scholarly journals The Allelic Correlation Structure of Gainj- and Kalam-Speaking People. II. The Genetic Distance Between Population Subdivisions

Genetics ◽  
1987 ◽  
Vol 117 (2) ◽  
pp. 273-283
Author(s):  
Jeffrey C Long ◽  
Peter E Smouse ◽  
James W Wood
Keyword(s):  
Genetic Distance ◽  
Group Size ◽  
Linguistic Diversity ◽  
Genetic Distances ◽  
Demographic Feature ◽  
Distance Methods ◽  
Tribal Populations ◽  
Geographic Differences ◽  
Population Subdivisions ◽  
Theoretical Considerations

ABSTRACT The patterning of allele frequency variability among 18 local groups of Gainj and Kalam speakers of highland Papua New Guinea is investigated using new genetic distance methods. The genetic distances proposed here are obtained by decomposing Sewall Wright's coefficient FST into a set of coefficients corresponding to all pairs of population subdivisions. Two statistical methods are given to estimate these quantities. One method provides estimates weighted by sample sizes, while the other method does not use sample size weighting. Both methods correct for the within-individual and between-individual-within-groups sums of squares. Genetic distances among the Gainj and Kalam subdivisions are analyzed with respect to demographic, geographic, and linguistic variables. We find that a demographic feature, group size, has the greatest demonstrable association with the patterning of genetic distances. The pattern of geographic distances among groups displays a weak congruence with the pattern of genetic distances, and the association of genetic and linguistic diversity is very low. An effect of differences in group size on genetic distances is not surprising, from basic theoretical considerations, but genetic distances have not often been analyzed with respect to these variables in the past. The lack of correspondence between genetic distances and linguistic and geographic differences is an unusual feature that distinguishes the Gainj and Kalam from most other tribal populations.

scholarly journals Genetic Variation Among Colletotrichum graminicola Isolates from Four Hosts Using Isozyme Analysis

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 402-406 ◽  
Author(s):  
B. J. Horvath ◽  
J. M. Vargas
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Geographic Origin ◽  
Creeping Bentgrass ◽  
Genetic Distances ◽  
Colletotrichum Graminicola ◽  
Annual Bluegrass ◽  
Close Relationship ◽  
Host Origin ◽  
Serious Disease

Anthracnose basal rot (ABR) is a serious disease of turfgrasses that is caused by the pathogen Colletotrichum graminicola. The relationships of isolates causing ABR on turfgrasses to those causing disease on important crop hosts (maize, sorghum) remain unresolved. Genetic variation among isolates from annual bluegrass, creeping bentgrass, maize, and sorghum was evaluated based on host origin and geographic origin. Isozymes were used to estimate the genetic variation of the isolates. Five enzyme systems comprising 16 alleles from 5 loci were used. Allele frequencies, genetic distance, and linkage disequilibrium values were calculated for isolates based on both host and geographic origin. Isolates from creeping bentgrass and annual bluegrass were the most closely related based on Nei's genetic distance, while isolates from maize and sorghum were the most distantly related, consistent with their known species-level relationship. Isolates from annual bluegrass and creeping bentgrass had different genetic distances to isolates from both maize and sorghum. Annual bluegrass isolates from different geographic regions had the smallest genetic distance values observed in this study, indicating a very close relationship regardless of geographic origin. Based on these data, it appears that host origin, not geographic origin, plays a more important role in the genetic diversity of these fungi.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

scholarly journals The optimal mating distance resulting from heterosis and genetic incompatibility

2018 ◽  
Vol 4 (11) ◽  
pp. eaau5518 ◽  
Author(s):  
Xinzhu Wei ◽  
Jianzhi Zhang
Keyword(s):  
Animal Model ◽  
Genetic Distance ◽  
Polynomial Function ◽  
Genetic Distances ◽  
Quadratic Polynomial ◽  
Model Organisms ◽  
Genetic Incompatibility ◽  
Large Numbers ◽  
Practical Implications

Theory predicts that the fitness of an individual is maximized when the genetic distance between its parents (i.e., mating distance) is neither too small nor too large. However, decades of research have generally failed to validate this prediction or identify the optimal mating distance (OMD). Respectively analyzing large numbers of crosses of fungal, plant, and animal model organisms, we indeed find the hybrid phenotypic value a humped quadratic polynomial function of the mating distance for the vast majority of fitness-related traits examined, with different traits of the same species exhibiting similar OMDs. OMDs are generally slightly greater than the nucleotide diversities of the species concerned but smaller than the observed maximal intraspecific genetic distances. Hence, the benefit of heterosis is at least partially offset by the harm of genetic incompatibility even within species. These results have multiple theoretical and practical implications for speciation, conservation, and agriculture.

