scholarly journals Habitat fragmentation decreased the genetic variability of Trichilia elegans A. Juss. (Meliaceae) in southern Brazil

2014 ◽  
Vol 63 (1-6) ◽  
pp. 133-138
Author(s):  
L. B. Slaviero ◽  
C. Valério-Júnior ◽  
R. I. Cardoso ◽  
A. Mielniczki-Pereira ◽  
R. L. Cansian ◽  
...  
Keyword(s):  
Habitat Fragmentation ◽  
Genetic Variability ◽  
Total Population ◽  
Local Population ◽  
Southern Brazil ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
The Mean ◽  
Genetic Responses ◽  
Average Sample

Abstract Habitat fragmentation and the creation of so-called edge effects may have different implications on flora and fauna, including complex genetic responses. This study aimed to analyze the genetic diversity in a local population of the shade tolerant tree Trichilia elegans A. Juss (Meliaceae), with emphasis to the evaluation of genetic variation towards an edge-interior gradient. The results of isoenzymes assays showed that the edge subpopulation experienced the highest allele loss, while fixed alleles increased towards the interior. The total polymorphic loci percentage was 76.67%, being higher in the Middle subpopulation, whilethe average sample size for a locus (N) and the mean number of alleles for a locus (Na) were significantly lower in the Edge subpopulation. The indices Ho, He and f showed good heterozygosity in the total population, indicating high genetic variability. The genetic distance Fst and Nm followed the same pattern, with Middle and Interior subpopulations showing higher similarity and the Edge as the farthest one, also showing less gene flow in relation to the others. Principal Coordinates Analysis (PCoA) allowed us to separate the three subpopulations with the first two axes explaining 65% of total variation, confirming that forest fragmentation affects the genetics of Trichilia elegans within the analyzed fragment.

Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

2018 ◽  
Vol 16 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Georgios F. Tsanakas ◽  
Photini V. Mylona ◽  
Katerina Koura ◽  
Anthoula Gleridou ◽  
Alexios N. Polidoros
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Morphological Analysis ◽  
Phenotypic Variability ◽  
Market Price ◽  
Genetic Distances ◽  
Reaction Products ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

Qualitative and quantitative variation in the macrobenthic fauna of the Original Lake and new lake areas of Great Lake and Arthurs Lake, Tasmania

1983 ◽  
Vol 34 (5) ◽  
pp. 787 ◽  
Author(s):  
W Fulton
Keyword(s):  
Great Lake ◽  
Quantitative Data ◽  
Benthic Fauna ◽  
Principal Coordinates Analysis ◽  
Qualitative And Quantitative ◽  
Principal Coordinates ◽  
Annual Biomass ◽  
Species Groups ◽  
The Mean ◽  
Flooded Areas

Faunal variation between sample sites in Great Lake and Arthurs Lake, using both qualitative and quantitative data, was analysed. Cluster analysis and principal coordinates analysis showed that the fauna of the original lake areas of both lakes is distinct from the fauna of the newly flooded areas. Closer relationships exist between the faunas of the old level of the two lakes than between the faunas of the old and new levels within either lake. The distinction is not attributable to depth but may be influenced by substrate differences. The effects of abnormal fluctuations in water level on benthic fauna are discussed. Biomass variation between the sample sites was examined in relation to component species groups. The sites at the old level were dominated by oligochaetes whereas chironomids contributed most to the sites at the new level. Consistent seasonal peaks were evident in the biomass at sites at the new level but not at sites at the old. The mean annual biomass levels (wet wt) for Great Lake (13.9 g m-2) and Arthurs Lake (35.9 g m-2) are compared with recorded values for other Australian and overseas lakes. Biomass levels of Australian lakes in general are also discussed.

scholarly journals Genetic variability of dairy cattle breeds in Lithuania

Biologija ◽  
2021 ◽  
Vol 67 (3) ◽  
Author(s):  
Romualdas Lapickis ◽  
Loreta Griciuvienė ◽  
Asta Aleksandravičienė ◽  
Indrė Lipatova ◽  
Algimantas Paulauskas
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dairy Cattle ◽  
Genetic Material ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Black And White ◽  
Cattle Breeds ◽  
Principal Coordinates ◽  
High Degree

