-2007-3302.
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Wu, Jing Li. "A Practical Heuristic Algorithm for the Minimum Founder Set Reconstructive Problem." Advanced Materials Research 393-395 (November 2011): 549–54. http://dx.doi.org/10.4028/www.scientific.net/amr.393-395.549.
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It has been generally accepted that current-day population evolved from a small number of specific sequences called founders, and the genomic sequences (called recombinants) of individuals within the population are composed of segments from the founders due to recombination. In this paper, the minimum founder set problem is studied. A practical heuristic algorithm HMFS is presented for solving the problem, which partitions the sites of founders into three parts and reconstructs them respectively. Experimental results show that HMFS can solve the minimum founder set problem fast and effectively. Furthermore, when the number of recombinants and SNP sites grows large, HMFS is still able to find satisfied solution to this problem very quickly. Hence it is practical in realistic applications
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DeVries, Ashleigh, Deborah Budge, Terry Schwaner, and Delilah Schwaner. "Genetic variation in founder populations of the Mediterranean gecko, Hemidactylus turcicus, across the southern United States." Amphibia-Reptilia 29, no. 3 (2008): 438–42. http://dx.doi.org/10.1163/156853808785112084.
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Abstract Populations initially founded by a small number of individuals risk chance increases in some genetic variants and experience periods during which only a few individuals survive to continue the existence of the population. Colonization of new locations by individuals from these founder populations is expected to result in further reduction of variation in founding populations. Tissue samples from the Mediterranean gecko, Hemidactylus turcicus, were subjected to allozyme electrophoresis to measure gene frequencies at two polymorphic loci for populations initially introduced to port cities along the Gulf Coast, and which are now distributed across the southern United States. We observed levels of polymorphism and heterozygosity that were markedly reduced in populations more distant from coastal localities, consistent with a hypothesis of founder effect.
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Davis, Michelle L., Carl Barker, Ian Powell, Keith Porter, and Paul Ashton. "Combining modelling, field data and genetic variation to understand the post-reintroduction population genetics of the Marsh Fritillary butterfly (Euphydryas aurinia)." Journal of Insect Conservation 25, no. 5-6 (2021): 875–86. http://dx.doi.org/10.1007/s10841-021-00354-3.
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Abstract The Marsh Fritillary butterfly (Euphydryas aurinia) is a Eurasian species which has suffered significant reductions in occurrence and abundance over the past century, particularly across the western side of its range, due to agricultural intensification and habitat loss. This loss has been particularly severe in the UK with extensive localised extinctions. Following sympathetic management, reintroduction was undertaken at four Cumbria (northern UK) sites in 2007 with stock from a captive admixture population descended from Cumbrian and Scottish founders. Annual population monitoring of the reintroductions was undertaken. Nine years post-reintroduction, the level of population genetic variation was assessed using microsatellites. Variation in historical Cumbrian samples was determined using museum samples and Scottish samples from current populations were assayed to characterise natural population variation. Half of the Scottish sites also served as indicators of the alleles present in the founder populations. The genetic contribution of the founder populations allied to population size data allowed patterns of genetic variation to be modelled. Alleles from Cumbrian and Scottish founders are present in the reintroduced populations. The four sites have levels of variation akin to natural populations and exhibit differentiation as predicted by statistical modelling and comparable with natural populations. This suggests that reintroduction following captive breeding can produce self-sustaining populations with natural levels of genetic diversity. These populations appear to be undergoing the same evolutionary dynamics with bottlenecks and drift as natural populations. Implications for insect conservation Reintroduction of captive bred individuals is a viable strategy for producing populations with natural levels of genetic diversity and evolutionary dynamics. Hybridisation of populations on the brink of extinction with those thriving can preserve some of the genetic distinctiveness of the declining population.
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Viluma, Agnese, Øystein Flagstad, Mikael Åkesson, et al. "Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population." Genome Research 32, no. 3 (2022): 449–58. http://dx.doi.org/10.1101/gr.276070.121.
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Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%–24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.
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Foote, Imogen, Stephanie S. Godfrey, and Bruce C. Robertson. "Mate choice explains high genetic diversity in a small founding population of the New Zealand sea lion (Phocarctos hookeri)." Australian Journal of Zoology 66, no. 6 (2018): 343. http://dx.doi.org/10.1071/zo19023.
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Founder populations are susceptible to reduced genetic diversity, which can hinder successful population establishment. A new genetic lineage of the New Zealand sea lion (Phocarctos hookeri) has recently colonised the historical range of the New Zealand mainland (Otago Peninsula). Despite a small founding population, previous research indicated that nuclear genetic diversity in the Otago Peninsula population is similar to that of the larger source population (Sandy Bay, Auckland Islands). Our research aimed to identify whether mechanisms of female mate choice could help to explain the unexpectedly high level of genetic diversity in the founder population. We used genetic data at 12 microsatellite loci for mother–pup pairs from both populations, and the software COLONY to identify putative paternal genotypes inferred from allele sharing between known mother–pup pairs. We found that mating pairs were, on average, more related at the Otago Peninsula location. However, Sandy Bay females were mating with males more related to themselves than expected by chance, while the Otago Peninsula females were not. These findings suggest that female choice in this otariid species appears important, although may be constrained in some situations. Our findings also help to explain how the recently founded population is able to maintain a viable, growing population.
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Karacaören, Burak. "Empirical comparison of association and admixture mapping for body weight using F<sub>2</sub> mice data set." Archives Animal Breeding 57, no. 1 (2014): 1–6. http://dx.doi.org/10.7482/0003-9438-57-005.
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Abstract. Recent advances in molecular genetics have provided hundreds of thousands of single nucleotide polymorphisms (SNPs) to detect mutations in genes related with complex traits. Undetected shared ancestry within samples of individuals could lead to the detection of false genomic signals in association mapping. Pedigree-based relationship matrices or genomic relationship matrices could be used in a mixed model to predict and correct for genetic stratifications. Genotypic information of founder populations could also be used to explore patterns of inheritance for complex traits by admixture mapping. An F2 population was created using M16 and ICR mouse lines for studying body weight at 8 weeks of age. Genotypes were collected for 1813 SNPs for each animal, including the founders. Bayesian residuals were used for population stratification in the admixture model. Association and admixture mapping detected similar genomic signals from chromosome 10. Our results provide empirical proof that gene flow from ancestral populations could be traced by admixture mapping with founder genotypes.