Detection of genetic diversity in rough fescue (Festuca campestris Rydb) populations of southern Alberta and British Columbia, Canada, using RAPD markers

2008 ◽  
Vol 88 (2) ◽  
pp. 307-312
Author(s):  
Zhao Mengli ◽  
Han Bing ◽  
Walter D Willms
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Gene Frequencies ◽  
Southern Alberta ◽  
Potential Adaptation ◽  
Rough Fescue

Mountain rough fescue (Festuca campestris Rydb.) is a tufted native grass in southern Alberta and British Columbia, Canada, and has attracted interest for use in reclamation. However, its seed is often available from only a few localized sources and may not be adapted for areas removed from the collection site. We conducted a study to determine the genetic variability among rough fescue populations to assess its potential adaptation. Thirty plants were collected from each of six populations and analyzed using Random Amplified Polymorphic DNA (RAPD). One population (Kamloops, BC) was separated by several mountain ranges from the five easterly Alberta populations.The Kamloops population was also separated from the Alberta populations by genetic distance in two clusters. Of the total genetic variation present in the data, 21% was found among populations while the remaining (79%) was found within populations. Nei’s genetic distances among populations were related to their geographical distances. Genetic differences among populations appeared to be caused primarily by differences in gene frequencies rather than rare genes. Also, genetic diversity appeared to increase from west to east suggesting that the more easterly populations had greater adaptation potential. We speculate that the more easterly populations are less likely to share genes since the prevailing winds are from the west. Germplasm from the more easterly populations may be used with suitable precautions within Alberta and possibly around Kamloops. Key words: Genetic distance, geographic distance, reclamation, potential adaptation

scholarly journals The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus

2020 ◽  
Vol 37 (12) ◽  
pp. 3654-3671
Author(s):  
Kevin H -C Wei ◽  
Aditya Mantha ◽  
Doris Bachtrog
Keyword(s):  
Genetic Distance ◽  
Allele Frequency ◽  
Recombination Rate ◽  
High Throughput Sequencing ◽  
Genetic Material ◽  
Cost Effective ◽  
Genetic Distances ◽  
Recombination Rates ◽  
Marker Selection ◽  
Cost Effective Approach

Abstract Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High-throughput sequencing approaches detect crossovers genome wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near chromosome-wide recombination rates by taking advantage of non-Mendelian allele frequency generated from a fitness differential at a locus under selection. As more crossovers decouple the selected locus from distal loci, the distorted allele frequency attenuates distally toward Mendelian and can be used to estimate the genetic distance. Here, we use marker selection to generate distorted allele frequency and theoretically derive the mathematical relationships between allele frequency attenuation, genetic distance, and recombination rate in marker-selected pools. We implemented nonlinear curve-fitting methods that robustly estimate the allele frequency decay from batch sequencing of pooled individuals and derive chromosome-wide genetic distance and recombination rates. Empirically, we show that marker-selected pools closely recapitulate genetic distances inferred from scoring recombinants. Using this method, we generated novel recombination rate maps of three wild-derived strains of Drosophila melanogaster, which strongly correlate with previous measurements. Moreover, we show that this approach can be extended to estimate chromosome-wide crossover interference with reciprocal marker selection and discuss how it can be applied in the absence of visible markers. Altogether, we find that our method is a simple and cost-effective approach to generate chromosome-wide recombination rate maps requiring only one or two libraries.

scholarly journals Genetic Diversity Based on ISSR Markers of Apple Genotypes in Ardahan/Turkey

2018 ◽  
Vol 10 (4) ◽  
pp. 554-558
Author(s):  
Emre SEVİNDİK ◽  
Hüseyin UYSAL ◽  
Zehra Tuğba MURATHAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Uv Light ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
The Matrix ◽  
Commercial Kits ◽  
Issr Primers

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program.  According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

Lack of isozyme similarity between Vigna unguiculata and other species of subgenus Vigna (Leguminosae)

