Genetic diversity among geographically separated populations of Nepenthes mirabilis

Biologia ◽  
2006 ◽  
Vol 61 (3) ◽  
Author(s):  
Arunrat Chaveerach ◽  
Alongkod Tanomtong ◽  
Runglawan Sudmoon ◽  
Tawatchai Tanee
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Geographical Area ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
High Genetic Diversity ◽  
Total Genetic Diversity ◽  
Environmental Variations ◽  
Diversity Profile ◽  
Great Genetic Diversity

AbstractThe distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H T) and inter-population genetic diversity (H S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.

scholarly journals High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Amali Malshani Samaraweera ◽  
Ranga Liyanage ◽  
Mohamed Nawaz Ibrahim ◽  
Ally Mwai Okeyo ◽  
Jianlin Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Microsatellite Markers ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Population Substructure ◽  
High Genetic Diversity ◽  
Naked Neck ◽  
Local Chicken ◽  
Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

scholarly journals Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau

2019 ◽  
Vol 11 (20) ◽  
pp. 5863 ◽  
Author(s):  
Qingqing Yu ◽  
Qian Liu ◽  
Yi Xiong ◽  
Yanli Xiong ◽  
Zhixiao Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tibetan Plateau ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Conservation Strategy ◽  
Conservation Strategies ◽  
Grass Species ◽  
Population Divergence ◽  
High Genetic Diversity ◽  
Widespread Species

Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.

Genetic diversity of oil-tea camellia germplasms revealed by ISSR analysis

2015 ◽  
Vol 08 (05) ◽  
pp. 1550070 ◽  
Author(s):  
Lan-Ying Zhou ◽  
Xiang-Nan Wang ◽  
Li-Ping Wang ◽  
Yong-Zhong Chen ◽  
Xiao-Cheng Jiang
Keyword(s):  
Genetic Diversity ◽  
Reaction System ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Hunan Province ◽  
Information Index ◽  
Group I ◽  
Issr Pcr ◽  
Simple Sequence

Genetic diversity of 51 oil-tea camellia germplasms was analyzed using the optimized inter-simple sequence repeat (ISSR)–PCR reaction system with 22 primers screened from a set of 100 ISSR primers. The results showed that 493 discernible loci with distinct electrophoretic bands were obtained, of which, 478 loci (96.78%) were polymorphic. This indicated that oil-tea germplasms possess abundant genetic diversities. By clustering analysis performed using softwares of NTSYS 2.10 and Winboot, 51 oil-tea germplasms were divided into two groups: Group I had 48 lines of Camellia oleifera Abel, while Group II had three C. oleifera Abel related species and their similarity coefficient was 0.62. Group I was further divided into Group I-1 and Group I-2, and their similarity coefficient (Gs) was 0.634. All members of Group I-1 originated from Hunan Province, while Group I-2 included the rest of Hunan lines and those originated from other regions of China. Analyzed by software POPGENE 1.32, the Shannon's information index (I*) of genetic polymorphism was 0.3852, the genetic diversity among different region populations (Ht) was 0.2537, the genetic diversity within populations (Hs) was 0.15545, the differentiation coefficient of genetic diversity among populations (Gst) was 0.3967, and the gene flow among populations (Nm*) was 0.8262. The Nei's genetic distances between the Hunan population and the populations originated from other regions of China implied that geographic isolation strongly influenced genetic differentiation among populations. Meanwhile, seedling rootstock grafting and high grafting for tree crown produced genetic variations among clonal offsprings.

scholarly journals Schinus Terebinthifolia Raddi: A Comparative Framework On Population Genetic Structure In A Restored Area After 12 Years*

2021 ◽  
Author(s):  
Erica Moraes Santos de Souza ◽  
Sheila Valéria Álvares-Carvalho ◽  
Robério Anastácio Ferreira ◽  
Renata Silva Mann
Keyword(s):  
Genetic Diversity ◽  
Continuous Monitoring ◽  
Diversity Index ◽  
Limiting Factor ◽  
Effective Population ◽  
Natural Area ◽  
High Genetic Diversity ◽  
Seed Sources ◽  
Adult Trees ◽  
Ssr Primers