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Borowska, Alicja, and Tomasz Szwaczkowski. "Pedigree analysis of Polish warmblood horses participating in riding performance tests." Canadian Journal of Animal Science 95, no. 1 (2015): 21–29. http://dx.doi.org/10.4141/cjas-2014-006.
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Borowska, A. and Szwaczkowski, T. 2015. Pedigree analysis of Polish warmblood horses participating in riding performance tests. Can. J. Anim. Sci. 95: 21–29. The aim of this study was to describe the population structure and genetic diversity in Polish warmblood horse population participating in the performance test. The reference population consisted of 596 stallions and 866 mares that participated in stationary performance tests conducted between 2002 and 2011 in Poland. The pedigree data contained 15 452 individuals. Completeness of pedigree information was assessed by two measures: percentage of animals with both parents known and discrete generation equivalent. Individual inbreeding coefficients, coancestry coefficient, individual increase in inbreeding, founder equivalent, founder genome equivalent, effective number of non-founders and genetic diversity loss were estimated to characterize the genetic diversity of the population. The average number of discrete generation equivalents reached 4.50 for observed stallions and 5.04 for mares, which shows good pedigree completeness. Pedigree analysis showed that 34% of the stallions and 44% of mares had inbreeding coefficients above zero. The average coancestry was 0.39% in the whole tested population. Average inbreeding rate of studied populations was very low (0.46%). The effective number of founders was 560. Generally, the inbreeding rate was low; genetic diversity was observed at a constant level for mares and only a small decrease was noticed for stallion. However, further studies are needed in this area.
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Paixão, Gustavo, Alexandra Esteves, Rita Payan-Carreira, and Nuno Carolino. "Demographic structure and genetic diversity of the endangered Bísaro pig: Evolution and current status." Czech Journal of Animal Science 63, No. 11 (2018): 452–61. http://dx.doi.org/10.17221/113/2018-cjas.
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Bísaro pig, a local endangered swine breed, has gained popularity in the recent years. A complete pedigree was used to evaluate the population structure and investigate the current breed’s genetic variability in two reference populations (AlivePop and AliveBpop). Since the breed’s foundation, the number of registered animals, producers, and farrowing records has increased. The mean progeny size for sires was 116.17 ± 210.81, and 3.24% of the breeding boars originated 26.54% of all registered births showing a marked unbalanced use of certain sires. The mean calculated equivalent generations was 4.54, and 98.1% of all the animals had known parents, indicating a good degree of pedigree completion and depth. Approximately half of the individuals were inbred, with average inbreeding values of 10.41, 9.02, and 8.58% for the whole and reference populations, respectively. Considering both reference populations, a low effective founder/ancestor ratio was obtained (1.12), showing a well-balanced founder/ancestor contribution, and subsequent genetic transfer. However, the effective founder/founder ratio was particularly low (0.06 and 0.12) compared with other native breeds. The founder genome/effective founder ratios were 0.37 and 0.41 for AlivePop and AliveBpop. Contrarily to the whole population, the random genetic drift weighted significantly more than the drift due to unequal founder contribution in the reference populations. The effective population size based on the increase in coancestry ranged from 62.39 and 54.66, and 16.74 and 24.84 based on the increase of individual inbreeding, for the whole and reference populations. The genetic conservation index steadily grew over the years with a mean value of 6.53 for the whole pedigree. Genetic variability losses and diffuse structuring might have occurred in the Bísaro population. Notwithstanding, the recent genetic variability indicators seem positive, yet supported by an open herdbook policy. These characteristics must be taken into account to define future mating policies and selection programs.
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Tournebize, Rémi, Gillian Chu, and Priya Moorjani. "Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals." PLOS Genetics 18, no. 6 (2022): e1010243. http://dx.doi.org/10.1371/journal.pgen.1010243.
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Founder events play a critical role in shaping genetic diversity, fitness and disease risk in a population. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods require large sample sizes or phased genomes. Thus, we developed ASCEND that measures the correlation in allele sharing between pairs of individuals across the genome to infer the age and strength of founder events. We show that ASCEND can reliably estimate the parameters of founder events under a range of demographic scenarios. We then apply ASCEND to two species with contrasting evolutionary histories: ~460 worldwide human populations and ~40 modern dog breeds. In humans, we find that over half of the analyzed populations have evidence for recent founder events, associated with geographic isolation, modes of sustenance, or cultural practices such as endogamy. Notably, island populations have lower population sizes than continental groups and most hunter-gatherer, nomadic and indigenous groups have evidence of recent founder events. Many present-day groups––including Native Americans, Oceanians and South Asians––have experienced more extreme founder events than Ashkenazi Jews who have high rates of recessive diseases due their known history of founder events. Using ancient genomes, we show that the strength of founder events differs markedly across geographic regions and time––with three major founder events related to the peopling of Americas and a trend in decreasing strength of founder events in Europe following the Neolithic transition and steppe migrations. In dogs, we estimate extreme founder events in most breeds that occurred in the last 25 generations, concordant with the establishment of many dog breeds during the Victorian times. Our analysis highlights a widespread history of founder events in humans and dogs and elucidates some of the demographic and cultural practices related to these events.
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Ghafouri-Kesbi, F. "Using pedigree information to study genetic diversity and re-evaluating a selection program in an experimental flock of Afshari sheep." Archives Animal Breeding 55, no. 4 (2012): 375–84. http://dx.doi.org/10.5194/aab-55-375-2012.
