scholarly journals Genetic Diversity and Population Dynamics of Leptobrachium leishanense (Anura: Megophryidae) as Determined by Tetranucleotide Microsatellite Markers Developed from Its Genome

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3560
Author(s):  
Chao Fu ◽  
Qingbo Ai ◽  
Ling Cai ◽  
Fuyuan Qiu ◽  
Lei Yao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Dynamics ◽  
Microsatellite Markers ◽  
Population Bottlenecks ◽  
Effective Population ◽  
High Genetic Diversity ◽  
The Public ◽  
Low Degree ◽  
Population Sustainability ◽  
Human Use

Persisting declination of amphibians around the world has resulted in the public attaching importance to the conservation of their biodiversity. Genetic data can be greatly helpful in conservation planning and management, especially in species that are small in size and hard to observe. It is essential to perform genetic assessments for the conservation of Leptobrachium leishanense, an endangered toad and receiving secondary protection on the list of state-protected wildlife in China. However, current molecular markers with low reliability and efficiency hinder studies. Here, we sampled 120 adult toes from the population in the Leishan Mountain, 23 of which were used to develop tetranucleotide microsatellite markers based on one reference L. leishanense genome. After primer optimization, stability detection, and polymorphism detection, we obtained 12 satisfactory microsatellite loci. Then, we used these loci to evaluate the genetic diversity and population dynamics of the 120 individuals. Our results show that there is a low degree of inbreeding in the population, and it has a high genetic diversity. Recently, the population has not experienced population bottlenecks, and the estimated effective population size was 424.3. Accordingly, stabilizing genetic diversity will be key to population sustainability. Recovering its habitat and avoiding intentional human use will be useful for conservation of this species.

scholarly journals Changes in Genetic Diversity and Demographic History of Jankowski’s Bunting (Emberiza Jankowskii), as Revealed by Mitochondrial DNA and Microsatellite Markers

2021 ◽  
Author(s):  
Long Huang ◽  
Guochen Feng ◽  
Dan Li ◽  
Weiping Shang ◽  
Lishi Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
Population Size ◽  
Demographic History ◽  
Effective Population ◽  
High Genetic Diversity ◽  
History Of ◽  
Eastern Inner Mongolia

Abstract The genetic variation and distribution of a population depend largely on the demographic history. For instance, populations that have recently experienced shrinkage usually have a lower genetic diversity. However, some endangered species with a narrow distribution have a high genetic diversity resulting from large historical population sizes and long generation times. In addition, very recent population bottlenecks may not be reflected in the population’s genetic information. In this study, we used a mitochondrial DNA marker and 15 microsatellite markers to reveal the genetic diversity, recent changes, inbreeding, and demographic history of a Jankowski’s bunting (Emberiza jankowskii) population in eastern Inner Mongolia. The results show that the genetic diversity of the population remained at a relatively stable and high level until recently. Severe population shrinkage did not result in a considerable lack of genetic variation because of the large historical population size and relatively short periods of human disturbance. In addition, introgression and gene flow among populations compensate for the loss of genetic variation to some extent. Considering the current small effective population size and the existence of inbreeding, we recommend that habitat protection be continued to maximize the genetic diversity of the Jankowski’s bunting population.

scholarly journals Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

2009 ◽  
Vol 99 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Laura I. Weber ◽  
Cintia G. Hildebrand ◽  
Anderson Ferreira ◽  
Gustavo Pedarassi ◽  
José A. Levy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Significant Degree ◽  
Southern Brazil ◽  
High Genetic Diversity ◽  
Low Degree ◽  
Faecal Samples ◽  
High Level ◽  
Degree Of Differentiation ◽  
Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

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 Structure of Latvian Tilia cordata Populations

2021 ◽  
Vol 75 (4) ◽  
pp. 261-267
Author(s):  
Dainis Edgars Ruņģis ◽  
Baiba Krivmane
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Vegetative Reproduction ◽  
Growth Conditions ◽  
Climatic Conditions ◽  
Tilia Cordata ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Broadleaf Tree ◽  
Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

scholarly journals The Sri Lankan paradox: high genetic diversity in Plasmodium vivax populations despite decreasing levels of malaria transmission

