scholarly journals Analysis of the mitochondrial CYTB gene sequence in human populations of northeastern Bosnia

2019 ◽  
Vol 82 (3) ◽  
pp. 221-238
Author(s):  
Adisa Ahmic ◽  
Irma Mujkic ◽  
Anel Ismailovic ◽  
Emir Halilovic ◽  
Lejla Lasic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Human Populations ◽  
Roma Population ◽  
Additional Information ◽  
Mitochondrial Cytochrome B ◽  
Different Populations ◽  
Two Populations ◽  
Maternal Gene

Abstract This study offers the first report on variation sequence of the mitochondrial cytochrome b (MT-CYTB) gene in populations from Bosnia (northeastern Bosnia). This study was designed on the analysis of the genetic diversity of two populations of different cultural-anthropological and genetic origin, Roma population and native/non-Roma population. The main aim of our study was to estimate the usefulness of the CYTB sequence in the analysis of genetic categorization of different populations and intergroup diversity, as well as to provide some additional information on haplogroup-associated polymorphisms within the CYTB region in defining haplogroup status. Estimation of the genetic diversity was done using intra and intergroup genetic indices. The population-specific polymorphisms have been found in both categories of the populations. The results of the analysis of genetic differentiation show significant pairwise Fst differences between the Romani and native populations. Also, registered significant genetic differentiation is illustrated on the level of genetic variation between subpopulations of the Roma and non-Roma origin. The important result in our study is the confirmation of the significance of the triad of polymorphisms T14783C-G15043A-G15301A, indicating the influence of Asian component of the maternal gene pool on the genetic structure of the studied population of the Roma. Our data show that the haplogroup polymorphisms exist in the CYTB region and can provide useful information on the haplogroups that were defined only by the control region of the mtDNA. The results of this study indicate the region of CYTB gene can be a benefit in providing some additional information in the analysis of genetic structure of human populations and can be additionally applied in population studies.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Genetic diversity in different populations of sloths assessed by DNA fingerprinting

2002 ◽  
Vol 62 (3) ◽  
pp. 503-508 ◽  
Author(s):  
N. MORAES ◽  
J. S. MORGANTE ◽  
C. Y. MIYAKI
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dna Fingerprinting ◽  
Genetic Similarity ◽  
Similarity Indices ◽  
Different Populations ◽  
Related Individuals ◽  
Low Levels ◽  
Dna Profiles ◽  
Two Populations

In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

Genetic differentiation of regional populations of the widespread Asiatic toad (Bufo gargarizans), as revealed by development of novel microsatellite markers

2018 ◽  
Vol 66 (6) ◽  
pp. 335
Author(s):  
T. Pan ◽  
P. Yan ◽  
M. Yang ◽  
H. Wang ◽  
I. Ali ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Yangtze River ◽  
The Yangtze River ◽  
Geographic Scale ◽  
Widespread Species ◽  
Bufo Gargarizans ◽  
Toad Bufo

Dispersal is a key component of a species’ life history, by influencing population persistence, genetic structure, adaptation and maintenance of genetic diversity. The Asiatic toad (Bufo gargarizans) is a widespread species in east Asia. However, we still have no knowledge of what kind of geographical scale equates to genetic differentiation within B. gargarizans. In this study, the population genetics of B. gargarizans was studied at five localities, with the Yangtze River running through the sampling area, in order to detect the level of genetic differentiation and the natural barriers to the species’ dispersal on a small geographic scale, by means of the development and use of novel microsatellite loci. These markers revealed a relatively high level of genetic diversity. Distinct genetic structure among populations in B. gargarizans was observed, as described by genetic distance, AMOVA, PCA and Geneland results. A weak but significant positive correlation between genetic distance and geographical distance. The combination of these findings suggests that the Yangtze River and geographic distance may act as effective barriers for B. gargarizans. These results serve as benchmark data for understanding the impacts of dispersal barriers and continued landscape research on B. gargarizans.