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Abstract. The purpose of this paper was to evaluate the inbreeding consequences of a short-term selection experiment which was initiated in 1998 in an Afshari sheep flock. Moreover, the conducted selection experiment was re-evaluated through assessing change in ranking of the first 10 influential ancestors when their genetic contributions were replaced with their breeding values. A total of 1714 animals were registered in the herdbook with a founder population comprised of 243 animals. The average coancestry (f) and inbreeding (F) in the reference population were 2.1% and 1.2%, respectively. Estimated value of the effective population size (Ne) was 50. The effective number of founders (fe) was estimated to be 40 and the effective number of ancestors (fa) was 34. Estimates of breeding values revealed that owing to phenotypic selection some ancestors with lower breeding values had greater contribution to the reference genome than those with greater breeding values and, for this reason, the population has been deprived from the maximum genetic improvement that could be achieved if selection was based on breeding values. The effective number of founder genomes (fg) was computed to be 23 and the effective number of non-founder genomes (fne) was 55. The index of genetic diversity decreased by almost 2.2% over the period studied. In general, decrease in genetic variability was low and Ne was not very low for a small-closed population under selection, indicating even in populations which undergo selection, besides achieving genetic gain, the rate of inbreeding is controllable if matings carefully planned.
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Stratford, Ken J., Abigail S. Guerier, Stuart J. Crawford, Sabina M. C. Stratford, Anne Schmidt-Küntzel, and Jacqueline M. Bishop. "Female Southern White Rhinoceros Can Select Mates to Avoid Inbreeding." Journal of Heredity 112, no. 4 (2021): 385–90. http://dx.doi.org/10.1093/jhered/esab028.
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Abstract Current management models for many endangered species focus primarily on demographic recovery, often ignoring their intrinsic ecological requirements. Across the protected area network of southern Africa, most southern white rhinoceros are managed in populations of less than 50 individuals, experiencing restricted dispersal opportunities, and limited breeding male numbers due to their exclusive home range requirements. In the absence of information on the breeding structure of these populations, poor management decisions may require females to either forego a breeding opportunity or select to inbreed with close relatives. Here, we use a combination of social pedigree data together with genetic analyses to reconstruct the parentage of all 28 offspring produced in a 5-year period in a managed free-ranging southern white rhinoceros population. During this period, all breeding females (founders and first-generation daughters) had access to both a founder male (father to most of the daughters) and two recently introduced inexperienced males. We report that while founder females were more likely to breed with the founder male, their daughters, in contrast, were more likely to breed with the introduced males, thus avoiding inbreeding. However, we also found evidence of father–daughter inbreeding in this population, and contend that in the absence of choice, rather than forego a breeding opportunity, female white rhinoceros will inbreed with their fathers. We argue that to effectively conserve the southern white rhinoceros, managers need to understand the breeding structure of these small populations, particularly in terms of parentage and kinship.
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Markov, Nikolay, Maryana Ranyuk, Elmar Babaev, et al. "Introduced, Mixed, and Peripheral: Conservation of Mitochondrial-DNA Lineages in the Wild Boar (Sus scrofa L.) Population in the Urals." Diversity 14, no. 11 (2022): 916. http://dx.doi.org/10.3390/d14110916.
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Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
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Ghavi Hossein-Zadeh, Navid. "Analysis of population structure and genetic variability in Iranian buffaloes (Bubalus bubalis) using pedigree information." Animal Production Science 56, no. 7 (2016): 1130. http://dx.doi.org/10.1071/an14738.
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The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P < 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.
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Gunundu, Rodreck, Hussein Shimelis, and Seltene Abady Tesfamariam. "Genetic diversity and population structure analyses of tropical maize inbred lines using Single Nucleotide Polymorphism markers." PLOS ONE 20, no. 1 (2025): e0315463. https://doi.org/10.1371/journal.pone.0315463.
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Analyses of the genetic distance and composition of inbred lines are a prerequisite for parental selection and to exploit heterosis in plant breeding programs. The study aimed to assess genetic diversity and population structure of a maize germplasm panel comprising 182 founder lines and 866 derived inbred lines using Single Nucleotide Polymorphism (SNP) markers to identify genetically unique lines for hybrid breeding. The founder lines were genotyped with 1201 SNPs, and the derived lines with 1484 SNPs. Moderate genetic variation, with genetic diversity ranging from 0.004 to 0.44 with a mean of 0.25, was recorded for the founder lines, while corresponding values of 0.004 to 0.34 with a mean of 0.13 were recorded for the derived lines. Heterozygosity values ranging from 0.00 to 0.24 and a mean of 0.08 were recorded for both lines. Of the SNP markers used, 82% of the 1201 markers and 84% of the 1484 markers exhibited polymorphism information content ranging from 0.25 to 0.50. Analysis of molecular variance revealed significant genetic differences (P ≤ 0.001) among and within populations in the founder and derived lines. Most detected variations, i.e., 97% and 88.38%, were attributed to within populations in the founder and derived lines, respectively. Population structure analysis identified three distinct subpopulations among founder lines and two among derived lines. Cluster analysis supported the population structure The following genetically distant founder and derived inbred lines were selected: G15NL337 and G15NL312 (Cluster 1), 15ARG152 and RGS-PL44 (Cluster 2), RGS-PL44 and 15ARG149 (Cluster 2), and RGS-PL33 and RGS-PL44 (Cluster 2), respectively. The selected lines are genetically distinct and recommended for marker-assisted hybrid maize breeding to exploit the frequency of beneficial alleles. This study provides valuable insights for maize breeding programs, enabling the exploitation of beneficial alleles and contributing to improved crop yields and food security through hybrid breeding.
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Wilson, Gregory A., Tara L. Fulton, and Karsten Heuer. "When Theory Meets Practice: Balancing Genetic Diversity and Behaviour When Choosing Founders for a Recently Reintroduced Bison (Bison bison) Herd in Banff National Park, Canada." Diversity 15, no. 3 (2023): 366. http://dx.doi.org/10.3390/d15030366.
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The tragic decline of plains bison (Bison bison bison) in North America is well known. By the turn of the 20th century, plains bison, once numbering in the tens of millions, were extirpated from the wild in Canada. Banff National Park, AB, Canada, is within the original range of bison in North America, and still contains suitable habitat for the species. In 2017, we used measures of genetic diversity, as well as age and reproductive status, to select 16 plains bison for reintroduction to an unoccupied corner of their former historic range in Banff National Park. However, five of the preferred founders from this genetically diverse group needed to be substituted for less ideal candidates when aggressive behavior was observed, which could have compromised animal welfare during translocation. The level of genetic diversity in the founding population was therefore lower than if all proposed founders had been used, although the difference was not substantial. As expected, adults in this small, reintroduced herd had lower observed heterozygosity and number of alleles than the larger source herd, but expected heterozygosity was higher, likely a result of preferentially choosing individuals with rare alleles. Another substantial contribution to genetic diversity was in unborn fetuses: sired by males that were not translocated, the calves born a few months later provided a boost to the genetic diversity of this small founder herd. Where opportunities allow, the inclusion of pregnant females can significantly increase the genetic diversity of small founder populations. When compared to other founded herds of bison, the techniques described here have ensured that the newly established Banff NP herd is one of the most diverse bison herds in Canada, despite its relatively small number of founders.