Parasitology ◽  
2014 ◽  
Vol 141 (7) ◽  
pp. 880-890 ◽  
Author(s):  
SHARMINI GUNAWARDENA ◽  
MARCELO U. FERREIRA ◽  
G. M. G. KAPILANANDA ◽  
DYANN F. WIRTH ◽  
NADIRA D. KARUNAWEERA
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Plasmodium Vivax ◽  
Malaria Transmission ◽  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency Distribution ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Mode Shift

SUMMARYHere we examined whether the recent dramatic decline in malaria transmission in Sri Lanka led to a major bottleneck in the local Plasmodium vivax population, with a substantial decrease in the effective population size. To this end, we typed 14 highly polymorphic microsatellite markers in 185 P. vivax patient isolates collected from 13 districts in Sri Lanka over a period of 5 years (2003–2007). Overall, we found a high degree of polymorphism, with 184 unique haplotypes (12–46 alleles per locus) and average genetic diversity (expected heterozygosity) of 0·8744. Almost 69% (n = 127) isolates had multiple-clone infections (MCI). Significant spatial and temporal differentiation (FST = 0·04–0·25; P⩽0·0009) between populations was observed. The effective population size was relatively high but showed a decline from 2003–4 to 2006–7 periods (estimated as 45 661 to 22 896 or 10 513 to 7057, depending on the underlying model used). We used three approaches – namely, mode-shift in allele frequency distribution, detection of heterozygote excess and the M-ratio statistics – to test for evidence of a recent population bottleneck but only the low values of M-ratio statistics (ranging between 0·15–0·33, mean 0·26) were suggestive of such a bottleneck. The persistence of high genetic diversity and high proportion of MCI, with little change in effective population size, despite the collapse in demographic population size of P. vivax in Sri Lanka indicates the importance of maintaining stringent control and surveillance measures to prevent resurgence.

scholarly journals Molecular Assessment of Genetic Diversity among Egyptian Landraces of Wheat (Triticum aestivum L.) Using Microsatellite Markers

2020 ◽  
pp. 46-58 ◽  
Author(s):  
Ahmed Medhat Mohamed Al-Naggar ◽  
Mohamed Abd El-Maboud Abd El-Shafi ◽  
Mohamed Helmy El-Shal ◽  
Ali Hassan Anany
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Triticum Aestivum L ◽  
Genetic Progress ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
High Polymorphism Information Content ◽  
Wheat Landraces

To increase the genetic progress in wheat (Triticum aestivum L.) yield, breeders search for germplasm of high genetic diversity, one of them is the landraces. The present study aimed at evaluating genetic diversity of 20 Egyptian wheat landraces and two cultivars using microsatellite markers (SSRs). Ten SSR markers amplified a total of 27 alleles in the set of 22 wheat accessions, of which 23 alleles (85.2%) were polymorphic. The majority of the markers showed high polymorphism information content (PIC) values (0.67-0.94), indicating the diverse nature of the wheat accessions and/or highly informative SSR markers used in this study. The genotyping data of the SSR markers were used to assess genetic variation in the wheat accessions by dendrogram. The highest genetic distance was found between G21 (Sakha 64; an Egyptian cultivar) and the landrace accession No. 9120 (G11). These two genotypes could be used as parents in a hybridization program followed by selection in the segregating generations, to identify some transgressive segregates of higher grain yield than both parents. The clustering assigned the wheat genotypes into four groups based on SSR markers. The results showed that the studied SSR markers, provided sufficient polymorphism and reproducible fingerprinting profiles for evaluating genetic diversity of wheat landraces. The analyzed wheat landraces showed a good level of genetic diversity at the molecular level. Molecular variation evaluated in this study of wheat landraces can be useful in traditional and molecular breeding programs.

scholarly journals Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

2019 ◽  
Vol 62 (1) ◽  
pp. 143-151 ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Nahid Parna ◽  
Pourya Davoudi ◽  
Majid Khansefid
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Snp Panel ◽  
Zandi Sheep

Abstract. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (> 10 Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

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