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Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases

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Abstract

A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two populations or species. To express the degree of polymorphism in a population at the nucleotide level, a measure called "nucleotide diversity" is proposed.

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... On the basis of these ISSR data, Nei and Li (1979) band-sharing distances and Nei genetic distances (Nei, 1972) were calculated using the PHYLIP (version 3.5c) package (Felsenstein, 1993). The difference between the two distance measures is that the first regards only the shared presence of a band, whereas the second gives equal weight to the shared absence and shared presence of a band. ...
... THE SIMILARITY TREE. The dendrogram generated from the ISSR band-sharing distance matrix (Nei and Li, 1979) using the neighbor-joining algorithm (Fig. 2) displays the similarities and divergences among lychee cultivars and accessions. The divergence can be deduced from the length of the horizontal branches. ...
... 2) Subgroup 2-2 includes two accessions (23, 49), which resemble the accessions of subgroup 2-3 morphologically, but are at a somewhat greater genetic distance. The third member (1) is a lo- Fig. 2. A similarity dendrogram of 66 lychee accessions, generated by neighborjoining analysis using Nei and Li (1979) band-sharing distances, based on the ISSR data. The numbers at the forks are bootstrap values, which are the number of times the grouping at the right of that fork was found in 1000 bootstrap resamplings. ...
Article
There is widespread confusion and uncertainty concerning the identity of lychee cultivars: the same cultivar may be known under different names and different cultivars may appear under the same name. In the present study, the potential of intersimple sequence repeat (ISSR) for the identification of 66 lychee cultivars and accessions and a determination of their genetic relationships was evaluated, using 32 primers containing different simple sequence repeat motifs. Of the 194 bands produced, 124 (64%) were polymorphic. A set of six ISSR primers was sufficient to distinguish all cultivars and accessions. Thus, cultivars which are morphologically very similar and have identical isozyme profiles can be distinguished by ISSR analysis. However, seven pairs of accessions, each considered to be the same cultivar, were found to be identical by ISSR analysis. Nei and Li band-sharing distances and Nei genetic distances were calculated among the cultivars and two similarity dendrograms were generated using the neighbor-joining algorithm. Results showed that the ISSR technique is a valuable tool for identification of lychee cultivars and analysis of their genetic relationships.
... Specialized software BIO-1D++, version 11.07 was used to create databases for the gliadin patterns of the studied genotypes. A Nei & Li (1979) genetic similarity coefficient was calculated for all pairs of electrophoregrams, using the results of the electrophoretic band pattern as a basis. The similarity matrix was used to construct the dendrogram by the UPGMA. ...
... In all the Agelops samples all bands were polymorphic and the mean diversity estimate was high (H = 0.947) (Table 6). Therefore, populations of the studied Aegilops species can be used to increase the Nei & Li (1979) BGR44236, 2-BGR43678, 3-BGR43704, 4-BGR44232, 5-BGR19081, 6-BGR43668, 7-C3E0144, 8-BGR43704 A, 9-BGR44234, 10-BGR44617, 11-BGRR43676, 12-BGR43660, 13-BGR43684, 14-BGR43687, 15-BGR43663, 16-BGR43702, 17-BGR43677, 18-BGR43675, 19-BGR43540, 20-BGR30391, 21-BGR9315 (Marquis). In our study, the international standard variety Marquis (Bushuk & Zillman, 1978;Metakovsky et al., 2018) was used to identify γ-45 and γ-42 in the studied genotypes (Yupsanis & Moustakas, 1988). ...
... In order to find the genetic relationship between the Aegilops accessions, the genetic similarity was calculated based on the Nei & Li (1979) coefficient. The average genetic similarity between all 20 genotypes range from 0.14 to 0.93 with a mean of 0.56. ...
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The objective of the study was to evaluate the genetic diversity in twenty Aegilops accessions belonging to five plant species with respect to specific grain morphometric parameters and gliadin proteins, employing digital image analysis and A-PAGE electrophoresis. The considerable variation was observed among accessions for grain morphometric traits-area, perimeter, length, width and colour of grain. A total of 96 gliadin polymorphic bands were identified, with the number of bands varying between 13 and 22 per accession. The overall genetic diversity in the samples based on the patterns observed for each of the four gliadin regions showed that the ω, γ and β regions had high genetic variation index (H = 0.950), while α regions (H = 0.938), respectively. The mean genetic diversity estimate was high (H = 0.947). The average genetic similarity between all 20 genotypes ranges from 0.14 to 0.93 with a mean of 0.56, indicating that the studied accessions exhibited considerable genetic variability. The study found that the clustering of Aegilops genotypes was not linked to their geographic origin. Two-dimensional Principal Coordinates Analysis (PCoA) based on the gliadin and morphometric analyses revealed wide genetic dissimilarity between most of the genotypes, explaining 97.16% of the variations, with the model explaining 97.16% of the observed variation. Of this, PCo1 accounted for 93.65% and PCo2 for 3.51%. Genotypes with analogous genomes were grouped in close proximity within the phylogenetic tree, indicating that their evolutionary relationships may have originated from the same parental lineage.
... Principal Coordinate Analysis (PCoA) was performed at the individual level using the Nei and Li (1979) coefficient in R (R Core Team 2025). Haplotype definition and genealogical relationships among haplotypes in datasets 6, 7, and 8 were independently inferred using the median-joining (MJ) method (Bandelt et al. 1999) in Network 5.0.0.3 (Fluxus Technology Ltd., Cambridge). ...
... The number of isolates of each lineage are shown in parenthesis in front of lineages names. Principal coordinate analysis (PCoA) was carried out onNei and Li (1979) coefficient using software R in UBL significantly deviated from the null hypothesis of a 1:1. None of the isolates contained both idiomorphs. ...
... The number of isolates is shown in front of each sub-lineage names. Principal coordinate analysis (PCoA) was carried out onNei and Li (1979) coefficient using software R Genetic clusters estimated by Bayesian analysis of population structure using the admixture model of BAPS. Clustering based on dataset 9 (N = 256, 3178 bp) containing fragment of four nuclear genes (ITS, cfp, tub and mcm7). ...
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The genus Cercospora is widely distributed and causes foliar diseases, including those affecting soybean. Cercosporoid species exhibit high intraspecific variation, and the lack of distinct morphological features has led to host plant association becoming a key criterion for species delimitation. Recently, in addition to C. kikuchii , other species such as C. cf. flagellaris, C. cf. sigesbeckiae , and C. cf. nicotianae have been linked to Cercospora Leaf Blight (CLB) and Purple Seed Stain (PSS) in soybean. In this study, phylogenetic and phylogeographic analyses were used to identify six Cercospora lineages responsible for causing CLB and PSS across Brazil. A total of 256 Cercospora isolates were obtained from eight states in Brazil, and DNA was extracted to sequence 10 polymorphic nuclear and mitochondrial gene fragments. Bayesian phylogenetic analysis was performed to infer relationships among the isolates. Eight lineages were associated with CLB and PSS, six of which were exclusively found in Brazil, while two were restricted to the United States. We propose that these lineages represent cryptic species of Cercospora , producing similar symptoms on leaves and seeds. Principal coordinate analysis supported the Bayesian phylogenetic results, explaining 84% of the variation through three principal coordinates. Bayesian population structure analysis detected no evidence of admixture among isolates. Additionally, nine out of ten tested lineages exhibited a 1:1 ratio of MAT1-1 to MAT1-2 mating-type alleles. Our findings reveal the presence of multiple Cercospora lineages causing CLB and PSS in soybean, demonstrating that species identification based solely on host association is unreliable.
... (iii) PI: The mean and the standard deviation of the expected heterozygosity across segregating sites (Nei and Li 1979). (iv) WinH: the mean and the standard deviation of the haplotypic heterozygosity computed for non-overlapping windows of size 50 kb. ...
... We computed the mean and the standard deviation of the length of AFIBS segments for the SNPs of frequency i for all i in [1, …, 2n].The among-population statistics classes were: (ix) Fst: the fixation index(Wright 1950). (x) Dxy: genetic divergence between the two populations(Nei and Li 1979). (xi) JSFS: Joint site frequency spectrum(Wakeley and Hey 1997): The percentage of SNPs where the derived allele is present at a frequency i in population 1 and j in population 2. ...
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The ever-increasing availability of high-throughput DNA sequences and the development of numerous computational methods have led to considerable advances in our understanding of the evolutionary and demographic history of populations. Several demographic inference methods have been developed to take advantage of these massive genomic data. Simulation-based approaches, such as approximate Bayesian computation (ABC), have proved particularly efficient for complex demographic models. However, taking full advantage of the comprehensive information contained in massive genomic data remains a challenge for demographic inference methods, which generally rely on partial information from these data. Using advanced computational methods, such as machine learning, is valuable for efficiently integrating more comprehensive information. Here, we showed how simulation-based supervised machine learning methods applied to an extensive range of summary statistics are effective in inferring demographic parameters for connected populations. We compared three machine learning (ML) methods: a neural network, the multilayer perceptron (MLP), and two ensemble methods, random forest (RF) and the gradient boosting system XGBoost (XGB), to infer demographic parameters from genomic data under a standard isolation with migration model and a secondary contact model with varying population sizes. We showed that MLP outperformed the other two methods and that, on the basis of permutation feature importance, its predictions involved a larger combination of summary statistics. Moreover, they outperformed all three tested ABC algorithms. Finally, we demonstrated how a method called SHAP, from the field of explainable artificial intelligence, can be used to shed light on the contribution of summary statistics within the ML models.