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Thavornkanlapachai, Rujiporn, Harriet R. Mills, Kym Ottewell, J. Anthony Friend, and W. Jason Kennington. "Temporal Variation in the Genetic Composition of an Endangered Marsupial Reflects Reintroduction History." Diversity 13, no. 6 (2021): 257. http://dx.doi.org/10.3390/d13060257.
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The loss of genetic variation and genetic divergence from source populations are common problems for reintroductions that use captive animals or a small number of founders to establish a new population. This study evaluated the genetic changes occurring in a captive and a reintroduced population of the dibbler (Parantechinus apicalis) that were established from multiple source populations over a twelve-year period, using 21 microsatellite loci. While the levels of genetic variation within the captive and reintroduced populations were relatively stable, and did not differ significantly from the source populations, their effective population size reduced 10–16-fold over the duration of this study. Evidence of some loss of genetic variation in the reintroduced population coincided with genetic bottlenecks that occurred after the population had become established. Detectable changes in the genetic composition of both captive and reintroduced populations were associated with the origins of the individuals introduced to the population. We show that interbreeding between individuals from different source populations lowered the genetic relatedness among the offspring, but this was short-lived. Our study highlights the importance of sourcing founders from multiple locations in conservation breeding programs to avoid inbreeding and maximize allelic diversity. The manipulation of genetic composition in a captive or reintroduced population is possible with careful management of the origins and timings of founder releases.
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Heyer, Evelyne, Bruno Toupance, Cesare Perri, Ornella De Vito, Jean-François Foncin, and Amalia Cecilia Bruni. "Manic depressive illness in a founder population." European Journal of Human Genetics 11, no. 8 (2003): 597–602. http://dx.doi.org/10.1038/sj.ejhg.5201001.
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Amaratunga, Chanaki, Benoit Witkowski, Dalin Dek, et al. "Plasmodium falciparum Founder Populations in Western Cambodia Have Reduced Artemisinin SensitivityIn Vitro." Antimicrobial Agents and Chemotherapy 58, no. 8 (2014): 4935–37. http://dx.doi.org/10.1128/aac.03055-14.
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ABSTRACTReducedPlasmodium falciparumsensitivity to short-course artemisinin (ART) monotherapy manifests as a long parasite clearance half-life. We recently defined three parasite founder populations with long half-lives in Pursat, western Cambodia, where reduced ART sensitivity is prevalent. Using the ring-stage survival assay, we show that these founder populations have reduced ART sensitivityin vitroat the early ring stage of parasite development and that a genetically admixed population contains subsets of parasites with normal or reduced ART sensitivity.
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Aboagye, Elvis Twumasi, Samuel Mawuli Adadey, Edmond Wonkam-Tingang, Lucas Amenga-Etego, Gordon A. Awandare, and Ambroise Wonkam. "Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment." Genes 14, no. 2 (2023): 399. http://dx.doi.org/10.3390/genes14020399.
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The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number “CRD42020198573”. Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants’ origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.
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Brune, Alexander, Martin Thomsen, and Christoph Watrin. "Family Firm Heterogeneity and Tax Avoidance: The Role of the Founder." Family Business Review 32, no. 3 (2019): 296–317. http://dx.doi.org/10.1177/0894486519831467.
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Family business research suggests that the population of family firms cannot be regarded as a homogenous group. Therefore, with respect to tax avoidance, we analyze the role of the founder as one dimension of family firm heterogeneity. Specifically, we consider socioemotional wealth loss aversion and find that founders may affect the level of tax avoidance not only when they have direct influence (i.e., serving as CEO) but also when they possess solely indirect influence (i.e., having substantial ownership or a seat on the board). Overall, our results suggest that founders remain attached to their firms despite giving up executive positions.
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Major, Tamás, Réka Gindele, Gábor Balogh, Péter Bárdossy, and Zsuzsanna Bereczky. "Founder Effects in Hereditary Hemorrhagic Telangiectasia." Journal of Clinical Medicine 10, no. 8 (2021): 1682. http://dx.doi.org/10.3390/jcm10081682.
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A founder effect can result from the establishment of a new population by individuals from a larger population or bottleneck events. Certain alleles may be found at much higher frequencies because of genetic drift immediately after the founder event. We provide a systematic literature review of the sporadically reported founder effects in hereditary hemorrhagic telangiectasia (HHT). All publications from the ACVRL1, ENG and SMAD4 Mutation Databases and publications searched for terms “hereditary hemorrhagic telangiectasia” and “founder” in PubMed and Scopus, respectively, were extracted. Following duplicate removal, 141 publications were searched for the terms “founder” and “founding” and the etymon “ancest”. Finally, 67 publications between 1992 and 2020 were reviewed. Founder effects were graded upon shared area of ancestry/residence, shared core haplotypes, genealogy and prevalence. Twenty-six ACVRL1 and 12 ENG variants with a potential founder effect were identified. The bigger the cluster of families with a founder mutation, the more remarkable is its influence to the populational ACVRL1/ENG ratio, affecting HHT phenotype. Being aware of founder effects might simplify the diagnosis of HHT by establishing local genetic algorithms. Families sharing a common core haplotype might serve as a basis to study potential second-hits in the etiology of HHT.
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Järvelä, Irma, Tuomo Määttä, Anushree Acharya, et al. "Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland." Human Genetics 140, no. 7 (2021): 1011–29. http://dx.doi.org/10.1007/s00439-021-02268-1.
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AbstractThe genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.
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Mitchell, Simon, Koushik Roy, Thomas A. Zangle, and Alexander Hoffmann. "Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation." Proceedings of the National Academy of Sciences 115, no. 12 (2018): E2888—E2897. http://dx.doi.org/10.1073/pnas.1715639115.