Large numbers of different scientific studies are conducted to preserve the breeds and improve the existing ones by introducing the variability of the plate genes, which best shows the phenotypic characteristics that can improve the health of dairy cattle and the quality of their production. The main purpose of this study was to perform an analysis of genetic variability of Lithuanian cattle breeds. Three subpopulation groups were studied: Lithuanian Black and White (95 individuals), Lithuanian Red (49), and Lithuanian White and Red (48). Bovine genetic material was genotyped using a total of 11 fluorescent microsatellite primers to estimate genetic variability. All loci presented a high degree of polymorphism and a total of 292 different alleles (Na) were detected. Thirty-two private alleles were detected in all evaluated subpopulations. After completing pairwise population assignment, which is based on the distribution of allelic frequencies, three populations showed the tendency to group into three separate clusters. However, the performed Principal Coordinates Analysis (PCoA), which is based on genetic distances, showed no anticipated clear grouping. Bayesian structure analysis revealed three genetic clusters. Analysis of FST (0.001–0.027) and Nei genetic distance (0.029–0.084) revealed that the genetic diversity of inter subpopulation in cattle groups was estimated to be lower than the genetic diversity of intra subpopulation.

scholarly journals Genetic diversity and relationships of Chinese donkeys using microsatellite markers

2019 ◽  
Vol 62 (1) ◽  
pp. 181-187 ◽  
Author(s):  
Lulan Zeng ◽  
Ruihua Dang ◽  
Hong Dong ◽  
Fangyu Li ◽  
Hong Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Mean Value ◽  
Principal Coordinates Analysis ◽  
Expected Heterozygosity ◽  
Principal Coordinates ◽  
Baseline Information ◽  
Grouping Pattern ◽  
The Mean

Abstract. Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99 % of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.

scholarly journals Acute coronary syndrome: which age group tends to delay call for help?

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Ahmed Ayuna ◽  
Ayyaz Sultan
Keyword(s):  
Acute Coronary Syndrome ◽  
Time Delay ◽  
Local Population ◽  
Age Groups ◽  
Age Group ◽  
Teaching Programme ◽  
The Road ◽  
Coronary Syndrome ◽  
The Mean ◽  
Mean Time

Abstract Background Early diagnosis and treatment of ACS can reduce the risk of complications and death. Delay calling for help can increase morbidity and mortality. It is unclear which age group among patients with acute coronary syndrome tend to delay their call for help. Results Our observational retrospective study showed that men and women in their 50s and 40s respectively tend to delay their call for help from symptoms onset. For the former, the mean time delays (590 ± 71.1 min), whereas for the latter it was (1084 ± 120.1 min). Moreover, these groups tend to have a longer time delay between symptoms onset and arrival at the hospital. Among deaths, we observed that the death rate was proportional to the time delay, which is not unexpected. Next step, we plan to perform a qualitative study in the form of questionnaires to target the individuals with a high risk of CVD within these age groups. Conclusion Middle age group of both genders tend to delay their call for help when they experience symptoms of ACS; moreover, regardless of the age, the longer the delay, the higher the mortality rate. The results of this study gave us a better understanding of our local population and will pave the road for a well-structured teaching programme for them to minimise the time delay for calling for help.

scholarly journals Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1803
Author(s):  
Valentino Palombo ◽  
Elena De Zio ◽  
Giovanna Salvatore ◽  
Stefano Esposito ◽  
Nicolaia Iaffaldano ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Fishery Management ◽  
Snp Array ◽  
Fine Scale ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Management Actions ◽  
Principal Coordinates ◽  
Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

scholarly journals Tree Species Diversity and Composition of Miombo Woodlands in South-Central Angola: A Chronosequence of Forest Recovery after Shifting Cultivation

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Francisco M. P. Gonçalves ◽  
Rasmus Revermann ◽  
Amândio L. Gomes ◽  
Marcos P. M. Aidar ◽  
Manfred Finckh ◽  
...  
Keyword(s):  
Shifting Cultivation ◽  
Stand Structure ◽  
Woody Species ◽  
Distinct Group ◽  
Forest Recovery ◽  
Miombo Woodlands ◽  
Principal Coordinates Analysis ◽  
South Central ◽  
Principal Coordinates ◽  
Management Plans

The study was carried out in the Cusseque area of the Municipality of Chitembo in south-central Angola. Our objectives were to assess the floristic diversity, the species composition, and stand structure of Miombo woodlands during regeneration after shifting cultivation. A total of 40 plots of 1000 m2were surveyed and analyzed, corresponding to mature forests/woodlands and three fallow types of different age. The analyses were based on plot inventories of all trees with DBH ≥ 5 cm. A total of 51 woody species, 38 genera, and 19 families were recorded. The dominant family was Fabaceae, with subfamily Caesalpinioideae being very abundant. Shannon Diversity and Evenness were highest in mature forests and young fallows, while the mature forest stands showed the highest species richness. A Principal Coordinates Analysis (PCoA) showed many species shared between the intermediate fallow types, but only few species were shared with young fallows. Mature forests formed a clearly distinct group. This study shows potential pathways of forest recovery in terms of faster regeneration after agricultural abandonment and, thus, the results presented here can be used in future conservation and management plans in order to reduce the pressure on mature forests.