... To estimate the genetic diversity within and divergence between species, F ST (Weir and Cockerham, 1984), d XY (Nei and Miller, 1990), and π (Nei and Li, 1979) were computed in 5 kb windows for all species pairs using pixy 1.2.7 (Korunes and Samuk, 2021) and the all-sites dataset. To ensure data reliability, windows with coverage below 50% (in each pairwise comparison) were discarded. ...
... To ensure data reliability, windows with coverage below 50% (in each pairwise comparison) were discarded. The means for each statistic and the net divergence between species (d a ; Nei and Li (1979)) were calculated. ...
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Speciation can be broadly understood within two non-mutually exclusive frameworks: genetic drift under isolation and natural selection under ecological divergence. Here, we examined the genomic diversity and differentiation of five Typha species, a group of plants foundational to freshwaters with widespread, partially sympatric distributions and at least one widespread hybrid zone. Using genome-wide data from 207 individuals, we examined the contributions of demographic fluctuations, selection, and hybridisation in driving their speciation history. Demographic reconstructions revealed sequential bottlenecks and expansions coincident with lineage splits, and indicated a drift-driven scenario with no migration events for all five species. The genomic landscapes showed balancing selection, sparse divergent selection, and low net divergence. Introgressions from T. latifolia to T. angustifolia and T. domingensis were found. Our findings suggest histories of allopatric speciation followed by range expansions and secondary contacts, leading to contemporary hybridisation between some species. Our results also emphasise the roles of balancing selection and introgression as sources of standing genetic variation. Allopatric speciation in T. latifolia and T. angustifolia could explain their ability to hybridise, highlighting the need to stop the human-mediated dispersal of Typha (e.g., the intercontinental sourcing via garden centres).
... Nucleotide diversity (π), divergence (d xy ), heterozygosity, and F ST are fundamental population genetic summary statistics that summarize key aspects of population history and structure. π measures genetic variation within populations (Nei and Li 1979), d xy quantifies genetic distance between populations (Nei and Li 1979), heterozygosity reflects genetic diversity at the individual level, and F ST measures population differentiation (Hudson et al. 1992;Bhatia et al. 2013). Accurate estimation of these statistics is essential for inferring demographic history, detecting selection, and understanding speciation processes (Hendricks et al. 2018;Luikart et al. 2018;Hohenlohe et al. 2021). ...
... Nucleotide diversity (π), divergence (d xy ), heterozygosity, and F ST are fundamental population genetic summary statistics that summarize key aspects of population history and structure. π measures genetic variation within populations (Nei and Li 1979), d xy quantifies genetic distance between populations (Nei and Li 1979), heterozygosity reflects genetic diversity at the individual level, and F ST measures population differentiation (Hudson et al. 1992;Bhatia et al. 2013). Accurate estimation of these statistics is essential for inferring demographic history, detecting selection, and understanding speciation processes (Hendricks et al. 2018;Luikart et al. 2018;Hohenlohe et al. 2021). ...
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The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversity (π) and divergence (dxy). Unbiased estimates of diversity require knowledge of missing data and existing tools require all-sites VCFs. However, generating these files is computationally expensive for large datasets. Here, we introduce Callable Loci And More (clam), a tool that leverages callable loci -- determined from depth information -- to estimate population genetic statistics using a variant-only VCF. This approach offers improvements in storage footprint and computational performance compared to contemporary methods. We benchmark clam using a large muskox dataset and demonstrate that it produces unbiased estimates of π while reducing runtime and storage requirements, compared to an existing approach. clam provides an efficient and scalable alternative for population genomic analyses, facilitating the study of increasingly large and diverse datasets. clam is available as a standalone program and integrated into snpArcher for efficient reproducible population genomic analysis.
... Otros datos como los obtenidos desde fuentes ecológicas y fisiológicas pueden ser considerados para sumar a la exploración de la delimitación de los taxones, traducidos en datos cualitativos o cuantitativos (Nei y Li, 1979;Palacio et al., 2020). ...
... Los análisis de distancias genéticas que evalúan las mutaciones pueden ser divididos en dos grandes grupos (a) los que reflejan la similitud entre poblaciones sin considerar a priori modelos evolutivos (distancias geométricas) (Cavalli-Sforza y Edwards, 1967;Rogers, 1972;Nei et al., 1983), y (b) los que presuponen modelos evolutivos a priori de sustitución nucleotídica (Tamura y Nei, 1993;Takezaki y Nei, 1996). En el primer caso (a), por ejemplo, si lo que se analiza son matrices de presencia/ausencia de bandas de ADN o de proteínas, obtenidas por electroforesis, el coeficiente más adecuado es el desarrollado por Dice en 1945, entre otros (Nei y Li, 1979; Núñez-Colín y Escobedo-López, 2011). En el segundo caso (b), uno de los coeficientes utilizados con mayor frecuencia es el de distancia de Nei (1972), que considera una tasa de mutación constante e igual para todos los loci, poblaciones con tamaños efectivos iguales y constantes a través de las generaciones y poblaciones en equilibrio mutación-deriva (Takezaki y Nei, 1996). ...
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La obra contiene ocho capítulos que siguen el programa vigente de la materia Introducción a la Taxonomía de la Facultad de Ciencias Naturales y Museo (UNLP). El material organiza y presenta las temáticas y ejercicios que se abordan a lo largo del curso. Cada capítulo consiste en una selección de ejercicios prácticos acompañados de una breve introducción teórica necesaria para su desarrollo. También se presentan tutoriales para la utilización de los programas informáticos necesarios para trabajar con las matrices brindadas en algunos ejercicios.
... where π total and π within are the total nucleotide diversity and nucleotide diversity observed within lineages, respectively 133 . The d XY is estimated as 1 n P m i¼1 p i1 q i2 þ p i2 q i1 , where p i1 and q i1 represent the frequencies of alternative alleles at locus i in lineage 1, and p i2 and q i2 are the frequencies of those alleles at the same locus in lineage 2. The value m stands for the count of variable sites, and n is the total count of both variable and unchanging sites in the interval used for estimating d XY 134 . Each statistic across comparisons was summarized by standardization and PCA by the scale and prcomp function in R. ...
... The first principal components of each standardized genetic statistic (i.e., PC1 π, PC1 zd XY , PC1 zF ST ), recombination rate, gene density, and mean f d were used for calculating Pearson's correlations 61 . The pairwise corrected estimate of sequence divergence (d a ), as the proxy of divergence time for each comparison, was further calculated by subtracting the mean π (π mean ¼ π x Àπ y 2 ) from the pairwise d XY for each window 134 . ...
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Cryptic diversity in evolutionary radiation offers an excellent system for investigating the intricacies of evolutionary progress. Understanding the evolution of cryptic diversity is imperative for unraveling the hidden complexities of biodiversity. However, empirical evidence elucidating the mechanisms behind cryptic radiation remains limited, particularly in plants. Here, we focus on a monophyletic group of Aquilegia species mainly distributed in the mountains of Southwest China, one of the world’s biodiversity hotspots. Using whole-genome resequencing of 158 individuals from 23 natural populations, we identify three to four paraphyletic lineages within each morphological species. Our findings reveal that 39 out of 43 detected instances of introgression occurred post-lineage formation. Identifying shared genomic regions indicates that the divergence of fixed singletons in lineages from morphological species A. kansuensis and A. rockii predates lineage formation, supporting a scenario where incomplete lineage sorting of standing variation contributes to morphological parallelism. Furthermore, strong positive correlations among genomic differentiation, divergence, and introgression suggest that standing variations and introgression from non-sister lineages contribute to the rapid genetic divergence. Our study illuminates the important roles of standing variations and introgression in plant cryptic radiation, advancing our understanding of the complex mechanisms behind the evolution of biodiversity in recent radiation events.
... Data analysis SRAP profile scoring of clearly visible amplified band was recorded as presence (1) and absence (0), the binary scored data was subjected to NTSYSpc version 2.02i to compute the similarity matrix based on the Dice coefficient (Rohlf 1990), also known as the similarity coefficient of (Nei and Li 1979). Clustering analysis was conducted using the unweighted pair-group method with arithmetic mean (UPGMA) to construct the dendrogram. ...