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Rapid antibody production in response to invading pathogens requires the dramatic expansion of pathogen-derived antigen-specific B lymphocyte populations. Whether B cell population dynamics are based on stochastic competition between competing cell fates, as in the development of competence by the bacterium Bacillus subtilis, or on deterministic cell fate decisions that execute a predictable program, as during the development of the worm Caenorhabditis elegans, remains unclear. Here, we developed long-term live-cell microscopy of B cell population expansion and multiscale mechanistic computational modeling to characterize the role of molecular noise in determining phenotype heterogeneity. We show that the cell lineage trees underlying B cell population dynamics are mediated by a largely predictable decision-making process where the heterogeneity of cell proliferation and death decisions at any given timepoint largely derives from nongenetic heterogeneity in the founder cells. This means that contrary to previous models, only a minority of genetically identical founder cells contribute the majority to the population response. We computationally predict and experimentally confirm nongenetic molecular determinants that are predictive of founder cells’ proliferative capacity. While founder cell heterogeneity may arise from different exposure histories, we show that it may also be due to the gradual accumulation of small amounts of intrinsic noise during the lineage differentiation process of hematopoietic stem cells to mature B cells. Our finding of the largely deterministic nature of B lymphocyte responses may provide opportunities for diagnostic and therapeutic development.
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Goleman, Małgorzata, Ireneusz Balicki, Anna Radko, Iwona Rozempolska-Rucińska, and Grzegorz Zięba. "Pedigree and Molecular Analyses in the Assessment of Genetic Variability of the Polish Greyhound." Animals 11, no. 2 (2021): 353. http://dx.doi.org/10.3390/ani11020353.
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The aim of the study was to assess the genetic variability of the Polish Greyhound population based on pedigree analysis and molecular DNA testing and to determine the degree of relatedness among individuals in the population. Pedigree data of 912 Polish Greyhounds recorded in pedigree books since they were opened for this breed were analyzed. For molecular testing, DNA was obtained from cheek swabs taken from 235 dogs of the tested breed. A panel of 21 markers (Short Tandem Repeat—STR) was used. The mean inbreeding determined for the Polish Greyhound population based on pedigree analyses was low and amounted to 11.8%, but as many as 872 individuals of the 912 dogs in the studied population were inbred. A total of 83 founders (at least one unknown parent) were identified, among which 27 founders had both unknown parents. Full-sibling groups consisted of 130 individuals, with a minimum and maximum litter size of 2 and 16, respectively. The average litter size was 5.969. Gene diversity calculated based on the mean kinship matrix was 0.862 and the population mean kinship was 0.138. The founder genome equivalent based on the mean kinship matrix was 3.61; the founder genome surviving level was 12.34; the mean Ne was estimated at 21.76; and the Ne/N ratio was 0.135. The FIS inbreeding coefficient for 21 STR was negative, and the mean FIS value for all loci had a low negative value (−0.018). These values suggest a low level of inbreeding in the examined breed as well as the avoidance of mating related animals.
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Степанов, В. А. "Population Genomics of Russian populations." Nauchno-prakticheskii zhurnal «Medicinskaia genetika», no. 7(216) (July 30, 2020): 6–7. http://dx.doi.org/10.25557/2073-7998.2020.07.6-7.
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Популяционная геномика человека является мощным современным подходом в популяционной генетике, базирующемся на технологиях геномного секвенирования, биоинформатики и анализа больших данных. Геномный анализ генетической вариабельности в популяциях является фундаментальной основой генетики болезней и разработки путей их диагностики, терапии и профилактики. В работе представлены собственные данные о геномном анализе генетического разнообразия населения России. Показано, что генофонд современных народов России формировался на протяжении многих тысяч лет в ходе совокупного влияния миграций, изоляции расстоянием, эффектов основателя и естественного отбора. Сформировавшиеся в ходе микроэволюции геномные паттерны современных популяций в существенной мере определяют композицию генетических факторов как частых хронических, так и редких моногенных заболеваний. Human population genomics is a powerful modern approach in population genetics based on technologies of genomic sequencing, bioinformatics, and big data analysis. Genomic analysis of genetic variability in populations is a fundamental basis for the genetics of diseases and the development of ways for their diagnosis, therapy and prevention. The work presents the own data on the genomic analysis of the genetic diversity of the Russian populations. It is shown that the gene pool of modern populations of Russia was formed over many thousands of years by the combined effects of migrations, isolation by distance, founder effects and natural selection. The genomic patterns of modern populations formed during microevolution substantially determine the composition of genetic factors of both frequent chronic and rare monogenic diseases.
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Mufwene, Salikoko S. "The Founder Principle in Creole Genesis." Diachronica 13, no. 1 (1996): 83–134. http://dx.doi.org/10.1075/dia.13.1.05muf.