scholarly journals Short-term movement patterns, population estimates and breeding biology of an island endemic bird, the Tristan Thrush

2019 ◽  
Vol 27 (4) ◽  
pp. 245-252
Author(s):  
Peter G. Ryan ◽  
Ben J. Dilley ◽  
Delia Davies ◽  
Trevor Glass ◽  
Fitsum Abadi
Keyword(s):  
Total Population ◽  
Data Augmentation ◽  
Local Population ◽  
Population Estimates ◽  
Limited Information ◽  
Short Term ◽  
Main Island ◽  
Island Endemic ◽  
Core Study ◽  
Land Bird

AbstractThe Tristan Thrush Turdus eremita is the only land bird that survived human colonisation of the main island of Tristan da Cunha and is listed as “Near Threatened”. Population estimates are confounded by the thrushes’ inquisitive and gregarious nature as well as limited information on their movements. We report the first measures of nest densities on Nightingale Island: 6 nests·ha-1 in Phylica arborea woodland and 4–5 nests·ha-1 in tussock habitat, which suggests that the population is approximately double the previous estimate. At Inaccessible Island, we individually color ringed 110 thrushes over two months to track their short-term movements and estimate the local population size. Individuals moved up to 950 m along the coast, but 96% of resightings were < 100 m. A Bayesian data augmentation approach estimated that some 260 thrushes visited the core study area, a 200-m stretch of cobble and boulder beach where birds come to drink, bathe and forage. This result suggests that the population on Inaccessible Island also is substantially larger than reported previously. We estimate the total population to be 8000–15,000 Tristan Thrushes. The main need is a population estimate for the nominate subspecies on the main island of Tristan.

scholarly journals Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Runzhi Zhang ◽  
Alejandro R. Walker ◽  
Susmita Datta
Keyword(s):  
Machine Learning ◽  
Error Rates ◽  
Average Error ◽  
Importance Score ◽  
Learning Methods ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Total Variability ◽  
The Common ◽  
Feature Selecting

Abstract Background Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets. Results Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively. Conclusions The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.

scholarly journals Association between stress and bilateral symmetrical alopecia in free-ranging Formosan macaques in Mt. Longevity, Taiwan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chen-Chih Chen ◽  
Ai-Mei Chang ◽  
Ming-Shan Tsai ◽  
Yen-Hua Huang ◽  
Kurtis Jai-Chyi Pei ◽  
...  
Keyword(s):  
Total Population ◽  
Causative Factor ◽  
Population Status ◽  
Adrenocortical Activity ◽  
High Incidence ◽  
Normal Hair ◽  
The Mean ◽  
The Individual ◽  
Free Ranging ◽  
The Impact

AbstractSince 2013, a high incidence of bilateral symmetrical alopecia has been observed in free-ranging Formosan macaques (Macaca cyclopis) in Mt. Longevity, Taiwan. We hypothesized that stress induces alopecia in this population. To verify our hypothesis, we evaluated the histopathological characteristics of skin biopsy and used a validated enzyme immunoassay (EIA) for fecal glucocorticoid metabolite (FGM) analysis, which act as an indicator of stress experienced by the individual. Follicular densities were lower (2.1–3.0 mm2) in individuals with symmetrical alopecia than in those with normal hair conditions (4.7 mm2). Furthermore, anagen to catagen/telogen ratios were lower in individuals with alopecia (0–1.4) than in those with normal hair (4.0). The histopathological characteristics of alopecia were similar to those of telogen effluvium, which indicates that stress is one of the possible etiologies. On the basis of the analytical and biological validation of EIAs for FGM analysis, 11β-hydroxyetiocholanolone was considered suitable for monitoring adrenocortical activity in both sexes of Formosan macaques. The mean concentrations (standard error; sample size) of 11β-hydroxyetiocholanolone were 2.02 (0.17; n = 10) and 1.41 (0.10; n = 31) μg/g for individuals with and without alopecia, respectively. Furthermore, the results of logistic regression analysis show that 11β-hydroxyetiocholanolone (p = 0.012) concentration was positively associated with alopecia. Thus, stress was the most likely to trigger symmetrical alopecia in Formosan macaques in Mt. Longevity. Although stress can decrease the fitness of an individual, considering the population status of Formosan macaques in Taiwan is stable and alopecia was only observed in our study area, which is isolated from other populations, the impact on the total population of Formosan macaque in Taiwan is limited. Nonetheless, stress-induced immunosuppression and alopecia might affect the local abundance and increase zoonosis risk due to frequent human–macaque contact in Mt. Longevity. Future studies are suggested to focus on the causative factor of stress and the effects of stress and alopecia on the health and welfare in the Formosan macaques.

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