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Tuberose (Agave amica), a commercially significant ornamental plant, exhibits limited genetic diversity due to restricted breeding efforts. Assessing genetic variation is essential for breeding advancements and conservation strategies. This study aimed to evaluate the agro-morphological differentiation and genetic diversity among 13 tuberose cultivars using multivariate phenotypic analysis and sequence-related amplified polymorphism (SRAP) markers. Multifactorial Analysis (MFA) identified four principal factors, explaining 84.103% of the total variation, with plant height, spike length, and flower length being major contributors. Agglomerative Hierarchical Clustering (AHC) further categorized genotypes based on floral traits and genetic similarity. The 80 SRAP primer combinations were tested, 14 produced consistent and scorable amplification patterns, generating 63 bands, of which 54 (81%) were polymorphic. The polymorphic information content (PIC) ranged from 0.07 to 0.92, with an average of 0.52, indicating high level of marker informativeness. Jaccard’s similarity coefficients ranged from 0.51 to 0.89, reflecting significant genetic variability. Unweighted pair-group method with arithmetic mean (UPGMA) clustering grouped the cultivars into two major clusters, aligning their genetic background and morphological traits. Comparative analysis of molecular and morphological clustering revealed both congruence and discrepancies, emphasizing the influence of genetic background and environmental factors on phenotypic expression. This study provides a robust framework for marker-assisted selection and conservation strategies, ensuring the genetic sustainability and improvement of tuberose cultivars.
... Moreover, the software program (GENEPOP) was used to determine the level of global genetic differentiation among populations and population pairs using F st measures. The genetic relationship among the genotypes studied was calculated using UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analysis of the similarity matrix obtained from the proportion of shared amplification fragments (Nei and Li, 1979) using the R software (R Core Team, 2021). The dendrogram obtained was formatted using ITOL v6.8.1 (Letunic and Bork, 2021). ...
... The OP672342 was thus discarded from the alignment for all the subsequent analyses. The program SPADS was also used to estimate the nucleotide diversity π (Nei and Li, 1979) within each country. ...
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African swine fever virus (ASFV) is a highly virulent DNA virus that causes African swine fever, a severe hemorrhagic disease affecting domestic and wild pigs, leading to significant animal health burdens and economic losses. Initially limited to the sub-Saharan African region, ASFV genotype II has spread globally and is now a major concern in Africa, Europe, Asia, the Pacific and, more recently, the Caribbean. In this study, we performed phylogenetic and phylogeographic analyses using newly sequenced ASFV genomes from Lithuania, combined with previously available complete genomes, to investigate the spatiotemporal dispersal dynamics of ASFV genotype II in Europe. Our analysis suggests that ASFV genotype II has not been recently imported to Europe from other regions; instead, the spread is largely driven by long-distance dispersal, followed by regional (within-country) circulation. The estimated dispersal metrics suggest that ASFV has a slower dispersion capacity compared to other pig-transmitted viruses and is associated with a notable degree of spatial structure. Despite these findings, significant uncertainty remains regarding certain ancestral locations, highlighting challenges related to applying phylodynamic methods to DNA viruses with low genetic variability. Nevertheless, in our study, we managed to implement a phylogeographic framework to investigate major patterns of ASFV dispersion in Europe and the contribution of international importations in the establishment of regional transmission chains. This framework could be further expanded as more genomes become available. Our study emphasizes the need for increased genomic surveillance to enlarge the ASFV genome database to support outbreak control.
... To assess intraspecific genetic diversity, we calculated nucleotide diversity (π), which represents the average number of nucleotide differences per site between pairs of sequences (Nei & Li, 1979). While other measures such as the number of haplotypes or haplotype diversity are often used, they were not suitable for our dataset. ...
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Aim To investigate how past climate change has shaped the genetic diversity and demographic responses of tarantulas across latitudes, and to test whether climate–demography relationships vary with latitude. Location Global; spanning tropical to temperate regions. Taxon Tarantulas (family Theraphosidae). Methods We compiled mitochondrial Cytochrome oxidase I (COI) sequences for 48 tarantula species worldwide, including newly generated sequences, to estimate nucleotide diversity (π) and Tajima’s D. Species distribution models (SDMs) were constructed under present-day and Last Glacial Maximum (LGM) climatic conditions to quantify changes in habitat suitability since the LGM. Using generalized linear models (GLMs), we tested whether genetic and demographic metrics were associated with latitude and climate-driven habitat change, and whether their relationship varied with latitude. Results Pairwise correlations among latitude, habitat change, and genetic metrics showed no significant associations. However, GLMs revealed a significant interaction: the effect of habitat suitability change on Tajima’s D was strongly positive at high latitudes but negative or negligible at low latitudes. This indicates that demographic responses to past climate change varied latitudinally. Several high-latitude species showed genetic signatures of demographic expansion and range increase since the LGM. Main conclusions Our results support the hypothesis that species at higher latitudes experience stronger demographic fluctuations due to historical climate change, aligning with Darwin’s early predictions. Moreover, patterns of demographic growth in temperate taxa suggest that some species may benefit from recent warming, consistent with Janzen’s climatic variability hypothesis. These findings demonstrate that climate-driven genetic and demographic responses in tarantulas are shaped by latitude, highlighting the importance of integrating phylogeography with ecological niche modeling to understand species’ resilience under climate change.
... Variance around the mean heterozygosity of each sample was calculated as the weighted standard deviation of estimates obtained from each of the 18 autosomes. Specifically, our estimator of heterozygosity is given as: Under the assumption of random mating, the heterozygosity as normalised here is an estimator of a population's nucleotide diversity π (i.e., the average number of nucleotide differences between two sequences per site) (Nei and Li 1979), a common measure of genetic diversity. This usage is consistent with much of population genetic literature, but we note that it differs from the measures of heterozygosity commonly used in microsatellite studies, which report heterozygosity values for loci known to be polymorphic. ...
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As the world is hit by the sixth mass extinction, it becomes increasingly important to understand the factors relevant to the conservation of species, so that we may protect biodiversity to the best of our abilities. Although genetic diversity is known to reflect population demography and contribute to genetic health and adaptability, it is not explicitly used as a criterion in assessments by the International Union for the Conservation of Nature (IUCN). Additionally, studies comparing diversity estimates between species often rely on summarizing results across studies, which use different methodologies and may not be suited for direct comparison. Here we performed a family-wide assessment of genomic diversity in Felidae, covering most extant species. We tested for correlations between autosomal heterozygosity and ecological traits across (sub)species, and whether a subspecies’ genetic diversity was associated with its IUCN threat category. We found evidence for genetic diversity to be strongly positively correlated with both geographic range size and population density, but not with census size. Furthermore, although genetic diversity showed significant correlation with IUCN status, with threatened species exhibiting lower levels of genetic diversity, it was not possible to clearly distinguish between categories on this basis alone. Our results confirm the association of population parameters and assessment of extinction risk with genetic diversity in one of the most iconic and threatened families of land carnivores. While mechanisms and causality behind these associations will need to be the subject of further investigation, our study adds further credence to the importance of incorporating genomic information in risk assessment and conservation efforts.
... Based on our characterisation of genetic structure, each mountain range was considered a different population (see Results). Nucleotide diversity for each population (Nei and Li 1979) and the count of all sequenced positions were computed from RAD tag sequences using custom scripts (https:// github. com/ ckast all/ Gquin quepu nctata_ phylo geo_ RADseq). ...
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Aim During the past few 100,000 years, repeated cycles of glaciation and warming episodes have radically altered the range of organisms. Numerous phylogeographic studies have investigated the impact of past climate changes on the range of temperate organisms in Europe, but we know substantially less about organisms that are adapted to colder climates. Their distributions are often currently fragmented and limited to relatively high elevations in mountainous regions and to the north of Europe. Our inferences of their range during the last glaciation appear contradictory: some studies indicate a range expansion through colonisation of the lowlands, while others suggest a range contraction because they were restricted to small refugia. In this study, we wished to identify which of these two alternative hypotheses explains best the current distribution of genetic variation in a European montane leaf beetle whose current range spans several mountains. Location Four European mountain systems: Alps, Vosges, Massif Central, Pyrenees. Time Period End of the Quaternary, focusing mainly on the last glaciation and the Holocene. Taxon Gonioctena quinquepunctata [Fabricius, 1787] (Coleoptera; Chrysomelidae). Results Modelling of the potential current and last glacial maximum species distributions suggested that climatic conditions were more favourable in the lowlands during the last glaciation, opening the possibility that this leaf beetle has colonised them at the time. Characterising genomic variation across its current range using RAD‐seq data and comparing alternative hypotheses about its evolution with coalescence models in a composite likelihood framework contradicted this hypothesis; however: these analyses inferred instead that the species was associated with a much smaller population size during the last glaciation, suggesting that its range was then restricted to the mountains' outskirts. Main Conclusions Comparing these results to those of other studies of European cold‐adapted species, we argue that phylogeographic evidence points towards a similar glacial contraction of the range of many similar organisms.
