scholarly journals Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

2020 ◽  
Vol 295 (6) ◽  
pp. 1315-1324
Author(s):  
Noora R. Al-Snan ◽  
Safia A. Messaoudi ◽  
Yahya M. Khubrani ◽  
Jon H. Wetton ◽  
Mark A. Jobling ◽  
...  
Keyword(s):  
Population Structure ◽  
Tandem Repeats ◽  
Arabian Gulf ◽  
Ethnically Diverse ◽  
Population Expansion ◽  
Northern Region ◽  
Geographical Regions ◽  
Low Diversity ◽  
Discrimination Capacity ◽  
Short Tandem

Abstract We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions—Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over the 17-locus Yfiler kit in discrimination capacity (from 77% to 87.5% overall), but discrimination capacity differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly resulting from recent rapid population expansion. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a likely originating in Africa, and H, L and R2 likely indicative of migration from South Asia. Haplogroup frequencies differed significantly between regions, with J2 significantly more common in the Northern region compared with the Southern, possibly due to differential settlement by Baharna and Arabs. Our study shows that paternal lineage population structure can exist even over small geographical scales, and that highly discriminating genetic tools are required where rapid expansions have occurred within tightly bounded populations.

scholarly journals Genetic variation at 27 y-strs in four regions of bahrain

2019 ◽  
Author(s):  
Noora R. Al-Snan ◽  
Safia A. Messaoudi ◽  
Yahya M. Khubrani ◽  
Jon H. Wetton ◽  
Mark A. Jobling ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Indigenous Population ◽  
Arabian Gulf ◽  
Northern Region ◽  
Rapid Expansion ◽  
Population Substructure ◽  
Social Variation ◽  
Geographical Regions ◽  
Population Databases ◽  
Short Tandem

AbstractBahrain location in the Arabian Gulf contributed to the diversity of its indigenous population descended from Christian Arabs, Persians (Zoroastrians), Jews, and Aramaic-speaking agriculturalists. The aim of this study was to examine population substructure within Bahrain using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit and to characterize the haplotypes of 562 unrelated Bahraini nationals, sub-divided into the four geographical regions - North, Capital, South and Muharraq. Yfiler Plus provided a significant improvement over the earlier 17-locus Yfiler kit in discrimination capacity, increasing it from 77% to 87.5%, but this value differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly as a consequence of the very rapid expansion in population size in the last 80 years. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a originating in Africa and H, L and R2 indicative of migration from the east. Haplogroup frequencies differed significantly between regions with J2 significantly more common in the Northern region compared with the Southern possibly as a result of differential settlement with Baharna (descended from populations in which J2 predominates) and Arabs (both indigenous and migrant Huwala who are expected to have a higher frequency of J1). Our study illustrated the importance of encompassing geographical and social variation when constructing population databases and the need for highly discriminating multiplexes where rapid expansions have occurred within tightly bounded populations.

scholarly journals Genetic diversity in a Brazilian bovine herd based on four microsatellite loci

2000 ◽  
Vol 23 (2) ◽  
pp. 345-350 ◽  
Author(s):  
Sabrina E. Matos Almeida ◽  
Márcia S.N. Machado ◽  
Clara Sabina Steigleder ◽  
Cleonice L. Gama ◽  
Mara Helena Hutz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Tandem Repeats ◽  
Geographic Origin ◽  
Low Diversity ◽  
Taurine Cattle ◽  
Red Angus ◽  
High Degree ◽  
First Time ◽  
Short Tandem

Microsatellites or short tandem repeats (STRs), DNA markers relatively abundant in the genome, have a high degree of polymorphism and therefore great potential for characterizing populations. The present study estimates genetic variability in a set of four microsatellites (BMS3013, BMS3004, HEL10 and TGLA122) in a Brazilian hybrid bovine breed (5/8 Aberdeen Angus x 3/8 Nelore). The objectives were to determine the effect of crossbreeding and selection in these animals' genetic diversity as well as to discover the herd's genetic relationship with that of other breeds. Low diversity was verified in BMS3013 and high diversity was detected in BMS3004, HEL10 and TGLA122. Two alleles in TGLA122 are described here for the first time (TGLA122*155 and TGLA122*163). These genes are possibly characteristics of Zebu animals since they have not been found in other taurine samples so far investigated. Low interpopulational diversity was observed among taurine cattle populations, and clusters obtained on TGLA122 phylogenetic trees agreed with the bovine herd's geographic origin. Therefore, despite TGLA122's high polymorphism and high levels of intrapopulational diversity, the system engenders consistent bovine phylogenies. We detected an intriguingly high similarity between Brangus Ibagé and Red Angus since the former is a hybrid having 3/8 of Nelore genes. Either these animals' environment or genetic selective practices applied to the breed probably favor the Angus genotype.

