scholarly journals Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

2021 ◽  
Author(s):  
Elizabeth G. Atkinson ◽  
Shareefa Dalvie ◽  
Yakov Pichkar ◽  
Allan Kalungi ◽  
Lerato Majara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Variant Interpretation ◽  
African Continent ◽  
Transmission Rates ◽  
Genetics Research ◽  
African Populations ◽  
The World ◽  
Eastern And Southern Africa ◽  
Language Transmission

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multigenerational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We further find significantly higher language transmission rates for matrilineal groups as compared to patrilineal. We highlight both the diversity of variation within the African continent, as well as how within-Africa variation can be informative for broader variant interpretation; many variants appearing rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity within Africa.

scholarly journals Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2504 ◽  
Author(s):  
Katarzyna Bilska ◽  
Monika Szczecińska
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Conservation Genetics ◽  
Ssr Markers ◽  
Full Range ◽  
Mantel Test ◽  
Evolutionary Potential ◽  
Functional Variation ◽  
Genetics Research ◽  
Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

scholarly journals Global Biodiversity Patterns of the Photobionts Associated with the Genus Cladonia (Lecanorales, Ascomycota)

2020 ◽  
Author(s):  
Raquel Pino-Bodas ◽  
Soili Stenroos
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sexual Reproduction ◽  
Geographical Distribution ◽  
Type I ◽  
Generalist Species ◽  
Climatic Regions ◽  
The World ◽  
Global Biodiversity ◽  
High Diversity

Abstract The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.

scholarly journals Assessment of genetic diversity in tomato landraces using ISSR markers

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 25-35 ◽  
Author(s):  
Mashhid Henareh ◽  
Atilla Dursun ◽  
Babak Abdollahi-Mandoulakani ◽  
Kamil Haliloğlu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Issr Markers ◽  
Vegetable Crops ◽  
North West ◽  
Expected Heterozygosity ◽  
The World ◽  
Commercial Cultivars ◽  
The Mean ◽  
Issr Primers

Tomato is one of the most economically important vegetable crops in many parts of the world. Turkey and Iran are the main producers of tomatoes in the world. The objective of this study was to assess the genetic variation of 93 tomato landraces from East Anatolian region of Turkey and North-West of Iran, along with three commercial cultivars using 14 ISSR primers. The percentage of polymorphic loci (PPL) for all primers was 100%. The mean of expected heterozygosity (He) for the primers varied from 0.153 (UBC808) to 0.30 (UBC848). The dendrogram placed the landraces and commercial cultivars into nine groups. The genotypes originating from the same region, often located in the same group or two adjacent groups. The highest likelihood of the data was obtained when population were located into 2 sub-populations (K = 2). These sub-populations had Fst value of 0.16 and 0.21.

Threats to the Economic Security of Russia in the Context of Trends in the Development of Africa

2020 ◽  
pp. 112-125
Author(s):  
Alexander I. Selivanov ◽  
Vladimir G. Starovoitov ◽  
Dmitriy V. Troshin
Keyword(s):  
National Economy ◽  
Economic Security ◽  
Economic Transformation ◽  
Economic Crime ◽  
African Continent ◽  
New Developments ◽  
External Threats ◽  
National Economic ◽  
The World ◽  
National Economic Security

Situation and value of the African continent on the economic and social cardmap of the world dynamically changes and will continue to change throughout all the 21st century with strengthening of the Africa positions in the world. In Russia all the complex of threats and problems which arise owing to political and economic transformation of Africa is not adequately estimated. The scientific literature on economic security issues presents an expanded set of internal and external threats to the national economy that goes beyond the traditional areas of the shadow economy, corruption, economic crime and related segments, including the internal economic stability of the national economy and inter-country competition, the quality of state strategic management, studies of the specifics of ensuring economic security in the conditions of the sixth technological order, intercultural communication and their impact on the economic relations between countries, etc. Incomplete use of such approach to strategy for the countries of Africa creates additional threats and risks for Russia. An analysis of security problems in Africa revealed that studies of economic security in the context of African development trends in Russia are conducted in an unsatisfactory volume, not always taking into account the results of new developments in the field of ensuring economic security. Even the large shifts happening on the African continent, forecasts of this dynamics sometimes are poorly known to experts of a profile of economic security, and many experts of an economic profile including working in the African subject often do not accurately distinguish problems of “economic cooperation” and “the Russian – African relations”, on the one hand, and “economic security of Russia” – with another. In this regard the new scientific problem is proved: need for deeper analysis of trends of economic and social development in Africa as an important component of a system of ensuring national economic security of Russia in the current period and in the future into account the new developments in the sphere of economic security. The main directions of activating scientific research and concentration of practical efforts to increase national economic security, neutralize threats and reduce risk for Russia in the designated context are formulated.

Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Allelic Variation ◽  
Germplasm Collection ◽  
Principal Component ◽  
Isozyme Loci ◽  
National Plant Germplasm System ◽  
The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

scholarly journals Edible Insects and Global Food Security

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 472
Author(s):  
Fabio Verneau ◽  
Mario Amato ◽  
Francesco La La Barbera
Keyword(s):  
Food Security ◽  
Central America ◽  
Mediterranean Basin ◽  
Edible Insects ◽  
African Continent ◽  
Global Food Security ◽  
The World ◽  
The Mediterranean ◽  
Global Food ◽  
The Mediterranean Basin

Starting in 2008 and lasting up until 2011, the crisis in agricultural and, in particular, cereal prices triggered a period of riots that spread from the Mediterranean basin to the rest of the world, reaching from Asia to Central America and the African continent. [...]

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals Genetic variation in the Middle East—an opportunity to advance the human genetics field

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Ahmad N. Abou Tayoun ◽  
Heidi L. Rehm
Keyword(s):  
Genetic Variation ◽  
Middle East ◽  
Human Genetics ◽  
High Impact ◽  
Limiting Factors ◽  
Sequencing Data ◽  
Clinical Sequencing ◽  
The World ◽  
Genomic Studies

AbstractWe highlight the current lack of representation of the Middle East from large genomic studies and emphasize the expected high impact of cataloging its variation. We discuss the limiting factors and possible solutions to generating and accessing research and clinical sequencing data from this part of the world.

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