... Genetic diversity within populations was estimated based on the number of haplotypes (H), haplotypic diversity (h) (Nei 1987), and nucleotide diversity (π) (Nei and Li 1979), using the DnaSP v.5 program (Librado and Rozas 2009). Haplotype networks were constructed in the POPART 1.7 program (Leigh et al. 2015) using the median-joining (MJ) algorithm (Bandelt et al. 1999) with 1000 interactions. ...
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Studies on population genetic differentiation are essential for understanding the ecological, biological, and behavioral aspects of species, as well as their diversification patterns and how populations evolve over time. The species Artibeus planirostris, one of the best-known Neotropical fruit bats, has a wide distribution. This species exhibits high dietary plasticity and plays a significant ecological role. While A. planirostris has been used as a model organism in various studies, no comprehensive research has yet explored its population dynamics. Here, we analyzed fragments of the mitochondrial Cytochrome b (Cyt b) and Cytochrome c Oxidase 1 (COI) genes to investigate the genetic diversity, population structure and demographic history of A. planirostris in the Neotropics. Our findings reveal a weakly structured geographic population pattern. Nevertheless, in peripheral populations, we have observed limited maternal gene flow due to isolation by distance or potentially geographic barriers. It suggests that local adaptations, shaped by specific environmental pressures and Pleistocene climatic fluctuations, may have influenced the dispersal and colonization abilities of A. planirostris in these regions. The demographic history of A. planirostris indicates a recent population expansion during the late Pleistocene, approximately 50,000-60,000 years ago.
... The indep-pairwise option was used with a window size of 100, a variant count of 5 to switch window at the end of each step, and a r 2 threshold of 0.5. Levels of genetic diversity were assessed using Nei and Li (1979) nucleotide diversity (Π) and individual observed heterozygosity (H o ) calculated using vcftools v0.1.14 (Danecek et al. 2011). ...
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The spatial distribution of the European anchovy has expanded in the northern part of its range in the Northeast Atlantic in recent decades. However, whether this results from a northward range shift of southern conspecifics or the expansion of a local northern population is unknown. Using for the first time whole‐genome sequencing, we explore current patterns of genetic diversity and population sub‐structuring of European anchovy in the Northeast Atlantic, with special focus on recently expanded North Sea areas. Genomic data suggested three distinct groups: Northern (North Sea and Kattegat), Southern (Ireland and Central Portugal) and Cadis (South Portugal). Despite most of the genome being homogenised by high levels of gene flow characteristic of small pelagic fish, several large regions of high genetic differentiation were observed. This suggests that genomic population boundaries might be maintained by local adaptation within chromosome structural variants (inversions). Admixture analysis indicates that the ongoing northern range shift involves both migrants of southern origin and expansion of the local North Sea population. Historical demographic inference suggests that anchovies survived the last glacial period with small population sizes, followed by a split into the current Northern and Southern groups at the end of the last glacial maximum. The Southern group then expanded into the North Sea as the ice sheets retreated, in an expansion involving a large number of individuals, which is consistent with the retention of most of the genetic diversity. In comparison with other small pelagic fish, the genetic patterns found in anchovies (deeply divergent groups, no loss of genetic diversity during expansion, mixing between groups) align well with those found in European sprat, while sardines fit the pattern of expansion of a leading‐edge population, with reduced genetic diversity and much shallower divergence between populations. This study contributes to a better understanding of population structure, range shifts and local adaptation in small pelagic fish under climate change, informing conservation and management efforts.
... RAPD phenotypes were scored as 1 (band present) or 0 (band absent), respectively, resulting in a 37 × 71 matrix. Dice (1945) coefficients [which is equivalent to Nei and Li (1979) genetic identity] were calculated for all possible pairwise combinations of pawpaw cultivars. As genetic diversity estimators, Nei's (1973) gene diversity (He) and Shannon and Weaver's (1949) index (I) were also calculated. ...
Article
Thirty-four extant pawpaw [ Asimina triloba (L.) Dunal] cultivars and advanced selections representing a large portion of the gene pool of cultivated pawpaws were investigated using 71 randomly amplified polymorphic DNA (RAPD) markers to establish genetic identities and evaluate genetic relatedness. All 34 cultivated pawpaws were uniquely identified by as few as 14 loci of eight primers. Genetic diversity of the existing gene pool of cultivated pawpaws, as estimated by Nei's gene diversity (He), was similar to that of wild pawpaw populations. The genetic relatedness among the cultivated pawpaws examined by UPGMA cluster analysis separated 34 cultivars and selections into two distinct clusters, a cluster of PPF (The PawPaw Foundation) selections and a cluster including a majority of the extant cultivars selected from the wild and their derived selections. The results are in general agreement with the known selection history and pedigree information available. The consensus fingerprint profile using the genetically defined RAPD markers is a useful and reliable method for establishing the genetic identities of the pawpaw cultivars and advanced selections. This also proved to be an improved discriminating tool over isozyme markers for the assessment of genetic diversity and relatedness. RAPD profiling of data presented in this study provides a useful reference for germplasm curators engaged in making decisions of sampling strategies, germplasm management and for breeders deciding which parents to select for future breeding efforts.
... A pairwise similarity matrix was generated using the Nei-Li similarity index (Nei and Li, 1979) according to the equation: Similarity = 2 N ab /(N a +N b ), Where N ab is the number of fragments (ISSRs and AFLPs) shared by two genotypes (a and b) and N a and N b are the total number of fragments analyzed in each genotype. A dendrogram was constructed based on the similarity matrix data by applying the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis using the Numerical Taxonomic and Multi-Variant Analysis System for PC (NTSYS-PC version 2) (Rohlf, 1993). ...
Article
Wide phenotypic diversity exists among American heirloom cultivars of watermelon ( Citrullus lanatus var. lanatus ). However, in published studies, low or no polymorphism was revealed among those heirlooms using isozyme or randomly amplified polymorphic DNA (RAPD) markers. In this study, experiments with inter-simple sequence repeat (ISSR) [also known as simple sequence repeat-(SSR-) anchored primers] and amplified fragment-length polymorphism (AFLP) markers produced high polymorphisms among watermelon heirloom cultivars. ISSR (111) and AFLP (118) markers (229 total) identified 80.2% to 97.8% genetic similarity among heirloom cultivars. The phylogenetic relations based on ISSR and AFLP markers are highly consistent with the parental records available for some of the heirloom cultivars, providing confidence in the dendogram constructed for heirlooms based on similarity values. As compared with RAPD markers, ISSRs and AFLPs are highly effective in differentiating among watermelon cultivars or elite lines with limited genetic diversity.
... For SRAP and AFLP molecular analysis, genetic distances (GD) among genotypes were calculated according to the Nei and Li (1979) similarity coeffi cient. Two types of analyses were applied: 1) unweighted pairgroup method, arithmetic mean (UPGMA), a SAHN clustering technique (Sneath and Sokal, 1973), which compresses the patterns of variation into two-dimension branch diagrams (dendrograms); and 2) principal coordinate analysis (PCoA), an ordination method analogue of PCA applicable to discrete variation data (Gower, 1966). ...
Article
Cucurbita maxima Duch. is one of the most morphologically variable cultivated species. The Center for Conservation and Breeding of the Agricultural Diversity (COMAV) holds a diverse germplasm collection of the Cucurbita genus, with more than 300 landraces of this species. Morphological and molecular characterization are needed to facilitate farmer and breeder use of this collection. With this aim, the morphological variation of a collection of 120 C. maxima accessions was evaluated. The majority of these accessions originated from Spain, which has acted as a bridge since the 16 th century for spreading squash morphotypes between the Americas and Europe. South American landraces (the center of origin of this species) were also included. Eight morphological types were established based on this characterization and previous intraspecific classifications. A subset of these accessions, selected from these classification and passport data, was employed for molecular characterization. Two marker types were used; sequence related amplified polymorphism (SRAP), which preferentially amplifies open reading frames (ORF), and amplified fragment length polymorphism (AFLP). In the main, SRAP marker analysis grouped accessions in accordance to their type of use (agronomic traits) and AFLP marker analysis grouped accessions as to their geographical origin. AFLP marker analysis detected a greater genetic variability among American than among Spanish accessions. This is likely due to a genetic bottleneck that may have occurred during the introduction of squash into Europe. The disparity of the results obtained with the two markers may be related to the different genome coverage which is characteristic of each particular marker type and/or to its efficiency in sampling variation in a population.
... For the purpose of examining the genetic relationships among the 48 cultivars and selections, allelic data were treated in binary format and scored as 1 (band present) or 0 (band absent), and were referred to as allelic phenotypes. Dice (1945) coeffi cients, which are equivalent to Nei and Li (1979) genetic identities, were calculated for all possible pairwise combinations of kiwifruit genotypes. A dendrogram was constructed based on the matrix of the Dice coeffi cients by unweighted pair-group mean analysis (UPGMA) using the software NTSYS-pc v.1.8 ...