Genetic differences within natural and planted stands of Quercus petraea

2011 ◽  
Vol 6 (4) ◽  
pp. 597-605 ◽  
Author(s):  
Jiří Dostálek ◽  
Tomáš Frantík ◽  
Miroslava Lukášová
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Spatial Genetic Structure ◽  
Quercus Petraea ◽  
Genetic Differences ◽  
Sessile Oak ◽  
Population Structures ◽  
Nuclear Microsatellite ◽  
The Impact ◽  
Two Populations

AbstractFive sessile oak [Quercus petraea (Matt.) Liebl.] stands from the Czech Republic were studied to learn about the impact of different types of forest management regimes on the genetic differences among tree populations and on population structures. One population had not been markedly affected by human activity, two populations represented unplanted stands that were extensively managed for a long period of time using the coppice system, and two populations were planted stands. Approximately 100 trees from each stand were mapped and subsequently genotyped using 10 nuclear microsatellite loci. We determined the spatial genetic structure of each population and the genetic differentiation among the populations. We found that: (i) the populations were genetically differentiated, but the differences between the unplanted and planted stands were not markedly significant; (ii) the genetic differentiation among the populations depended on the geographical distribution of the populations; (iii) within unplanted stands, a strong spatial genetic structure was seen; and (iv) within planted stands, no spatial genetic structure was observed. Our findings implies that the analysis of spatial genetic structure of the sessile oak forest stand can help reveal and determine its origin.

scholarly journals Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

2020 ◽  
Author(s):  
Godfrey Kinyori Wagutu ◽  
Xiangrong Fan ◽  
Wenlong Fu ◽  
Wei Li ◽  
Yuanyuan Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Local Adaptation ◽  
Landscape Heterogeneity ◽  
Maximum Temperature ◽  
Zizania Latifolia ◽  
Precipitation Seasonality ◽  
Isolation By Environment

AbstractGlobal aquatic habitats are undergoing rapid degradation and fragmentation as a result of land-use change and climate change. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the role of environment, landscape heterogeneity and geographical distance in shaping the genetic structure of 28 natural populations of Zizania latifolia (Griseb.) Turcz. Ex Stapf in China based on 25 microsatellite markers. Genetic structure was investigated by analysis of molecular variance (AMOVA), estimation of FST, Bayesian clustering and Thermodynamic Integration (TI) methods. Isolation by environment (IBE), isolation by resistance (IBR) and isolation by distance (IBD) hypotheses were compared using a reciprocal causal model (RCM). Further, generalized linear models and spatially explicit mixed models, by using geographic, landscape and genetic variables, were developed to elucidate the role of environment in driving Z. latifolia genetic diversity. The genetic differentiation across all populations was high: FST = 0.579; Øpt = 0.578. RCM exclusively supported IBE in shaping genetic structuring, only partial support for IBR, but not for IBD. Maximum temperature of the warmest month and precipitation seasonality were the plausible parameters responsible for genetic diversity. After controlling for spatial effect and landscape complexity, precipitation seasonality was significantly associated with genetic diversity. Based on these findings, genetic structure of Z. latifolia across China seem to be as a result of local adaptation. Environmental gradient and topographical barriers, rather than geographical isolation, influence genetic differentiation of aquatic species across China resulting in instances of local adaptation.

scholarly journals The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

2021 ◽  
Author(s):  
Yuan Li ◽  
Fangrui Lou ◽  
Hai Li ◽  
Rui Wang ◽  
Zizi Cai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Expansion ◽  
Nucleotide Polymorphisms ◽  
Stress Reactions ◽  
Long Distance ◽  
Evolutionary Mechanisms ◽  
Inflammatory Reactions ◽  
Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

scholarly journals Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Shumiao Zhang ◽  
Chao Li ◽  
Yiping Li ◽  
Qi Chen ◽  
Defu Hu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Size ◽  
Population Genomics ◽  
Distribution Area ◽  
History Of ◽  
Père David’S Deer ◽  
Free Ranging ◽  
Elaphurus Davidianus

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David’s deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David’s deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David’s deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David’s deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David’s deer, and low levels of genome-wide genetic diversity were observed in Père David’s deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David’s deer, especially between the captive population in Beijing Père David’s deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David’s deer started to decline ~25.8ka, and the similar levels of three populations’ LD reflected the genetic impacts of long-term population bottlenecks in the Père David’s deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.

scholarly journals Increased genetic diversity in Greek populations of the genus Ligidium (Crustacea: Isopoda: Oniscidea) revealed by RFLP analysis of mtDNA segments

2005 ◽  
Vol 74 (3-4) ◽  
pp. 255-264 ◽  
Author(s):  
Elena Klossa-Kilia ◽  
George Kilias ◽  
Spyros Sfenthourakis
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
16S Rdna ◽  
Central Europe ◽  
Phylogenetic Relationships ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Nominal Species ◽  
Nucleotide Divergence ◽  
Different Populations

