Genetic differentiation in populations of Canada geese (Branta canadensis)

1986 ◽  
Vol 64 (4) ◽  
pp. 940-947 ◽  
Author(s):  
Carol E. Van Wagner ◽  
Allan J. Baker
Keyword(s):  
Minimum Spanning Tree ◽  
Population Sample ◽  
Branta Canadensis ◽  
Three Dimensions ◽  
Structural Genes ◽  
Random Drift ◽  
Genetic Structuring ◽  
Principal Coordinates Analysis ◽  
Morphometric Characters ◽  
Principal Coordinates

Electrophoretic data for 35 structural gene loci were obtained from 249 individuals in 11 populations of Branta canadensis across North America. Twenty-four loci were polymorphic in at least one population sample, average observed heterozygosity ranged from 0.031 to 0.083, Rogers' genetic distance ranged from 0.014 to 0.063, and Wright's measure of genetic structuring among populations was 0.065. Samples of B. c. minima from Willows, California, and B. c. interior from Akimiski Island, Northwest Territories, exhibited both the highest levels of genetic variability within populations and the greatest divergence from other populations. Principal coordinates analysis on the genetic distances, followed by nonmetric scaling in three dimensions and supplemented by construction of a minimum spanning tree, gave a more informative and less distorted picture of relationships among populations than cluster analysis. Differentiation in structural genes was neither equivalent to morphometric differentiation (in magnitude and pattern) nor consistent with conventional subspecies designations. This suggests that structural genes are selectively neutral in Branta canadensis and are differentiating through random drift, in contrast to morphometric characters which have diverged markedly under different selective pressures.

scholarly journals Principal coordinate analysis of genotype × environment interaction for grain yield of bread wheat in the semi-arid regions

Genetika ◽  
2013 ◽  
Vol 45 (3) ◽  
pp. 691-701 ◽  
Author(s):  
Naser Sabaghnia ◽  
Mohtasham Mohammadi ◽  
Rahmatollah Karimizadeh
Keyword(s):  
Grain Yield ◽  
Spanning Tree ◽  
Arid Regions ◽  
Minimum Spanning Tree ◽  
Principal Coordinate Analysis ◽  
Ge Interaction ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Main Effects ◽  
Semi Arid

Multi-environmental trials have significant main effects and significant multiplicative genotype ? environment (GE) interaction effect. Principal coordinate analysis (PCOA) offers a more appropriate statistical analysis to deal with such situations, compared to traditional statistical methods. Eighteen bread wheat genotypes were grown in four semi-arid regions over three year seasons to study the GE interaction and yield stability and obtained data on grain yield were analyzed using PCOA. Combined analysis of variance indicated that all of the studied effects including the main effects of genotype and environments as well as the GE interaction were highly significant. According to grand means and total mean yield, test environments were grouped to two main groups as high mean yield (H) and low mean yield (L). There were five H test environments and six L test environments which analyzed in the sequential cycles. For each cycle, both scatter point diagram and minimum spanning tree plot were drawn. The identified most stable genotypes with dynamic stability concept and based on the minimum spanning tree plots and centroid distances were G1 (3310.2 kg ha-1) and G5 (3065.6 kg ha-1), and therefore could be recommended for unfavorable or poor conditions. Also, genotypes G7 (3047.2 kg ha-1) and G16 (3132.3 kg ha-1) were located several times in the vertex positions of high cycles according to the principal coordinates analysis. The principal coordinates analysis provided useful and interesting ways of investigating GE interaction of barley genotypes. Finally, the results of principal coordinates analysis in general confirmed the breeding value of the genotypes, obtained on the basis of the yield stability evaluation.

Genetic diversity and structure in the northern populations of European hazelnut (Corylus avellana L.)

Genome ◽  
2019 ◽  
Vol 62 (8) ◽  
pp. 537-548
Author(s):  
Pirjo Tanhuanpää ◽  
Maarit Heinonen ◽  
Lidija Bitz ◽  
Veli-Matti Rokka
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Plant Conservation ◽  
Corylus Avellana ◽  
Ice Age ◽  
Genetic Structuring ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Corylus Avellana L

European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.

Rhizobium screening of Stylosanthes species for effectiveness in nitrogen fixation

1979 ◽  
Vol 30 (1) ◽  
pp. 85 ◽  
Author(s):  
RA Date ◽  
DO Norris
Keyword(s):  
Nitrogen Fixation ◽  
Minimum Spanning Tree ◽  
Wide Spectrum ◽  
Dry Weight ◽  
Data Matrix ◽  
Strain Specificity ◽  
Principal Coordinates Analysis ◽  
Screening Programs ◽  
Principal Coordinates ◽  
Glasshouse Screening