Article
Forty-eight kiwifruit cultivars and selections, representing more than 90% of total world kiwifruit production, were investigated using nine SSR markers to establish genetic identities, and evaluate genetic diversity and relatedness. These nine SSRs were polymorphic and a total of 213 alleles were detected, resulting in a mean number of 23.7 alleles per locus, ranging from nine to 38 alleles. One hundred and thirty-three alleles were found to be common to both A. chinensis and A. deliciosa , while 33 and 36 were specific to A. chinensis and A. deliciosa , respectively. In addition, 34 alleles were specific to one single genotype and provided a set of valuable alleles for cultivar identification. A single SSR locus UDK 96-414 could differentiate all 48 genotypes except two presumable clones. Mean number of alleles per locus (A), percentage of polymorphic loci (P), and direct count heterozygosity (H o ) assessed for each genotype over all loci revealed considerable differences among these 48 genotypes. On average, A = 2.6, P = 89.4% and H o = 0.546 were found in A. chinensis cultivars, while A = 3.5, P = 97.0% and H o = 0.671 in A. deliciosa cultivars. Consensus fingerprint profiling using SSR markers is a useful and reliable method for establishing genetic identities of kiwifruit cultivars and selections. It also improves evaluation effectiveness of genetic diversity and relatedness compared to RAPD markers.
... Quantity One software (Version 4.6.2) was used to analyze the colored bands to determine the relative mobilities (Rfs), band quantity (Qty), and band percentage (B%) of the electrophoretically separated bands. The percentages of genetic distances (GD%) and similarity indices (SI%) between each treated group and the control were computed using a method developed by Nei and Li [31]. ...
... The matrix of chemical constituents of the different study plant species were analyzed by PAST (free programs on web) software (Hampl et al., 2001). Similarity of quantitative data was calculated using the Nei and Li/Dice similarity index (Nei and Li, 1979), and similarity estimates were analyzed using UPGMA (unweighted pair group method using arithmetic averages). The matrices of mutual coefficients of similarity calculated by PAST were clustered (Agglomerative Clustering) and resulting clusters were expressed as dendrogram. ...
... Quantity One software (Version 4.6.2) was used to analyze the colored bands to determine the relative mobilities (Rfs), band quantity (Qty), and band percentage (B%) of the electrophoretically separated bands. The percentages of genetic distances (GD%) and similarity indices (SI%) between each treated group and the control were computed using a method developed by Nei and Li [31]. ...
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One of the atypical antipsychotic drugs is olanzapine (OLZ). Enhancing metabolic and detoxifying activities requires zinc (Zn). Thus, the objective of the current study was to determine if Zn supplementation might effectively reduce hepatic lesions induced by OLZ. The oxidative stress, inflammatory, and fibrotic indicators of the liver tissues were evaluated, and electrophoretic methods were used to analyze the native protein and isoenzyme patterns. Furthermore, the liver tissues were examined histopathologically. The dynamic motion of the extracted hemoglobin was also examined. In addition to the serious damage identified histopathologically, our results show that OLZ treatment altered the liver tissue’s antioxidant and inflammatory indicators. The zinc sulfate (ZnSO4) salt solution, given in a dose-dependent fashion, reduced these changes. Additionally, the ZnSO4 salt solution enhanced the natural protein, lipid, and calcium moieties of the protein pattern that were electrophoretically detected and changed by OLZ. In terms of the isoenzyme patterns, the ZnSO4 salt solution reduced the electrophoretic catalase (CAT), peroxidase (POX), and β-esterase (β-EST) isoenzyme patterns that were hampered by OLZ in a dose-dependent manner. Rats treated with OLZ in addition to ZnSO4 showed an increase in heme-heme interactions, suggesting that zinc therapy stabilized oxyhemoglobin. This promotes a more effective folding process that improves the use of oxygen. A dosage of 100 mg/kg of ZnSO4 was shown to normalize physiological, histological, and biochemical markers. It also improved interactions between heme molecules.
... The proportion of heterozygous genotypes between samples was estimated using TASSEL5 (Bradbury et al., 2007). The nucleotide diversity (π; Nei & Li, 1979) was measured in a sliding window of 1000 bp every 500 bp across the genome using -window-pi and -window-pi-step options of VCFtools (Danecek et al., 2011). ...
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Cannabis (Cannabis sativa L.), once sidelined by decades of prohibition, has now gained recognition as a multifaceted and promising plant in both medical research and commercial applications following its recent legalization. This study leverages a genome‐wide association study (GWAS) on 174 drug‐type Cannabis accessions from the legal Canadian market, focusing on identifying quantitative trait loci (QTL) and candidate genes associated with eleven cannabinoid traits using 282K common single‐nucleotide polymorphisms. This approach aims to transform our understanding of Cannabis genetics. We have pinpointed 33 significant markers that significantly influence cannabinoid production, promising to drive the development of Cannabis varieties with specific cannabinoid profiles. Among the notable findings is a massive haplotype of ∼60 Mb on chromosome 7 in Type I (i.e., tetrahydrocannabinol [THC]‐dominant) accessions, highlighting a major genetic influence on cannabinoid profiles. These insights offer valuable guidance for Cannabis breeding programs, enabling the use of precise genetic markers to select and refine promising Cannabis varieties. This approach promises to speed up the breeding process, reduce costs significantly compared to traditional methods, and ensure that the resulting Cannabis varieties are optimized for specific medical and recreational needs. This study marks a significant stride toward fully integrating Cannabis into modern agricultural practices and genetic research, paving the way for future innovations.
... A sliding-window approach (40-kb windows sliding in 10-kb steps) was used to quantify polymorphism levels (θπ, pairwise nucleotide variation as a measure of variability) (24) and genetic differentiation (Fst) (25) between RJFs and two chmsicken breeds. Based on this, we further combined θπ with the Fst statistic and implemented a selective sweep screening method to identify genomic regions that may be affected by natural selection in different populations of Puan Panjiang Black-bone Chicken. ...
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Introduction Polydactyly—the presence of extra digits—is a heritable limb anomaly observed in several chicken breeds. The Puan Panjiang black-bone chicken uniquely exhibits both four- and five-toed phenotypes, yet the genetic and transcriptional bases of this trait remain unclear. This study aimed to elucidate the genomic variants and gene expression changes underlying polydactyly in this breed. Methods We performed whole-genome resequencing (WGS) on 43 Puan Panjiang chickens (22 four-toed, 21 five-toed) and integrated publicly available data from 17 red junglefowl (RJF). After stringent quality filtering, we aligned reads to GRCg7b, identified high-confidence SNPs and InDels, and conducted sliding-window analyses of nucleotide diversity (θπ) and genetic differentiation (F ST) to detect selective sweeps. Concurrently, we carried out RNA-seq on embryonic foot tissues at days 6–9 (24 four-toed, 24 five-toed samples), quantified transcript levels (TPM), and identified differentially expressed genes (DEGs) with DESeq2 (adjusted P < 0.01, |log2FC|> 2). Fuzzy c-means clustering delineated temporal expression patterns, and enrichment analyses (KEGG, GO) characterized candidate pathways. Results Genomic scans revealed 1,339 and 1,035 positively selected genes in five-toed and four-toed chickens, respectively, with 335 shared loci relative to RJF. Top candidates in polydactylous birds included AUH, SEMA4D, and ROR2, while four-toed birds showed strong signals at RYR2, KITLG, and PGR. KEGG enrichment highlighted the MAPK signaling pathway in both groups, and uniquely in five-toed birds, lipid metabolism and vascular signaling pathways (e.g., sphingolipid and apelin signaling). Transcriptome profiling demonstrated that the greatest transcriptional divergence between phenotypes occurred at embryonic Days 8–9, pinpointing a critical window for extra-digit differentiation. Clustering analyses indicated coordinated regulation of genes involved in ribosome biogenesis, extracellular matrix organization, and muscle development across stages. Discussion Our integrated analyses pinpoint MAPK pathway genes and lipid-vascular interactions as central to extra-toe formation, with the Days 8–9 embryonic window being pivotal. These findings offer clear targets for functional validation and may guide selective breeding for limb traits in poultry.
... Nei's genetic distances of the 10 populations and similarity coefficients were assessed by PopGene32 [12]. In this study, 10 bighead carp populations were clustered based on Nei's genetic distance using the UPGMA method in MEGA 7.0 software [13]. ...
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Background: Bighead carp (Hypophthalmichthys nobilis), a vital species in China’s freshwater ecosystems and aquaculture, has experienced significant population declines due to habitat degradation and intensive farming. Methods: In this study, eight polymorphic microsatellite markers were utilized to examine the genotypes and genetic diversity of 320 individuals of bighead carp populations located in the middle Yangtze River. This included four wild populations (ZX, DTH, SS, WH) and six cultured populations (HH, XZ, CH, QC, CD, HG). Results: Wild populations exhibited significantly higher genetic diversity (mean Na = 12.25 ± 0.63, Ho = 0.802 ± 0.063) than cultured groups (mean Na = 8.85 ± 1.21, He = 0.779 ± 0.032). Low differentiation (Fst < 0.05) among wild populations indicated high connectivity with low genetic structure, whereas cultured populations CH and HG showed moderate-to-high differentiation (Fst = 0.156–0.293). Bayesian analysis (K = 7) revealed a distinct clustering of wild populations, while cultured stocks exhibited admixed genetic ancestries. Bottleneck tests confirmed recent genetic bottlenecks in three cultured populations. Conclusions: Wild bighead carp populations retain a critical genetic diversity, serving as reservoirs for conservation, while intensive aquaculture practices threaten genetic integrity through allele loss and inbreeding.