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SUMMARY In this paper, the author discusses one of the aspects of creole genesis from a population genetics perspective, analogizing 'language' with 'population' (rather than 'organism', the tradition in linguistics) and 'linguistic feature' with 'gene'. With language contact analogized to population contact, individual speakers are given a greater role than traditionally accorded them in the literature and variation within language is made more natural. Like genes, linguistic features are shown as competing with each other for selection into creoles' systems, in the different, though similar, ecologies of individual language contacts. It is argued here that the founder populations, including speakers of both lexifiers and substrate languages, played greater roles than hitherto considered in determining which specific features received selective advantage over their competitors during the formation of creoles. The Founder Principle explains why some European languages in their nonstandard forms became the principal lexifiers when others could have and why some specific features prevailed in the new systems. The competition-of-features perspective allows deterministic influences of both the lexifiers and substrate languages, thanks to convergence and other markedness principles, with the bioprogram qua Universal Grammar serving as the body of principles regulating the development of the new vernaculars. RÉSUMÉ Dans cet article l'auteur discute un des aspects de la genèse des creoles du point de vue de la génétique des populations. Il y compare la notion de 'langue' à celle de 'population' (plutôt qu'à celle d"organisme', la tradition en linguistique) et celle de 'trait linguistique' à celle de 'gène'. Cette comparaison du contact de langues à celui de populations accorde aux locuteurs un rôle plus grand qu'il n'est de coutume dans la littérature; la variation dans la langue se montre ainsi plus naturelle. Comme les gènes, les traits linguistiques se présentent en compétition mutuelle pour être sélectionnés dans les systèmes des creoles, dans des écologies différentes, bien que semblables, des contacts langagiers individuels. Selon mon hypothèse, la population fondatrice, y compris les locuteurs autant des langues lexificatrices que des langues substrates, ont joué des rôles plus importants qu'on leur reconnaît à présent en déterminant quels traits spécifiques ont eu un avantage sélectif par rapport à leurs alternatives pendant la formation des creoles. Le Principe Fondateur explique pourquoi quelques langues européennes dans leurs formes non standard sont devenues les principales lexificatrices, plutôt que d'autres langues qui auraient pu faire autant, et pourqoi quelques traits spécifiques se sont imposés dans les nouveaux systèmes. La perspective de la compétition des traits rend possible des influences déterministes à la fois des langues lexificatrices que des langues substrates, étant donné la convergence de certains de leurs traits et grace à d'autres principes sur lesquels est basé l'opposition marqué/non marqué. La Grammaire Universelle fonctionne dans mon hypothèse comme un corps de principes régissant le développement des nouveaux vernaculaires. ZUSAMMENFASSUNG Im vorliegende Beitrag diskutiert der Autor einen Aspekt der Genese von Kreolsprachen aus der Sicht einer Bevölkerungsgenetik, dabei eine Analogie zwischen 'Sprache' und 'Population' (anstelle von 'Organismus', wie es in der Linguistik Tradition ist) und zwischen 'sprachlicher Erscheinung' und 'Gen' herstellend. Wenn Sprachkontakt mit Populationskontakt in Analogie gesetzt wird, erhalten die Einzelprecher eine größere Rolle als ihnen gewöhnlich in der Forschung zuerkannt werden, und Variation innerhalb einer Sprache wird auf diese Weise ein weit natürlicherer Vorgang. Genen vergleichbar, konkurrieren linguïstische Eigenschaften untereinander um die Auswahl für das System einer Kreolsprache innerhalb der verschiedenen, wenngleich ähnlichen, 'Ökologien' individueller Sprachkontakte. Es wird hier die Behauptung aufgestellt, daß die 'Gründungspopulationen', inklusive der Sprecher von sowohl lexifizierenden als auch Substratsprachen, größere Rollen spielen als man bisher bei der Bestim-mung berücksichtigt hat, welche besondere Eigenschaften selektive Vorteile gegenüber anderen bei der Herausbildung von Kreolsprachen erhalten haben. Das 'Gründerprinzip' erklärt, weshalb einige europäische Sprachen in ihren nicht-standardisierten Formen die hauptsachlichen Lieferanten von Wortstruk-turen geworden sind, wenn andere es hatten werden können, und weshalb gewisse Eigenschaften in diesen neuem System die Oberhand gewannen. Der Gesichts-punkt eines Wettkampfs zwischen Eigenschaften ermöglicht bestimmbare Ein-flüsse auf sowohl von lexifizierenden als auch Substratsprachen, und zwar dank einer Konvergenz und anderer Merkmalprinzipien, wobei ein 'Bioprogramm' oder eine Universaliengrammatik als die Grundlage dazu dient, die Entwicklung neuer Volkssprachen zu regulieren.
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REYES-VALDÉS, M. HUMBERTO, and CLAIRE G. WILLIAMS. "An entropy-based measure of founder informativeness." Genetical Research 85, no. 1 (2005): 81–88. http://dx.doi.org/10.1017/s0016672305007354.
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Optimizing quantitative trait locus (QTL) mapping experiments requires a generalized measure of marker informativeness because variable information is obtained from different marker systems, marker distribution and pedigree types. Such a measure can be derived from the concept of Shannon entropy, a central concept in information theory. Here we introduce entropy-based founder informativeness(EFI), a new measure of information content generalized across pedigrees, maps, marker systems and mating configurations. We derived equations for inbred- and outbred-derived mapping populations. Mathematical properties of EFI include enhanced sensitivity to mapping population type and extension to any number of founders. To illustrate the use of EFI, we compared experimental designs for QTL mapping for three examples: (i) different marker systems for an F2 pedigree, (ii) different marker densities and sampling sizes for a BC1 pedigree and (iii) a comparison of haplotypic versus zygotic analyses of an outbred pedigree. As an a priori generalized measure of information content, EFI does not require phenotypic data for optimizing experimental designs for QTL mapping.
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Macedo, F., R. Félix Soares, T. Cunha Pereira, et al. "Founder mutations BRCA2 c.156_157insAlu in Portuguese population." Annals of Oncology 30 (May 2019): iii20. http://dx.doi.org/10.1093/annonc/mdz095.060.
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Carr, Aisling, JM Polke, J. Wilson, et al. "MFN2 DELETION FOUNDER MUTATION IN THE UK POPULATION." Journal of Neurology, Neurosurgery & Psychiatry 85, no. 10 (2014): e4.80-e4. http://dx.doi.org/10.1136/jnnp-2014-309236.170.
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Moreau, Claudia, Jean-François Lefebvre, Michèle Jomphe, et al. "Native American Admixture in the Quebec Founder Population." PLoS ONE 8, no. 6 (2013): e65507. http://dx.doi.org/10.1371/journal.pone.0065507.
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Mogga, Jacob, and Friedrich Ruttner. "Apis Floreain Africa: Source of the Founder Population." Bee World 69, no. 3 (1988): 100–103. http://dx.doi.org/10.1080/0005772x.1988.11098960.
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Haddad, Nizar, Stefan Fuchs, H. Randall Hepburn, and Sarah E. Radloff. "Apis floreain Jordan: source of the founder population." Apidologie 40, no. 4 (2009): 508–12. http://dx.doi.org/10.1051/apido/2009011.
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Tan, Eng-King, Lisa Skipper, Louis Tan, and Jian-Jun Liu. "LRRK2 G2019S founder haplotype in the Chinese population." Movement Disorders 22, no. 1 (2007): 105–7. http://dx.doi.org/10.1002/mds.21206.