Abstract The success of restoration projects depends upon the genetic diversity of the implanted species. It is a limiting factor, often because the seed sources are immersed in highly fragmented landscapes. This work was carried out to compare the genetic diversities of the juveniles and the adult trees of Schinus terebinthifolia Raddi in a mixed reforestation area, both in the restoration process and in the remaining natural area in the Atlantic Forest. Through five SSR primers, it was observed that the implanted population showed a greater genetic diversity index (He) (0.553 adults and 0.505 juveniles) when compared to the wild population (0.487 adults and 0.483 juveniles). It indicated that the forested area was established with individuals of high genetic diversity. There was a reduction of genetic diversity, with the loss of exclusive alleles and maintenance of inbreeding and coancestry in the juveniles of the reforested population. It can be inferred that there was a low gene flow among the fragments. The effective population size in both populations (adults and juveniles) was lower than that recommended for conserving populations in the short and long terms. These results have shown that continuous monitoring of this particular area is of absolute necessity and for applying techniques that can promote the connectivity of the fragments. It would allow for a more significant reduction of genetic drift and the persistence of the planted populations.

scholarly journals ISSR analysis of two founding plant species on the volcanic island Surtsey, Iceland: grass versus shrub

2015 ◽  
Vol 13 ◽  
pp. 17-30 ◽  
Author(s):  
Agnieszka Sutkowska ◽  
Kesara Anamthawat-Jónsson ◽  
Borgthór Magnússon ◽  
Wojciech Bąba ◽  
Józef R. Mitka
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Diversity Indices ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Plant Colonization ◽  
Common Source ◽  
High Genetic Diversity ◽  
Early Arrival

Prior to the present study there was limited knowledge about the genetic basis of plant colonization on the 50-year-old island of Surtsey, South Iceland. The aim here was to compare genetic structure of two contrasting species, Festuca rubra (arctic fescue) and Empetrum nigrum (crowberry), which have colonized Surtsey since 1973 and 1993, respectively. Inter-simple sequence repeat (ISSR) markers were used to assess genetic diversity and population structure. Two census periods were compared: 1996-1997 and 2005-2006. Using six ISSR primers, we obtained 103 and 139 discernible DNA fragments from F. rubra and E. nigrum respectively. Although the two species displayed similarly high genetic diversity indices (h = 0.238 and 0.235; I = 0.384 and 0.380, respectively), they differed significantly in their genetic profiles. Festuca was genetically structured at the subpopulation level (FST = 0.034, p = 0.007), whereas Empetrum showed a lack of genetic differentiation. A Bayesian STRUCTURE computation further revealed temporal and spatial genetic structure of the species. The early arrival grass F. rubra has expanded from a local genepool. The population was however initially established from different sources, forming a genetic melting pot on Surtsey. On the other hand, the late arrival shrub E. nigrum probably derived from a common source of immigrants.

Genetic Diversity and Genetic Differentiation of Rheum palmatum by Chloroplast matK Sequences

2020 ◽  
Vol 10 (2) ◽  
pp. 96-103
Author(s):  
Xiaoqin Zhang ◽  
Na Lin ◽  
Liping Chen ◽  
Zunjing Zhang ◽  
Houxing Lei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Diversity Index ◽  
Geographic Distance ◽  
High Genetic Diversity ◽  
Rheum Palmatum ◽  
Wild Resources ◽  
Nj Tree ◽  
Matk Sequence ◽  
Over Exploitation

Background: Rheum palmatum is a medically important plant in the Polygonaceae family. Its wild resources have been declining due to over-exploitation. It is important and urgent to investigate the genetic diversity for the conservation of R. palmatum. Methods: The Chloroplast DNA matK sequences were used to assess genetic diversity among and within populations in this species. The genetic diversity index was calculated by Dnasp, PERMUT and Arlequin 3.0 software, and a Neighbor-Joining (NJ)-tree was constructed by MEGA 5.0 software. Results: Nine haplotypes were obtained based on the matK sequence analysis in fifteen populations. We found a relatively high genetic diversity in species level (Hd = 0.7414), and the genetic diversity among populations (FST = 0.81582) was higher than that within populations (FSC = 0.69526) according to the AMOVA analysis. The genetic distance between populations ranged from 0 to 0.0044, which within populations ranged from 0 to 0.001761. There was a significant correlation between genetic distance and geographic distance (r = 0.601, P < 0.001) according to the SPSS analysis. Conclusion: The genetic diversity among populations was higher than that within populations due to geographic isolation and decline in gene flow among populations. This study is significant for further studies concerned with efficient collection and preservation of wild resource of R. palmatum.

scholarly journals Morphological and Isozyme Variation in Natural Populations of the Genus Medicago L. Prospected in Northern Algeria

2015 ◽  
Vol 43 (1) ◽  
pp. 86-95 ◽  
Author(s):  
Imane MEDOUKALI ◽  
Ines BELLIL ◽  
Douadi KHELIFI
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Morphological Characteristics ◽  
Genetic Distances ◽  
Glutamate Oxaloacetate Transaminase ◽  
High Genetic Diversity ◽  
Isozyme Markers ◽  
Northern Algeria ◽  
Isozyme Variability ◽  
High Level