... Nucleotide diversity (π) measures the average number of nucleotide differences per site between any two DNA sequences chosen randomly from the population. [54] It's a measure of genetic variation within a population. Nucleotide diversity π was calculated for 3,818 coding genes with more than one CDSs of valid ORF which varied between 0 to 7.09e-3. ...
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Tuberculosis is a major public health threat resulting in more than one million lives lost every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China including 344 Lineage 2 strains, 69 Lineage 4 strains, six Lineage 3 strains, and one Lineage 1 strain. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 are core genes. However, due to 99,694 interruptions in 2,447 coding genes, we can only confidently confirm 1,651 of these genes are translated in all samples. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structural variations, mostly small indels. Assuming a proportion of these interruptions are artifacts, the number of active core genes would still be much lower than 3,438. We further described differential evolutionary patterns of genes under the influences of selective pressure, population structure and purifying selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations are concentrated in 1,310 genes. Genes involved in cell wall biogenesis are under the strongest selective pressure, while the biological process of disruption of host organelles indicates the direction of the most intensive positive selection. This study provides a comprehensive view on the genetic diversity and evolutionary patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.
... The absolute nucleotide divergence, d XY , measures the average genetic distance between two populations by calculating pairwise differences among individuals from the two populations (Nei and Li, 1979). Despite its frequent use for assessing population divergence, current implementations of d XY similarly rely on accurately called genotypes and may be biased when applied to low-depth sequencing data. ...
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Motivation: Next-generation sequencing (NGS) has transformed population genetics and evolutionary biology, but the data produced in studies of non-model organisms, ancient DNA, and environmental DNA often consist of low- or medium-depth sequencing. Analyses of these data rely on computational methods that utilize genotype likelihoods (GLs) to account for genotype uncertainty. Nevertheless, many widely-used analysis methods, such as analysis of molecular variance (AMOVA) and methods for estimating phylogenetic trees using nucleotide divergence (dXY) still lack the probabilistic frameworks necessary to accommodate GLs. Results: We introduce ngsAMOVA, a novel probabilistic framework for analyzing molecular variation in population hierarchies with low- and medium-depth sequencing data. It employs an Expectation Maximization algorithm to first estimate the joint genotype probabilities for pairs of individuals, accounting for genotype uncertainty using GLs. It then uses these estimates to generate a pairwise distance matrix, which can be used for AMOVA, estimation of dXY, and for estimating phylogenetic trees using Neighbor-Joining. Hypothesis testing is facilitated using genomic block-bootstrapping. Through extensive simulations, we demonstrate that ngsAMOVA provides more accurate results compared to genotype calling at low and medium read depths. Overall, ngsAMOVA represents a methodological advance in the analysis of molecular variance and divergence under sequencing uncertainty. It provides a robust framework, opening up numerous possibilities for gaining insights into the evolutionary histories through its applications. ngsAMOVA is available as a fast, efficient, and user-friendly program written in C/C++.
... However, before the high-throughput genome-wide resequencing developed in crops, the earlier studies could measure the ordinary allele frequency changes based on some microsatellites and/or a small number of nucleotide polymorphism markers. Accordingly, some genetic statistics, including genetic diversity (π) (Nei & Li, 1979), genetic differentiation index (F ST ) (Weir & Cockerham, 1984), selection sweeps or cross-population composite likelihood ratio (XP-CLR) for selective signals Zhou et al., 2015), relative identical by descent for introgressions (X. Wang et al., 2019), and genomic evolutionary rate profiling for deleterious mutations (Kim et al., 2021), were used in charactering the evolutionary processes. ...
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Previous studies on population evolution relied primarily on allele frequency analysis using molecular markers or genome sequence segments, like selective sweeps. With the sequencing technique developed, we suggest the genome‐wide locus–allele comparison to detect the genomic structure variation among populations. Its key point lies in taking SNP linkage disequilibrium block as uniform genomic marker for genome‐wide gene and inter‐gene regions to meet the requirement of multiple alleles in natural populations. A sample composed of 750 annual wild accessions (WAs), landraces (LRs), and released cultivars (RCs) of soybean from southern, northern, and northeastern China eco‐regions (SC, NC, and NEC, respectively) were analyzed for their evolution dynamics involving four evolutionary processes (WA→LR→RC, WASC→WANC→WANEC, LRSC→LRNC→LRNEC, and LRSC→RCSC/LRNC→RCNC/LRNEC→RCNEC). Our major finding was the discovery of allele and locus zero/one variation between/among ancestor‐filial populations involving a large part of the whole population alleles and loci, 25.10% and 18.62% in domestication and modern breeding stages, respectively, which was not detected by selective sweeps. The essence of population evolution is the allele zero/one changes based on ordinary allele frequency changes, which causes the locus zero/one changes. The allele/locus zero/one variation happened more often when their frequency was at 0.0–0.3 and 0.8–0.99 in the previous stage generation, respectively. The WA and LR geographic evolution are different processes due to different combination of allele/locus zero/one changes by natural versus artificial selection pressures. Compared to per‐year allele exclusion, the rate of per‐year allele emergence is relatively stable in domestication and modern breeding (2.75E‐5 vs. 1.34E‐5 and 1.42E‐3 vs. 1.10E‐5), respectively.
... Genetic diversity within a species is commonly measured as the nucleotide diversity, defined by Nei and Li (81) in 1979 as the average number of nucleotide differences per site between two DNA sequences in all possible pairs in the sample population. In this sense, genetic diversity is equivalent to genetic distance or sequence mismatches. ...
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Genetic equidistance phenomenon (GEP): A simpler species is equally distantly related to two or more complex species in a sequence alignment when the genetic distance is measured by the identity matrix or percentage non-identity. Maximum genetic diversity (MGD): The upper limit in genetic distance or diversity, as measured by the identity matrix or percentage differences, that can be reached during evolution over long periods. Microevolution: In the MGD theory, the term encompasses evolutionary changes both within a species and between species over both short and long periods, as long as these changes do not involve major epigenetic modifications. Macroevolution: In the MGD theory, the term describes new species formation that involves both genetic and epigenetic
... Genetic diversity analysis: To assess the level of polymorphism between and within populations, we calculated the nucleotide diversity (Pi) at each locus using the R package PopGenome [90]. The Pi was defined as the average number of nucleotide differences per site between two sequences [91]. Furthermore, we determined Tajima's D index per gene, a neutrality derived from comparing the mean number of segregating-sites and the average pairwise differences [92]. ...
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Background: Insecticide resistance challenges the vector control efforts towards malaria elimination and proving the development of complementary tools. Targeting the genes that are involved in mosquito fertility and susceptibility to Plasmodium with small molecule inhibitors has been a promising alternative to curb the vector population and drive the transmission down. However, such an approach would require a comprehensive knowledge of the genetic diversity of the targeted genes to ensure the broad efficacy of new tools across the natural vector populations. Methods: Four fertility and parasite susceptibility genes were identified from a systematic review of the literature. The Single Nucleotide Polymorphisms (SNPs) found within the regions spanned by these four genes, genotyped across 2784 wild-caught Anopheles gambiae s.l. from 19 sub-Saharan African (SSA) countries, were extracted from the whole genome SNP data of the Ag1000G project (Ag3.0). The population genetic analysis on gene-specific data included the determination of the population structure, estimation of the differentiation level between the populations, evaluation of the linkage between the non-synonymous SNPs (nsSNPs), and a few statistical tests. Results: As potential targets for small molecule inhibitors to reduce malaria transmission, our set of four genes associated with Anopheles fertility and their susceptibility to Plasmodium comprises the mating-induced stimulator of oogenesis protein (MISO, AGAP002620), Vitellogenin (Vg, AGAP004203), Lipophorin (Lp, AGAP001826), and Haem-peroxidase 15 (HPX15, AGAP013327). The analyses performed on these potential targets of small inhibitor molecules revealed that the genes are conserved within SSA populations of An. gambiae s.l. The overall low Fst values and low clustering of principal component analysis between species indicated low genetic differentiation at all the genes (MISO, Vg, Lp and HPX15). The low nucleotide diversity (>0.10), negative Tajima’s D values, and heterozygosity analysis provided ecological insights into the purifying selection that acts to remove deleterious mutations, maintaining genetic diversity at low levels within the populations. None of MISO nsSNPs were identified in linkage disequilibrium, whereas a few weakly linked nsSNPs with ambiguous haplotyping were detected at other genes. Conclusions: This integrated finding on the genetic features of major malaria vectors’ biological factors across natural populations offer new insights for developing sustainable malaria control tools. These loci were reasonably conserved, allowing for the design of effective targeting with small molecule inhibitors towards controlling vector populations and lowering global malaria transmission.
