scholarly journals Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations

2021 ◽  
Author(s):  
Angela M Taravella Oill ◽  
Carla Handley ◽  
Emma K Howell ◽  
Anne C. Stone ◽  
Sarah Mathew ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Genomic Analysis ◽  
Human Populations ◽  
Demographic Information ◽  
Geographic Scale ◽  
Northern Kenya ◽  
Predominant Factor ◽  
Cultural Similarity

Objectives: The aim of this study was to characterize the genetic relationships within and among four neighboring populations in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation. Materials and Methods: We collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals. Results: Here we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations. Discussion: Overall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.

scholarly journals Evaluating the genetic variability of rubber hybrid progenies of the two crosses PB260 x RO44/71 and PB260 x RO62/54 by RAPD technique

2019 ◽  
Vol 2 (3) ◽  
pp. 36-43
Author(s):  
Thien Minh Nguyen ◽  
Tien Thi My Pham
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Similarity ◽  
Field Experiments ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Genetic Material ◽  
Population Based ◽  
Shannon Index ◽  
Polymorphic Bands

The agronomic values of this population have been evaluated in the field experiments based on their phenotypic performance of agronomic traits, but the genetic variability of this population needs to be evaluated via techniques based on genetic material - DNA. In this study, the genetic variability in the investigated population of 71 hybrids and their parents was evaluated by RAPD technique, using eight selected arbitrarily primers; Genetic parameters and dendrogram expressing the genetic relationships among the investigated population were analyzed by GenALEx 6.1, Popgene 1.31 and NTSYSpc 2.1 softwares. Eight primers were used to generate the amplify products on each individual in the investigated population. From 74 genotypes, a total of 109 fragments were generated, among which, there were 89 polymorphic bands representing 81.65% with an average of 11 polymorphic bands/primer. Genetic similarity coefficient among the investigated population, based on DICE coefficient, ranged from 0.560 (LH05/0822 and PB260) to 0.991 (LH05/0781 and LH05/0841) with an average of 0,796, meaning that the genetic distance among ranged from 0.009 to 0.440 with an average of 0.231. The Shannon index and mean heterozygosity values were 0.328 and 0,176, respectively. This indicated that the progenies of the two investigated crosses possessed a relatively high range of genetic variability. The analysis of molecular variance (AMOVA) showed that genetic variation within population represented 62%, while genetic variation among two different crosses contributes 38% to the total genetic variability. Dendrogram based on DICE’s genetic similarity using UPGMA method showed that the hybrids divide into two major genetic groups (0.75), but the crosses were scattered independently of the hybrid.

scholarly journals Variasi Genetik dalam Populasi Kultivar Kopi Arabika Berbuah Kuning di Lahan Petani Berdasarkan Penanda SSRs

2016 ◽  
Vol 3 (2) ◽  
pp. 83
Author(s):  
Dani Dani ◽  
Nur Kholilatul Izzah ◽  
Enny Randriani
Keyword(s):  
Genetic Variation ◽  
Environmental Conditions ◽  
Genetic Similarity ◽  
Binary Data ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Arabica Coffee

<p><em>Identification of the genetic diversity within populations of yellow-berried Arabica coffee cultivar based on morphological characters faced an obstacle in finding identical environmental conditions at farmers field. Therefore, an approach which is not influenced by differences in environmental conditions is required, for instance based on DNA polymorphism. The research aimed to analyze genetic variation within populations of yellow-berried Arabica coffee cultivar based on SSRs markers. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, from April until June 2015. The leaf samples for DNA extraction were obtained from yellow-berried Arabica coffee cultivar (AGK-1) and two red-berried cultivars  as controls, namely  ABP-1 (dwarf type) and Typica (tall type). AGK-1 and ABP-1 cultivars consisted of 17 and 5 individual numbers, respectively, whereas Typica cultivar comprised three individuals. PCR amplification was carried out using 12 SSR primers. Four primers (M24, SSRCa052, M32, and M42) produced polymorphic band. The binary data obtained in this research was subsequently processed using NTSYS-PC program version 2.1. The genotypes were grouped  based on a genetic similarity matrix using the unweighted pair group method arithmetic mean (UPGMA). The result showed the existence of genetic variation among individual of AGK-1 cultivars, which forming three clusters at the genetic similarity value of 67%. One cluster exhibited close genetic relationships between some individuals within the population of AGK-1 cultivar and Typica cultivar. Meanwhile, the other two clusters showed high genetic similarity between AGK-1 cultivar and ABP-1 cultivar. The result demonstrated the possibility of gene flow between genotypes or residual heterozygosity within the population of  AGK-1 cultivar at farmers field, which required a further study.</em><em></em></p>