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Kalaydjieva, Luba, Bharti Morar, Raphaelle Chaix, and Hua Tang. "A newly discovered founder population: the Roma/Gypsies." BioEssays 27, no. 10 (2005): 1084–94. http://dx.doi.org/10.1002/bies.20287.
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Wittke-Thompson, Jacqueline K., Nicoline Ambrose, Ehud Yairi, et al. "Genetic studies of stuttering in a founder population." Journal of Fluency Disorders 32, no. 1 (2007): 33–50. http://dx.doi.org/10.1016/j.jfludis.2006.12.002.
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Max-Aguilar, Adriana, Humberto Villarreal, Ignacio Leyva-Valencia, et al. "Genetic diversity of divergent redclaw crayfish Cherax quadricarinatus (Von Martens, 1868) populations evaluated to initiate a breeding program in Mexico." Latin American Journal of Aquatic Research 49, no. 2 (2021): 272–79. http://dx.doi.org/10.3856/vol49-issue2-fulltext-2630.
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Cherax quadricarinatus is a decapod crustacean of interest to the aquaculture industry. In Mexico, a significant effort has been made to improve biological requirements, but the genetic characteristics are unknown. We examined the genetic diversity and differentiation in four populations in Mexico (three commercial farms and one feral population), as well as one research line from Argentina, used as reference. To initiate a founder stock in a genetic improvement program, we analyzed five microsatellite markers. The genetic diversity in terms of the number of alleles was low to moderate (2.8-6.2) in Mexican populations than the Argentinean sample (8.8). A pairwise Wright's Fst analysis showed that all populations were significantly different (P < 0.5). Cross-breeding organisms from a different population are suggested to increase genetic variability before initiating a founder stock with higher genetic variation.
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de Bruyn, Mark, Malin L. Pinsky, Brenda Hall, Paul Koch, Carlo Baroni, and A. Rus Hoelzel. "Rapid increase in southern elephant seal genetic diversity after a founder event." Proceedings of the Royal Society B: Biological Sciences 281, no. 1779 (2014): 20133078. http://dx.doi.org/10.1098/rspb.2013.3078.
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Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal ( Mirounga leonina ) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.
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Álvarez, I., L. J. Royo, L. Pérez-Pardal, I. Fernández, L. Payeras, and F. Goyache. "Assessing losses of genetic variability in the endangered Mallorquí horse." Czech Journal of Animal Science 55, No. 10 (2010): 456–62. http://dx.doi.org/10.17221/1700-cjas.
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Information contained in the studbook of the endangered Mallorqu&iacute; horse was analysed to assess the genetic variability of the breed. Also, the effect of selection for coat colour variation was assessed using a set of 15 microsatellites genotyped on 68 Mallorqu&iacute; reproductive individuals previously diagnosed for the presence of the chestnut allele on the melanocortin-1 receptor gene. Mean inbreeding for the whole pedigree (310 individuals) was 2.5% while that for the individuals born during the last three years of recording (reference population) was 4.7%. Only 70% of all the founders have genetic representation in the reference population. A comparison of the parameters such as effective number of founders, effective number of ancestors and founder genome equivalents documented that the losses of founder genes occurred very soon after the implementation of conservation strategies. The parameter F<sub>IS</sub> computed from genealogical information was positive (0.029) for the whole population and negative (&ndash;0.024) for the reference population, thus illustrating the effort of the Mallorqu&iacute; horse breeders to avoid matings between relatives in later generations. A total of 14 individuals were heterozygotes for the chestnut allele (allele frequency of 10.6%). The rejection for reproduction of the chestnut heterozygote individuals would not affect the overall gene diversity of the population. However, the total allelic richness would decrease both at the within-subpopulation (1.2%) and total contribution level (0.4%). The chestnut heterozygote individuals are a within-breed reservoir of rare alleles that should be preserved to avoid risks for the future viability of the breed.
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Khaldari, M., A. N. Javaremi, A. Pakdel, H. M. Yeganeh, and P. Berg. "Management of genetic diversity using gene dropping method based on pedigree information." Archives Animal Breeding 56, no. 1 (2013): 518–26. http://dx.doi.org/10.7482/0003-9438-56-050.
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Abstract. Preservation of genetic diversity in populations is an important task to ensure a possible longterm response to selection in animal breeding. The purpose of this study was to consider how pedigree analysis and gene dropping method could be used for management plans in order to maintain genetic variation in a population under selection of Japanese quail. Therefore, the distributions of alleles frequencies originated from founders were estimated on an actual pedigree using gene dropping simulation software. Then, genetic contribution of founders to the current population, components such as the F-statistics and effective population size were estimated. The results show that from 156 founders there are only 64 of them (22 males and 42 females) in the last generation. The average genetic contribution of a founder male and female contributing to the last generation were 1.87 and 1.40 %, respectively. A total of 87 and 95 % of the genome in the last generation were constituted by 34 and 42 founders, respectively. The effective population size decreased as inbreeding increases. The allele frequency averaged over replicates agreed with the genetic contribution. Some useful information regarding the management of genetic diversity such as the probability of allele extinction, the probability of alleles surviving at a critically low frequency and risk of future allele extinction were derived by using these distributions. Results show that pedigree analysis and gene dropping are valuable tools in optimizing decisions to preserve genetic variability.
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Sarmiento, Derly Rodríguez, Emanuela Tullo, and Rita Rizzi. "Pedigree-based analysis of genetic variability in the registered Normande cattle breed in Colombia." Animal Production Science 57, no. 3 (2017): 422. http://dx.doi.org/10.1071/an15057.
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Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.
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Ahlroth, Petri, Rauno V. Alatalo, Anne Holopainen, Tomi Kumpulainen, and Jukka Suhonen. "Founder population size and number of source populations enhance colonization success in waterstriders." Oecologia 137, no. 4 (2003): 617–20. http://dx.doi.org/10.1007/s00442-003-1344-y.
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Anseeuw, Dieter, Joost A. M. Raeymaekers, Paul Busselen, Erik Verheyen, and Jos Snoeks. "Low Genetic and Morphometric Intraspecific Divergence in Peripheral Copadichromis Populations (Perciformes: Cichlidae) in the Lake Malawi Basin." International Journal of Evolutionary Biology 2011 (May 14, 2011): 1–11. http://dx.doi.org/10.4061/2011/835946.