... We used VCFtools [33] to estimate nucleotide diversity for each breed, employing window sizes of 50 kb with 20 kb step while keeping other parameters at default settings. The π-ratio [34] was calculated as the ratio of nucleotide diversity between Simmental and Hubei indigenous cattle (π Simmental /π Hu ) and between indicine cattle and Hubei indigenous cattle (π Indicine /π Hu ). The identified key genes were analyzed and illustrated using HTIRDB (https://yanglab.hzau.edu.cn/HTIRDB#/expression/single_all_species, ...
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Hubei indigenous cattle have adapted to diverse environmental conditions, exhibiting unique genetic traits associated with both economic and adaptive characteristics. Understanding their adaptive selection offers insight into their evolutionary history and genetic enhancements. In this study, we analyzed whole-genome sequencing (WGS) data from five Hubei indigenous cattle breeds to identify selection signals. Selective sweep analysis revealed the candidate genes (USH2A, TMTC2, ABCC12, and SUGT1) associated with sensory perception, backfat thickness, reproduction, and immune function. The further integration of cis-regulatory elements (CREs) and expression quantitative trait loci (eQTL) highlighted regulatory variants, influencing adaptive traits. Notably, positively selected genes such as RPS6KA2, CRLS1, MGST3, GPCPD1, and LDLRAP1 were associated with lipid metabolism, meat quality, and reproductive traits, influencing aldehyde volatile organic compounds (VOCs) and fat deposition. These findings highlight the understanding of the genetic basis of adaptation and production traits in Hubei indigenous cattle and provide valuable insights for their conservation and potential breeding strategies.
... Comparing the locations of the bands with the standard size index after converting the results to binary character tables indicated a band presence (1) and a band absence (0). In determining the genetic relationship among the examined Rosa L. species, transforming all characterization data into similarity data used the following equations (Nei and Li, 1979;Yao et al., 2007). ...
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The innovative research employed rbcL (ribulose bisphosphate carboxylase) primers in detecting the internal transcribed spacer (ITS) region on the chloroplast cpDNA of five species of the genus Rosa L., using the polymerase chain reaction (PCR) and phylogenetic relationship. The species are R. gallica, R. hemisphaerica, R. foetida, Rosa x damascene, and R. centifolia. The results revealed the presence of a major band (1700 bp) in all studied species. Based on a phylogenetic analysis of the rbcL gene sequence data, two major clusters were evident in the dendrogram. The species R. gallica and R. hemisphaerica have a good bootstrap value of 99%. The rest of the three species (R. centifolia, R. foetida, and Rosa x damascene) has a bootstrap value ranging between 55%-57%. The study also authenticated the species R. hemisphaerica and R. foetida were newly recorded species in the international GenBank NCBI (National Center for Biotechnology Information).
... The software Arlequin [42] was used to calculate the genetic diversity indices of each population: observed heterozygosity (Ho), expected heterozygosity (He), molecular variance analysis (AMOVA) and Fst between groups to measure possible differences between different groups. The method of Nei & Li [43] was used to analyze the population nucleotide diversity (π) and calculate the single nucleotide diversity index (Pi). ...
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Background: Sophora alopecuroides L. is a perennial herb of Leguminosae. It is mainly distributed in northwest China and has important medicinal, feeding and ecological restoration values. However, in recent years, due to the intensification of human activities, its wild population resources have plummeted and genetic diversity has continued to decline. In order to fully reveal the genetic diversity and population structure characteristics of S. alopecuroides in the natural distribution area. In this study, Single nucleotide polymorphism (SNP) molecular markers combined with seed phenotypic traits were used to systematically study 65 wild samples of S. alopecuroides in northwest China. Results: The results showed that the coefficient of variation (CV) of 8 phenotypic traits of S. alopecuroides seeds ranged from 2.87 % to 7.94 %, and the diversity index (H) ranged from 1.639 to 1.767. There was a significant correlation between phenotypic traits (P < 0.01), indicating that the phenotypic diversity of S. alopecuroides seeds was rich. Cluster analysis based on phenotypic traits divided the S. alopecuroides population into two groups. At the same time, based on SNP molecular markers, the genetic diversity of S. alopecuroides was relatively low. The average values of expected heterozygosity (He), observed heterozygosity (Ho) and single nucleotide diversity index (Pi) were 0.22, 0.17 and 0.19, respectively. The results of molecular variance analysis (AMOVA) showed that the level of variation between individuals (132.83%) was higher than that between populations and within populations. The Pairwise population differentiation (Fst) was between 0.00 and 0.04, which confirmed that there was no obvious differentiation among the populations. Population structure analysis, principal component analysis (PCA) and phylogenetic tree analysis roughly divided all populations into two clusters, which was consistent with the phenotypic clustering results. It is worth noting that the distribution patterns of the samples in the Southern Tianshan Mountains (TSNL) and the Altai Mountains (ARTS) are more complex. In addition, redundancy analysis (RDA) showed that the cumulative interpretation rates of environmental factors on phenotypic traits and genetic diversity were 99.75 % and 67.89 %, respectively. Among them, the mean temperature of the driest quarter (MTD) and annual mean wind speed (YWS) were identified as the primary factors influencing phenotypic traits, while the precipitation of the coldest quarter (PC), isothermality (ISO), and precipitation of the wettest quarter (PWE) have an important impact on genetic diversity. Conclusions: This study provides a foundation for the genetic evaluation and conservation of S. alopecuroides genetic resources in China and offers important insights for its breeding programs.
... To capture diversity of structural variation across the genome, we developed a statistic called "SVπ". Akin to nucleotide [62] and synteny diversity [63], this statistic captures the average number of SVs per kb between all pairs of individuals. We found that SVπ was positively skewed when calculated for 50-kb sliding windows across the genome (Fig. 3A). ...
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Background An understanding of plant pathogen evolution is important for sustainable management of crop diseases. Plant pathogen populations must maintain adequate heritable phenotypic variability to survive. Polymorphisms ≥ 50 bp, known as structural variants (SVs), could contribute strongly to this variability by disrupting gene activities. SV acquisition is largely driven by mobile genetic elements called transposons, though a less appreciated source of SVs is erroneous meiotic double-strand break repair. The relative impacts of transposons and recombination on SV diversity and the overall contribution of SVs to phenotypic variability is elusive, especially in host generalists. Results We use 25 high-quality genomes to create a graphical pan-genome of the globally distributed host-generalist crop pathogen Sclerotinia sclerotiorum. Outcrossing and recombination rates in this self-fertile species have been debated. Using bisulfite sequencing and short-read data from 190 strains, we show that S. sclerotiorum has many hallmarks of eukaryotic meiosis, including recombination hot and cold spots, centromeric and genic recombination suppression, and rapid linkage disequilibrium decay. Using a new statistic that captures average pairwise structural variation, we show that recombination and transposons make distinct contributions to SV diversity. Furthermore, despite only 5% of genes being dispensable, SVs often had a stronger impact than other variants across 14 life history traits measured in 103 distinct strains. Conclusions Transposons and recombination make distinct contributions to SV diversity in S. sclerotiorum. Despite limited gene content diversity, SVs may strongly impact phenotypic variability. This sheds light on the genomic forces shaping adaptive flexibility in host generalists.
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Astragalus L. is regarded as the most extensive genus of vascular plants globally, encompassing around 3092 species and distributed across Eurasia and the America. Türkiye hosts 493 species categorized into 63 distinct taxonomic groups. This study examines the restricted molecular diversity studies pertaining to the sections of the genus Astragalus. The study primarily investigated ten (10) Astragalus taxa native to Türkiye. The Randomly Amplified Polymorphic DNA (RAPD) method was utilized to evaluate the existence of genetic polymorphisms. The phylogenetic analysis revealed that the sections Anthylloidei DC (A. anthylloides, A. halicacabus, and A. ermineus), Macrophyllium Bunge (A. oleaefolius and A. dipodurus), and Hymenostegis Bunge (A. lagopoides, A. velenowskyi, and A. hirticalyx) are closely related whereas the sections Poterion Bunge (A. russelli) and Hymenocoleus Bunge (A. vaginans) are situated in distinct locations. This study seeks to enhance the molecular characterization of Astragalus taxa, create molecular biodiversity inventories, and elucidate phylogenetic relationships. The results concerning genetic diversity and evolutionary relationships bear substantial implications for future research and underscore Astragalus species that possess economic significance in diverse domains, such as traditional medicine, agriculture, and landscaping.