1993 ◽  
Vol 71 (4) ◽  
pp. 586-591 ◽  
Author(s):  
R. E. Vaillancourt ◽  
N. F. Weeden
Keyword(s):  
Genetic Distance ◽  
Vigna Unguiculata ◽  
Genetic Distances ◽  
Close Relative ◽  
Tropical Africa ◽  
The Third ◽  
Upgma Cluster Analysis ◽  
Isozyme Loci ◽  
The Relationship ◽  
Nei's Genetic Distance

The cowpea (Vigna unguiculata (L.) Walp.) is an important crop of tropical Africa, Asia, and South America. However, the relationship between the cowpea and other species of subg. Vigna is relatively unknown. The objective of this study was to assess the genetic distance among species of subg. Vigna using isozymes. Twenty-four populations of the cowpea species and 39 populations from 10 other species (at least one species per section of subgenus Vigna) were sampled. Nei's genetic distance was calculated from allelic frequencies at 26 isozyme loci. UPGMA cluster analysis was performed. The range of genetic distance among species of subg. Vigna (0.41 – 2.69) was greater than previously reported in most plant genera. Three clusters of species were apparent. The first cluster included three species of sect. Vigna (V. luteola, V. oblongifolia, and V. subterranea (the Bambara groundnut)). The second cluster grouped together sections Liebrechtsia and Macrodontae. The third cluster included V. unguiculata, V. reticulata, and V. vexillata. The distances between species of this cluster were large and of similar size in all combinations (range from 0.92 to 0.95). None of the species included in this survey can be called a close relative of V. unguiculata. Key words: Vigna, cowpea, isozymes, genetic distances.

scholarly journals Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA–trnH intergenic region

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 15-20 ◽  
Author(s):  
Shangguo Feng ◽  
Kaili Jiao ◽  
Yujia Zhu ◽  
Hongfen Wang ◽  
Mengying Jiang ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Genetic Distances ◽  
Success Rates ◽  
Medicinal Species ◽  
Distance Methods ◽  
Identification Of Species ◽  
Related Plant

Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among species of Physalis make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA–trnH intergenic region, in the identification of species of Physalis. Thirty-six psbA–trnH regions of species of Physalis and of the closely related plant Nicandra physalodes were analyzed. The success rates of PCR amplification and sequencing of the psbA–trnH region were 100%. MEGA V6.0 was utilized to align the psbA–trnH sequences and to compute genetic distances. The results show an apparent barcoding gap between intra- and interspecific variations. Results of both BLAST1 and nearest-distance methods prove that the psbA–trnH regions can be used to identify all species examined in the present study. In addition, phylogenetic analysis using psbA–trnH data revealed a distinct boundary between species. It also confirmed the relationship between species of Physalis and closely related species, as established by previous studies. In conclusion, the psbA–trnH intergenic region can be used as an efficient DNA barcode for the identification of species of Physalis.

scholarly journals 468 PB 333 RAPDS ANALYSIS OF GENETIC DISTANCE BETWEEN WILD AND CULTIVATED TEPARY BEAN LINES

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 498c-498
Author(s):  
Jan E. Paul Debaene ◽  
Laren Robison
Keyword(s):  
Genetic Distance ◽  
Arid Regions ◽  
Genetic Distances ◽  
Tepary Bean ◽  
Phaseolus Acutifolius ◽  
Pinto Bean ◽  
Heat Tolerant

Tepary beans (Phaseolus acutifolius A. Gray) are considered drought and heat tolerant, desirable characteristics for arid regions. Knowing the genetic distances among tepary lines can indicate both compatibility for intraspecific crosses and potential for Interspecific P. acutifolius × P. vulgaris hybrids. Fifteen tepary lines, including cultivars and landraces, were compared to two pinto bean varieties using random amplified polymorphic DNA's (RAPDs). At the present time polymorphisms have been clearly identified between wild and cultivated teparies and the pinto bean. An ammo acid profile is also being determined using HPLC. More work needs to be completed before relationships among cultivated teparies can be established.

scholarly journals Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7754
Author(s):  
Dora Serdari ◽  
Evangelia-Georgia Kostaki ◽  
Dimitrios Paraskevis ◽  
Alexandros Stamatakis ◽  
Paschalia Kapli
Keyword(s):  
Species Delimitation ◽  
Ad Hoc ◽  
Hepatitis Virus ◽  
Genetic Distances ◽  
Phenotypic Traits ◽  
Virus Taxonomy ◽  
Hepatitis Viruses ◽  
Virus Classification ◽  
Distance Methods

Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.

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