We investigated mtDNA genetic differentiation and the phylogenetic relationships of 11 populations of the oniscidean genus Ligidium. We studied nine populations from Greece, assigned to three nominal species (L. euboicum, L. germanicum and L. beieri), and two from central Europe (L. germanicum and L. hypnorum), applying RFLP analysis of two mtDNA segments (12S rDNA and 16S rDNA) amplified by PCR. The analysis revealed seven monomorphic and four polymorphic populations, and 17 different haplotypes, each one present in one population only. Several restriction enzymes produced population specific patterns, enabling discrimination among the different populations. The estimated net nucleotide divergence between populations ranges from 1.06 to 16.52%, while the high NST value (0.96) indicates the existence of increased interpopulation genetic differentiation that can be attributed to the extreme isolation among Ligidium populations. The relationships between haplotypes and populations are not congruent with their geographical distribution and the established taxonomy within the genus.

scholarly journals Different Habitats Show Similar Genetic Structure of Bunias orientalis L. (Brassicaceae)in Lithuania

2013 ◽  
Vol 41 (2) ◽  
pp. 396 ◽  
Author(s):  
Jolanta PATAMSYTĖ ◽  
Tatjana ČĖSNIENĖ ◽  
Donatas NAUGŽEMYS ◽  
Violeta KLEIZAITĖ ◽  
Virginija TUNAITIENĖ ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Difference ◽  
Habitat Type ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Baltic Countries ◽  
Bunias Orientalis ◽  
The Impact

We studied genetic diversity within and among populations of warty cabbage (Bunias orientalis L.), which is an alien species in Lithuania and other Baltic countries. In Lithuania, this weed colonises two main types of habitats: railway/roadsides and meadows on riversides. The aim of this study was to assess the genetic structure of invasive populations of B. orientalis in Lithuania and consider the impact of diverse habitats on the partitioning of genetic diversity using inter-simple sequence repeat (ISSR) markers. An analysis of molecular variance (AMOVA) carried out on the basis of ISSR showed that there is high genetic differentiation (46%) among populations of B. orientalis, which is probably caused by the founder effect and limited gene flow. However, we observed no impact of habitat on the genetic difference among populations. Similar levels of ISSR polymorphic loci were observed in riverside (P = 31.67%) and railway/roadsides (P = 30.51%) populations. UPGMA cluster analysis and principal coordinate analysis (PCoA) also did not show grouping of studied populations according to habitat type. High genetic differentiation among populations, as indicated by ISSR markers, confirm multiple independent introductions of this species in Lithuania.

scholarly journals Genetic Diversity and Population Genetic Structure of Erythrophleum fordii Oliv., an Endangered Rosewood Species in South China

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 636 ◽  
Author(s):  
Jing Tan ◽  
Zhi-Gang Zhao ◽  
Jun-Jie Guo ◽  
Chun-Sheng Wang ◽  
Jie Zeng
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Endangered Species ◽  
Genetic Differentiation ◽  
South China ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
The Mean ◽  
Erythrophleum Fordii ◽  
Private Alleles

Erythrophleum fordii Oliv. is a valuable rosewood species indigenous to the tropical and warm sub-tropical zones of Vietnam, Laos, and South China. The natural forests have been heavily fragmented mostly due to over-exploitation and over-utilization, and alteration to croplands and fast-growing plantations. Therefore, it has been included in the IUCN Red List of Endangered Species as an endangered species. In the present study, genetic diversity and population genetic structure of 11 populations were estimated by SSR makers in South China. Five high polymorphic loci were studied with a total of 34 alleles, among which, seven were private alleles. The mean number of alleles per locus (A), the mean number of efficient alleles per locus (Ae), the observed (Ho) and expected (He) heterozygosity, and Shannon’s index (I) of the 11 populations were 3.40, 2.31, 0.52, 0.56, and 0.90, respectively. Correlation analysis between genetic parameters and geographical factors showed that He and I were in significant negative correlation with longitude, indicating that genetic diversity of E. fordii reduced gradually from West to East in south China. FIS of eight populations with above five samples was on average 0.01, most loci conformed to Hardy-Weinberg equilibrium in these populations; their genetic differentiation coefficient (FST) was 0.18, indicating that genetic differentiation among populations was relatively low and there existed 18% genetic variation among populations. Gene flow (Nm) between these populations was 1.28. The Mantel test showed that genetic distance was not significantly correlated with geographical distance (p > 0.05). It was concluded that populations with high genetic diversity or private alleles, especially Longmen, Wuming and Pingxiang populations should be a priority for in situ conservations, meanwhile more populations and as many families as possible in each population should be collected for ex situ conservations of germplasm resources of this species in the future.

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