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An estimation of the DNA sequence divergence between defined DNA sequences of individuals or species may be made from comparison by gel elec-trophoresis of restriction endonuclease digests. This analysis is applicable to purified DNA sequences of moderate complexity (1−100 × 106 daltons) which have diverged by base substitution of 0.5 to 25% of nucleotides.
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Mitochondrial DNA from several mammalian species has been digested with a site-specific restriction endonuclease (HaeIII) from Haemophilus aegyptius. A quantitative analysis of the resulting specific fragments indicates that the mtDNA of any individual mammal is predominantly a single molecular clone. Gel analysis of specific cleavage products has proven quite sensitive in detecting differences in mtDNA: mtDNAs from the more distantly related mammals studied (e.g., donkey and dog) are found to have few bands in common and very closely related mammals (e.g., donkey and horse) share only about 50% of their bands. This procedure has detected several intraspecies mtDNA differences. Six distinct human patterns have been found, with one pattern usually differing from another in two or three bands. mtDNAs from different organs of single individuals have also been analyzed, and no differences have been found.
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Mitochondrial DNA from an Old World mouse, Mus musculus, and from an Old World rat, Rattus norvegicus, contain 19 and 22 distinct sites, respectively, for the 8 restriction encfonucleases, BamHI, EcoRI, HaeII, HhaI, HincII, HindIII, HpaI and PstI. The relative positions of the sites have been mapped by the study of partial and double enzyme digests. Some sites may have been conserved between the mouse and rat mitochondrial genomes.
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In this study we introduce to natural population analysis a molecular technique that involves the use of restriction endonucleases to compare mitochondrial DNA (mtDNA) sequences. We have examined the fragment patterns produced by six restriction endonucleases acting upon mtDNA isolated from 23 samples of three species of the rodent Peromyscus. Our observations confirm the following conclusions derived from previous experiments with laboratory animals: (1) mtDNA within an individual homogeneous; (2) at least the majority of mtDNA present in an individual is inherited from the female parent. Our experiments demonstrate for the first time that there is detectable heterogeneity in mtDNA sequences within and among natural geographic populations of a species and that this heterogeneity can readily be used to estimate relatedness between individuals and populations. Individuals collected within a single locale show less than 0.5% sequence divergence, while those collected from conspecific populations separated by 50 ti 500 miles differ by approximately 1.5%. The mtDNAs of the closely related sibling species P. polionotus and P. maniculatus differ from each other by 13 to 17%; nonsibling species differ by more than 20%. Qualitative and quantitative approaches to analysis of digestion patterns are suggested. The results indicate that restriction analysis of mtNDA may become the most sensitive and powerful technique yet available for reconstructing evolutionary relationships among conspecific organisms.
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Watterson's (1975) formula for the steady-state distribution of the number of nucleotide differences between two randomly chosen cistrons in a finite population has been extended to transient states. The rate for the mean of this distribution to approach its equilibrium value is 1/2N and independent of mutation rate, but that for the variance is dependent on mutation rate, where N denotes the effective population size. Numerical computations show that if the heterozygosity (i.e., the probability that two cistrons are different) is low, say of the order of 0.1 or less, the probability that two cistrons differ at two or more nucleotide sites is less than 10 percent of the heterozygosity, whereas this probability may be as high as 50 percent of the heterozygosity if the heterozygosity is 0.5. A simple estimate for the mean number (-d) of site differences between cistrons is d = h/(1 - h) where h is the heterozygosity. At equilibrium, the probability that two cistrons differ by more than one site is equal to h2, the square of heterozygosity.
Article
Mitochondrial DNA (mtDNA) from sheep and goat was compared by restriction endonuclease analysis and heteroduplex mapping in the electron microscope. The fragment patterns produced by endonuclease Hae III from three individual sheep and two goat mtDNAs all differed from each other. The three sheep mtDNAs had identical Eco RI and Hind III fragments, but the two goat mtDNA patterns differed from each other as well as from sheep mtDNA. We estimate that each sheep mtDNA differs from each other by 0.5-1% of its nucleotide sequences, the two goat mtDNAs by 1-2%, and there is a 6-11% sequence difference between sheep and goat mtDNAs. We have mapped the Eco RI and Hind III sites of goat and sheep mtDNA and determined the positions of the D loop, which marks the replication origin, relative to the restriction map. The D loops are at homologous positions on the mtDNAs from both species, but the goat D loop is only 75% as long as the sheep D loop. Regions with a high degree of sequence divergence occur at both ends of the D loop. We suggest that a duplication of about 150 base pairs has occurred in the region where the sheep and goat D loops differ in length. We discuss mtDNA evolution in terms of divergence of isolated "mitochondrial DNA clones."
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The distribution is obtained for the number of segregating sites observed in a sample from a population which is subject to recurring, new, mutations but not subject to recombination. After allowance is made for the different effective population sizes, the results apply approximately to three population models, due to Wright, Burrows and Cockerham, and Moran. Included as extreme special cases are the distributions of the number of segregating sites in the whole population and of the number of heterozygous sites in a diploid individual. Some results of Fisher, Haldane, Kimura, and Ewens concerning the means of the distributions for different models are confirmed, but the variances, and the distributions themselves, are new.
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Xenopus laevis and Xenopus mulleri are related amphibian species which can be crossed to give viable hybrid progeny. Their mitochondrial DNAs (mtDNAs)1 have been compared with respect to size, composition, and sequence. Both are circular molecules with a molecular weight of 11.5 to 11.7 × 106 daltons. Their densities in CsCl and thermal denaturation profiles in two solvents are indistinguishable; from these values their nucleotide composition has been calculated to be 41% GC. The large and small mitochondrial rRNA encoded by the mtDNA of X. laevis and X. mulleri have the same or a very similar size.The nucleotide sequences of mtDNA in X. laevis differ from those in X. mulleri. Separated strands of mtDNA of both species were reannealed in all possible combinations, and the thermal stability of the products analyzed. This experiment led to the conclusion that (i) about 30% of the sequences in mtDNA of X. laevis and X. mulleri do not interact, indicating that about half of all bases in these regions differ; (ii) about 50% of the mtDNAs form a heteroduplex with an average of 27% mismatched bases; (iii) 20% of the mtDNAs form a heteroduplex with an average of 6% mismatched bases.Hybridization of mtDNA with different RNAs showed that the sequences coding for mitochondrial rRNA and 4 S RNA are more similar in the two Xenopus species than the other sequences in the DNA. These expressed rRNA and 4 S RNA regions account for the 20% of mtDNA whose sequences have diverged least during evolution. It is suggested that the remaining, rapidly evolving sequences of mtDNA may be equivalent to the “spacer” sequences which have been found within certain nuclear DNAs.
Article
The assumptions underlying the use of the Poisson distribution are essentially that the probability of an event is small but nearly identical for all occurrences and that the occurrence of an event does not alter the probability of recurrence of such events. These assumptions do not seem to be met for evolutionary events since (i) the probability of fixing nucleotide codon substitutions is not equal for all substitutions at a codon, and probably varies for the same substitution in different lineages; (ii) the probability of fixing codon substitutions varies among positions of a cistron; and (iii) the fixation of a nucleotide codon substitution at one position in a cistron modifies, and may even promote, the fixation of a codon substitution elsewhere along the cistron. Natural selection presumably is the causative factor that acts to modify the probability of a nucleotide codon substitution's being fixed in a population. The use of the negative binomial distribution is consistent with the evidence that selective pressure on amino acid or nucleotide codon positions varies both among codon positions of a cistron and at a particular position during evolutionary time. If the number of fixations of nucleotide codon substitutions per position of cistrons encoding cytochromes c are phyletically inferred (phylogeny based on a paleontological record) rather than phenetically inferred (based on paired comparisons of extant species' differences in the absence of a phylogeny) the distribution of these fixation data cannot be described adequately by a single Poisson distribution. The fit of these same data to a negative binomial distribution is very satisfactory. It has been argued that the fit of phenetically inferred fixation data, which do not take account of parallel or reverse fixations, to the Poisson distribution was supportive evidence for the hypothesis that protein evolution results from the fixation of selectively neutral codon substitutions. This argument now appears to be undercut by the evidence that data on nucleotide codon fixation are more probably distributed according to the negative binomial distribution. The fact that fixation data can be described by a particular discrete probability distribution does not of itself provide insight into the mechanisms of the evolutionary process. However, the facts—(i) that the assumptions underlying the use of the negative binomial distribution adequately deal with the varying probability of fixing amino acid or nucleotide codon substitutions at and among the positions of a cistron and (ii) that the negative binomial distribution provides an excellent fit for the phyletically inferred fixation data—suggest that the negative binomial is a very appropriate discrete probability distribution for describing evolutionary events. Amino acids or their nucleotide codon substitutions may be fixed at a position of a cistron as though selectively neutral relative to the codon being replaced, even though the codon position will not be selectively neutral, since many amino acids cannot function there. The negative binomial distribution treats this situation well whereas a single Poisson distribution could only be satisfactory if all codon positions that could vary were selectively neutral.
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