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Peripheral isolated populations may undergo rapid divergence from the main population due to various factors such as a bottleneck or a founder effect followed by genetic drift or local selection pressures. Recent populations of two economically important Copadichromis species in Lake Malombe, a satellite lake of Lake Malawi, were neither genetically nor morphometrically distinct from their source populations in the main lake. Evidence was found for a founder effect which had a different impact on the genetic composition of the two species. In addition, the increased fishing pressure in Lake Malombe may have led to a reduction of the body sizes of both species.
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Borg, Åke, Anne Dørum, Ketil Heimdal, Lovise Mæhle, Eivind Hovig, and Pål Møller. "BRCA1 1675delA and 1135insA Account for One Third of Norwegian Familial Breast-Ovarian Cancer and Are Associated with Later Disease Onset than Less Frequent Mutations." Disease Markers 15, no. 1-3 (1999): 79–84. http://dx.doi.org/10.1155/1999/278269.
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A total of 845 women from breast-ovarian cancer kindreds were enrolled in a clinical follow-up program for early disease diagnosis; 35 women were prospectively identified with cancer. In order to estimate the role of genetic factors for cancer predisposition in this well-defined set of patients, considered as representative for familial breast-ovarian cancer in the Norwegian population, the BRCA1 gene was investigated for germline mutations. The entire coding region of BRCA1 was analysed using a protein truncation test, direct sequencing and a screen for known large genomic deletions and insertions. Twenty one (60%) of the 35 patients were identified as carriers of 11 distinct BRCA1 mutations. Two previously described founder mutations, 1675delA and 1135insA, were found to account for more than half (11/21) of all BRCA1 cases and for almost one third (11/35) of all breast and ovarian cancers. Supported by a previous population-based analysis of these founder mutations in ovarian cancer, our findings suggest that a significant proportion of women at risk for developing inherited breast and ovarian cancer can be identified. This is particularly obvious in certain geographic regions where these founder mutations are prevalent. Women carrying the two founder mutations had a significantly older age of disease onset as compared to women with other BRCA1 mutations. This observation indicates that BRCA mutation penetrance estimates from populations with strong founder effects may be biased. One reason why some deleterious mutations are allowed to prevail in a population may be coupled to penetrance and the fact that they seldom induce disease in women in child-bearing ages. Eleven out of 12 (92%) breast cancers in BRCA1 mutation carriers were estrogen receptor negative, versus 4 out of 9 (44%) in mutation negative patients (p = 0.03). Histopathological characteristics of the prospectively detected cancers indicated an unfavourable prognosis in mutation carriers.
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Zhan, J., C. C. Mundt, and B. A. McDonald. "Using Restriction Fragment Length Polymorphisms to Assess Temporal Variation and Estimate the Number of Ascospores that Initiate Epidemics in Field Populations of Mycosphaerella graminicola." Phytopathology® 91, no. 10 (2001): 1011–17. http://dx.doi.org/10.1094/phyto.2001.91.10.1011.
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Restriction fragment length polymorphisms (RFLPs) and DNA fingerprints were used to assess temporal variation and estimate the effective population size of the wheat pathogen Mycosphaerella graminicola over a 6-year period. In each year, the fungal population was founded by ascospores originating from outside the sampled fields. A total of 605 fungal isolates were included in this study. Our results indicate that the genetic structure of these M. graminicola populations were stable over the 6-year period. The common alleles at each RFLP locus were present at similar frequencies each year. More than 99% of gene diversity was distributed within populations sampled from the same year and less than 1% was attributed to differences among years. The lack of population differentiation among collections taken in different years indicated that the effective size of the source population was sufficiently large that genetic drift was insignificant in this location. It also suggests that the initial colonists from ascospore founder populations were a fair reflection of the source population. We estimate that the effective sizes of these field populations ranged from 3,400 to 700,000 individuals, depending on the size of the field sampled and assumptions about mutation rates. Estimates of the number of ascospores initiating epidemics of leaf blotch disease in each field plot and factors that contribute to the large effective population size of M. graminicola are discussed.
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Trinderup, M., J. N. Jørgensen, and M. Hansen. "Inbreeding and loss of founder alleles in four variations of a conservation programme using circular mating, for Danish Shorthorn Cattle." Animal Genetic Resources Information 25 (April 1999): 99–106. http://dx.doi.org/10.1017/s1014233900003485.
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SummaryThe beef cattle breed Danish Shorthorn is used as a model for simulation of four variations of the circular mating scheme running for 50 years. Schemes 1 and 2 used a fixed exchange of bulls between female groups while schemes 3 and 4 used a random exchange of bulls between female groups. The number of bulls used in schemes 1 and 4 was 16 while the number of bulls used in schemes 2 and 3 was 8. Inbreeding levels were computed and gene dropping was applied to estimate the risk of founder allele loss. In the population of year 50 the inbreeding levels for the four mating schemes are not statistically different. The male founder alleles contribute strongly to the population of year 50. The female founder alleles are in greater risk of being lost than the male founder alleles.
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Forsman, Anders, Lena Wennersten, Magnus Karlsson, and Sofia Caesar. "Variation in founder groups promotes establishment success in the wild." Proceedings of the Royal Society B: Biological Sciences 279, no. 1739 (2012): 2800–2806. http://dx.doi.org/10.1098/rspb.2012.0174.
Full textAbstract:
Environmental changes currently pose severe threats to biodiversity, and reintroductions and translocations are increasingly used to protect declining populations and species from extinction. Theory predicts that establishment success should be higher for more variable groups of dissimilar individuals. To test this ‘diversity promotes establishment’ hypothesis, we introduced colour polymorphic pygmy grasshoppers ( Tetrix subulata ) to different sites in the wild. The number of descendants found at the release sites the subsequent year increased with increasing number of colour morphs in the founder group, and variation in founder groups also positively affected colour morph diversity in the established populations. Since colour morphs differ in morphology, physiology, behaviour, reproductive life history and types of niche used, these findings demonstrate that variation among individuals in functionally important traits promotes establishment success under natural conditions, and further indicate that founder diversity may contribute to evolutionary rescue and increased population persistence.