The Rhizobium strain specificity and effectiveness in nitrogen fixation of 336 accessions of the genus Stylosanthes were determined in glasshouse screening trials. In preliminary screening, against a wide-spectrum strain CB756, 224 accessions were effective (> 50% dry weight of nitrogen control). Sixty-two of these were evaluated subsequently against a spectrum of 22 strains of Rhizobium selected on the basis of host and geographic origins. Thirty-three were effective with 10 or more strains. Seventy-two accessions that were ineffectively nodulated in preliminary tests were also screened against the 22 strains. Fifty-four of these were effective with one or more strains of Rhizobium. A minimum spanning tree (MST) analysis was used to examine the interrelationships between, and the distribution of, accessions according to their effectiveness response (ER) to the 22 strains of Rhizobium. Accessions were classified into six groups, also according to their effectiveness response, by the program MULTBET. Groups I–IV were nodulated effectively by a large number of strains (mean 9.4) and groups V and VI by a limited number of strains (mean 1.3). Significant and wide-ranging Stylosanthes accession x strain of Rhizobium interactions for effectiveness in nitrogen fixation were observed, particularly in S. guianensis and S. hamata. Various reclassifications were made by MULTBET on a reduced number of strains which were selected on the basis of discriminatory powers between groups (eident values), contribution to the classification (Cramér measures) and intuitively on the basis of level of effectiveness specificity and soil pH adaption. Classifications based on Cramér measures gave least (9%) non-conforming accessions, but intuitively selected strains the widest range of effective associations. The majority of non-conforming accessions were found in effectiveness response groups ER-III and ER-IV and were mostly S. guianensis from M–A groups 2 and 14 andS. hamata M–A 28. For future screening programs strains CB 82, CB 159, CB 530, CB 756, CB 1408 and CB 2126 will be used as diagnostic strains for classification of accessions by effectiveness response, and strains CB 82, CB 1650 and CB 2126 as 'key strains' for provision of inocula for experimental purposes.Classification of strains of Rhizobium into six groups was obtained by a MULTCLAS analysis of the data matrix. A principal coordinates analysis suggested distinct clustering of strains on the basis of host specificity for effective nodulation. These corresponded very closely to the six classificatory groups.

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.

Morphometric discrimination of pelagic fish stocks challenged by variation in body condition

2017 ◽  
Vol 75 (2) ◽  
pp. 711-718
Author(s):  
George Geladakis ◽  
Nikolaos Nikolioudakis ◽  
George Koumoundouros ◽  
Stylianos Somarakis
Keyword(s):  
Body Condition ◽  
Prey Availability ◽  
Eastern Mediterranean ◽  
Morphological Differentiation ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Morphometric Characters ◽  
Mesozooplankton Biomass ◽  
Stock Discrimination ◽  
Principal Coordinates

Abstract Morphometric characters have traditionally been used to describe the population structure of fishes. Body shape variation, which is often environmentally induced, may provide a good record of short-term population structuring. However, factors unrelated to environmental or genetic influences on body morphology may complicate sampling and the use of morphometric features for stock discrimination. In the present study, we used geometric morphometric variables to compare the European sardine Sardina pilchardus putative stocks of the Aegean and Ionian Seas (eastern Mediterranean). Landmark data of fish collected at seven different sites were subjected to canonical analysis of principal coordinates (CAP). The average body condition of sardines from these sites was strongly and linearly related to corresponding scores along CAP1, the axis exhibiting the highest correlation with the morphometric data cloud. The average scores along CAP2 and CAP3 appeared to be linked to morphological differentiation related to temperature effects and prey availability (mesozooplankton biomass). Despite the primary and confounding effect of body condition, discrimination of different morphotypes corresponding to the Aegean and the Ionian Sea stocks was highly significant with 81% correct reallocations for the respective CAP model.

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 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.

Genetic analysis of a heritage variety collection

2018 ◽  
Vol 17 (03) ◽  
pp. 232-244 ◽  
Author(s):  
J. M. Preston ◽  
B. V. Ford-Lloyd ◽  
L. M. J. Smith ◽  
R. Sherman ◽  
N. Munro ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Group Method ◽  
Niche Markets ◽  
Principal Coordinates Analysis ◽  
Pair Group ◽  
Landrace Diversity ◽  
Principal Coordinates ◽  
Length Polymorphisms ◽  
Seed Saving ◽  
History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”

2014 ◽  
Vol 92 (2) ◽  
pp. 149-162 ◽  
Author(s):  
Christina M. Davy ◽  
Robert W. Murphy
Keyword(s):  
Population Genetics ◽  
Freshwater Turtles ◽  
Population Declines ◽  
Isolated Populations ◽  
Principal Coordinates Analysis ◽  
Turtle Species ◽  
Principal Coordinates ◽  
Clemmys Guttata ◽  
Spotted Turtle ◽  
Cast Doubt

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.

Use of multivariate methods in forest research site selection

1991 ◽  
Vol 21 (11) ◽  
pp. 1573-1580 ◽  
Author(s):  
Andrew J. Burton ◽  
Carl W. Ramm ◽  
Kurt S. Pregitzer ◽  
David D. Reed
Keyword(s):  
Site Selection ◽  
Large Scale ◽  
Multivariate Methods ◽  
Data Bases ◽  
Principal Coordinates Analysis ◽  
Research Site ◽  
Principal Coordinates ◽  
Alternative Sites ◽  
Existing Data ◽  
Selection Of

In large-scale gradient studies, selection of the best research sites is critical but time-consuming and costly. Multivariate methods can be used to quickly identify suitable sites from existing data bases. Based on a study of acid deposition in the Great Lakes region (the Michigan Gradient Study), we illustrate the use of multivariate methods in screening potential research sites for similarity. Sites were examined using cluster analysis, principal coordinates analysis, and correspondence analysis. The graphical displays generated by the multivariate methods were used to identify similar sites across the gradient. A list of 31 potential sites was reduced to 5 similar research sites and several alternative sites. The results of the multivariate methods compared well with more traditional methods of research site selection but allowed for multiple comparisons of many potential sites using a variety of data from existing data bases. By eliminating sites that are unacceptable with respect to available data, the multivariate methods reduce the number of sites that require field visitation prior to final site verification. This process represents a substantial savings in time and effort when dealing with a long list of potential research sites.

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