scholarly journals Genetic diversity of Carica papaya as revealed by AFLP markers

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 503-512 ◽  
Author(s):  
M S Kim ◽  
P H Moore ◽  
F Zee ◽  
M MM Fitch ◽  
D L Steiger ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Related Species ◽  
Genetic Similarity ◽  
Carica Papaya ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Gene Pools ◽  
Breeding Lines ◽  
Similar Gene

Genetic relationships among Carica papaya cultivars, breeding lines, unimproved germplasm, and related species were established using amplified fragment length polymorphism (AFLP) markers. Seventy-one papaya accessions and related species were analyzed with nine EcoRI–MseI primer combinations. A total of 186 informative AFLP markers was generated and analyzed. Cluster analysis suggested limited genetic variation in papaya, with an average genetic similarity among 63 papaya accessions of 0.880. Genetic diversity among cultivars derived from the same or similar gene pools was smaller, such as Hawaiian Solo hermaphrodite cultivars and Australian dioecious cultivars with genetic similarity at 0.921 and 0.912, respectively. The results indicated that self-pollinated hermaphrodite cultivars were as variable as open-pollinated dioecious cultivars. Genetic diversity between C. papaya and six other Carica species was also evaluated. Carica papaya shared the least genetic similarity with these species, with an average genetic similarity of 0.432; the average genetic similarity among the six other species was 0.729. The results from AFLP markers provided detailed estimates of the genetic variation within and among papaya cultivars, and supported the notion that C. papaya diverged from the rest of Carica species early in the evolution of this genus.Key words: DNA fingerprinting, germplasm, genetic relationship, molecular phylogeny, polymorphism.

scholarly journals 090 Identification and Genetic Relatedness among Pecan Cultivars Detected by Randomly Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 404B-404
Author(s):  
Patrick J. Conner ◽  
Bruce W. Wood
Keyword(s):  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Carya Illinoinensis ◽  
Randomly Amplified Polymorphic Dna

Genetic variation among pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint was produced for each of the pecan genotypes studied. The genetic relatedness between 44 cultivars was estimated using more than 100 RAPD markers. Genetic distances based on the simple matching coefficient varied from 0.91 to 0.59. The phenetic dendogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships. Using RAPD information in determining genetic relationships among pecan cultivars with unknown or questionable pedigrees and the integration of that knowledge into the breeding program is discussed.

Genetic Relationships of Cory's Shearwater: Parentage, Mating Assortment, and Geographic Differentiation Revealed by DNA Fingerprinting

The Auk ◽  
2000 ◽  
Vol 117 (3) ◽  
pp. 651-662 ◽  
Author(s):  
Corinne Rabouam ◽  
Vincent Bretagnolle ◽  
Yves Bigot ◽  
Georges Periquet
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Dna Fingerprinting ◽  
Genetic Relatedness ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Cory’S Shearwater ◽  
Genetic Structure Of Populations ◽  
The Social ◽  
Calonectris Diomedea

Abstract We used DNA fingerprinting to assess genetic structure of populations in Cory's Shearwater (Calonectris diomedea). We analyzed mates and parent-offspring relationships, as well as the amount and distribution of genetic variation within and among populations, from the level of subcolony to subspecies. We found no evidence of extrapair fertilization, confirming that the genetic breeding system matches the social system that has been observed in the species. Mates were closely related, and the level of genetic relatedness within populations was within the range usually found in inbred populations. In contrast to previous studies based on allozymes and mtDNA polymorphism, DNA fingerprinting using microsatellites revealed consistent levels of genetic differentiation among populations. However, analyzing the two subspecies separately revealed that the pattern of genetic variation among populations did not support the model of isolation by distance. Natal dispersal, as well as historic and/or demographic events, probably contributed to shape the genetic structure of populations in the species.

Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
Author(s):  
Wenguang Cao ◽  
G Scoles ◽  
P Hucl ◽  
R N Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
Similarity Coefficients ◽  
Morphological Classification ◽  
Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

scholarly journals Parasite variation and the evolution of virulence in a Daphnia-microparasite system

Parasitology ◽  
2007 ◽  
Vol 135 (3) ◽  
pp. 303-308 ◽  
Author(s):  
T. J. LITTLE ◽  
W. CHADWICK ◽  
K. WATT
Keyword(s):  
Genetic Variation ◽  
Rank Order ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Host Genotype ◽  
Relative Growth ◽  
Trade Off ◽  
Relative Growth Rates ◽  
Pasteuria Ramosa ◽  
Evolution Of Virulence

SUMMARYUnderstanding genetic relationships amongst the life-history traits of parasites is crucial for testing hypotheses on the evolution of virulence. This study therefore examined variation between parasite isolates (the bacterium Pasteuria ramosa) from the crustacean Daphnia magna. From a single wild-caught infected host we obtained 2 P. ramosa isolates that differed substantially in the mortality they caused. Surprisingly, the isolate causing higher early mortality was, on average, less successful at establishing infections and had a slower growth rate within hosts. The observation that within-host replication rate was negatively correlated with mortality could violate a central assumption of the trade-off hypothesis for the evolution of virulence, but we discuss a number of caveats which caution against premature rejection of the trade-off hypothesis. We sought to test if the characteristics of these parasite isolates were constant across host genotypes in a second experiment that included 2 Daphnia host clones. The relative growth rates of the two parasite isolates did indeed depend on the host genotype (although the rank order did not change). We suggest that testing evolutionary hypotheses for virulence may require substantial sampling of both host and parasite genetic variation, and discuss how selection for virulence may change with the epidemiological state of natural populations and how this can promote genetic variation for virulence.

Habitat differentiation between estuarine and inland Hibiscus tiliaceus L. (Malvaceae) as revealed by retrotransposon-based SSAP marker

2011 ◽  
Vol 59 (6) ◽  
pp. 515 ◽  
Author(s):  
Tian Tang ◽  
Lian He ◽  
Feng Peng ◽  
Suhua Shi
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Distance ◽  
Genetic Variance ◽  
Genetic Relationships ◽  
Principal Coordinate Analysis ◽  
Geographical Isolation ◽  
Tidal Zone ◽  
Ecological Scale ◽  
Habitat Differentiation

Hibiscus tiliaceus L. (Malvaceae) is a pantropical coastal tree that extends to the tidal zone. In this study, the retrotransposon sequence-specific amplified polymorphism (SSAP) technique was used in order to understand the genetic variation between four population pairs of H. tiliaceus from repeated estuarine and inland habitat contrasts in China. The estuarine populations were consistently more genetic variable compared with the inland ones, which may be attributed to extensive gene flow via water-drifted seeds and/or retrotransposon activation in stressful estuarine environments. An AMOVA revealed that 8.9% of the genetic variance could be explained by the habitat divergence within site, as compared with only 4.9% to geographical isolation between sites, which indicates significant habitat differentiation between the estuarine and inland populations. The estuarine populations were less differentiated (ΦST = 0.115) than the inland (ΦST = 0.152) implying frequent gene interchange in the former. Accordingly, the principal coordinate analysis of genetic distance between individuals revealed that genetic relationships are not fully consistent with the geographic association. These results suggest that despite substantial gene flow via sea-drifted seeds, habitat-related divergent selection could be one of the primary mechanisms that drive habitat differentiation in H. tiliaceus at a local ecological scale.

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