As part of the evaluation and enhancement of genetic resources, morphological and isozyme variability within and among 169 accessions, representing 14 species of the genus Medicago L. collected in northern Algeria, was assessed using twelve quantitative traits and two enzymatic systems. Phenotype frequencies were scored in six enzyme zones to determine isozyme variability within and among populations. The data analysis resolved a high level of genetic diversity. Ten morphometric characteristics contributed to the discrimination of the species. The relationship between the collection site environment and phenotypic characteristics was also studied. Esterase (EST) enzyme system was more polymorphic than glutamate oxaloacetate transaminase (GOT) system. Were scored 2 zones with 10 bands and 21 phenotypes for GOT (glutamate oxaloacetate transaminase) and 4 zones with 22 bands and 71 phenotypes for EST (esterase) Polymorphism index and Jaccard’s genetic distances revealed the existence of a high genetic diversity within and among the studied populations. The annual species M. polymorpha presented an intraspecific polymorphism index of 0.57, which was higher than all other species indices. Clustering of the species based on isozyme markers was in agreement with taxonomic criteria and showed no significant correlation with morphological characteristics. Conservation programs should take into account the level of genetic diversity within and between populations revealed by isozyme markers.

scholarly journals Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Bei Li ◽  
Hao-Rui Si ◽  
Yan Zhu ◽  
Xing-Lou Yang ◽  
Danielle E. Anderson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Active Surveillance ◽  
Large Scale ◽  
Next Generation ◽  
High Genetic Diversity ◽  
High Background ◽  
Field Samples ◽  
Great Genetic Diversity ◽  
Generation Sequencing

ABSTRACT Coronaviruses (CoVs) of bat origin have caused two pandemics in this century. Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV both originated from bats, and it is highly likely that bat coronaviruses will cause future outbreaks. Active surveillance is both urgent and essential to predict and mitigate the emergence of these viruses in humans. Next-generation sequencing (NGS) is currently the preferred methodology for virus discovery to ensure unbiased sequencing of bat CoVs, considering their high genetic diversity. However, unbiased NGS is an expensive methodology and is prone to missing low-abundance CoV sequences due to the high background level of nonviral sequences present in surveillance field samples. Here, we employ a capture-based NGS approach using baits targeting most of the CoV species. Using this technology, we effectively reduced sequencing costs by increasing the sensitivity of detection. We discovered nine full genomes of bat CoVs in this study and revealed great genetic diversity for eight of them. IMPORTANCE Active surveillance is both urgent and essential to predict and mitigate the emergence of bat-origin CoV in humans and livestock. However, great genetic diversity increases the chance of homologous recombination among CoVs. Performing targeted PCR, a common practice for many surveillance studies, would not reflect this diversity. NGS, on the other hand, is an expensive methodology and is prone to missing low-abundance CoV sequences. Here, we employ a capture-based NGS approach using baits targeting all CoVs. Our work demonstrates that targeted, cost-effective, large-scale, genome-level surveillance of bat CoVs is now highly feasible.

scholarly journals Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline

2006 ◽  
Vol 2 (2) ◽  
pp. 316-319 ◽  
Author(s):  
Frank Hailer ◽  
Björn Helander ◽  
Alv O Folkestad ◽  
Sergei A Ganusevich ◽  
Steinar Garstad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Generation Time ◽  
Population Decline ◽  
High Genetic Diversity ◽  
Effective Time ◽  
Total Genetic Diversity ◽  
Persistent Pollutants ◽  
Conservation Actions ◽  
Ringing Data ◽  
Loss Of Genetic Diversity

Most of the white-tailed eagle ( Haliaeetus albicilla ) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban of DDT and other persistent pollutants, populations are currently recovering. We show that despite passing through demographic bottlenecks, white-tailed eagle populations have retained significant levels of genetic diversity. Both genetic and ringing data indicate that migration between populations has not been a major factor for the maintenance of genetic variability. We argue that the long generation time of eagles has acted as an intrinsic buffer against loss of genetic diversity, leading to a shorter effective time of the experienced bottleneck. Notably, conservation actions taken in several small sub-populations have ensured the preservation of a larger proportion of the total genetic diversity than if conservation had focused on the population stronghold in Norway. For conservation programmes targeting other endangered, long-lived species, our results highlight the possibility for local retention of high genetic diversity in isolated remnant populations.

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