scholarly journals Canine echinococcosis: genetic diversity of Echinococcus granulosus sensu stricto (s.s.) from definitive hosts

2015 ◽  
Vol 89 (6) ◽  
pp. 689-698 ◽  
Author(s):  
B. Boufana ◽  
W. Lett ◽  
S. Lahmar ◽  
A. Griffiths ◽  
D.J. Jenkins ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Echinococcus Granulosus ◽  
Population Expansion ◽  
Sensu Stricto ◽  
Geographical Regions ◽  
Self Fertilization ◽  
Adult Tapeworm ◽  
Asymptomatic Disease

AbstractCanids, particularly dogs, constitute the major source of cystic echinococcosis (CE) infection to humans, with the majority of cases being caused by Echinococcus granulosus (G1 genotype). Canine echinococcosis is an asymptomatic disease caused by adult tapeworms of E. granulosus sensu lato (s.l.). Information on the population structure and genetic variation of adult E. granulosus is limited. Using sequenced data of the mitochondrial cytochrome c oxidase subunit 1 (cox1) we examined the genetic diversity and population structure of adult tapeworms of E. granulosus (G1 genotype) from canid definitive hosts originating from various geographical regions and compared it to that reported for the larval metacestode stage from sheep and human hosts. Echinococcus granulosus (s.s) was identified from adult tapeworm isolates from Kenya, Libya, Tunisia, Australia, China, Kazakhstan, United Kingdom and Peru, including the first known molecular confirmation from Gaza and the Falkland Islands. Haplotype analysis showed a star-shaped network with a centrally positioned common haplotype previously described for the metacestode stage from sheep and humans, and the neutrality indices indicated population expansion. Low Fst values suggested that populations of adult E. granulosus were not genetically differentiated. Haplotype and nucleotide diversities for E. granulosus isolates from sheep and human origin were twice as high as those reported from canid hosts. This may be related to self-fertilization of E. granulosus and/or to the longevity of the parasite in the respective intermediate and definitive hosts. Improved nuclear single loci are required to investigate the discrepancies in genetic variation seen in this study.

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

1997 ◽  
Vol 45 (3) ◽  
pp. 265-270 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
Mark Seielstad ◽  
Eva Mateu ◽  
David Comas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset

2020 ◽  
Vol 19 (2) ◽  
Author(s):  
Koji Tsukuda ◽  
Shuhei Mano ◽  
Toshimichi Yamamoto
Keyword(s):  
Sample Size ◽  
Classification Accuracy ◽  
Tandem Repeats ◽  
Bayes Factor ◽  
Characteristic Curve ◽  
Geometric Mean ◽  
Previous Method ◽  
Threshold Adjustment ◽  
Two Populations ◽  
Short Tandem

AbstractShort Tandem Repeats (STRs) are a type of DNA polymorphism. This study considers discriminant analysis to determine the population of test individuals using an STR database containing the lengths of STRs observed at more than one locus. The discriminant method based on the Bayes factor is discussed and an improved method is proposed. The main issues are to develop a method that is relatively robust to sample size imbalance, identify a procedure to select loci, and treat the parameter in the prior distribution. A previous study achieved a classification accuracy of 0.748 for the g-mean (geometric mean of classification accuracies for two populations) and 0.867 for the AUC (area under the receiver operating characteristic curve). We improve the maximum values for the g-mean to 0.830 and the AUC to 0.935. Computer simulations indicate that the previous method is susceptible to sample size imbalance, whereas the proposed method is more robust while achieving almost identical classification accuracy. Furthermore, the results confirm that threshold adjustment is an effective countermeasure to sample size imbalance.

Conditional Genotypic Probabilities for Microsatellite Loci

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1973-1980
Author(s):  
Jinko Graham ◽  
James Curran ◽  
B S Weir
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Dirichlet Distribution ◽  
Forensic Dna ◽  
Match Probability ◽  
Microsatellite Genotype ◽  
Allelic State ◽  
Forensic Assessments ◽  
Dna Profiles ◽  
Short Tandem

Abstract Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2–5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.

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