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

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.

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A comparative analysis of mathematical methods for homogeneity estimation of the Lithuanian population

Acta medica Lituanica ◽

10.6001/actamedica.v26i4.4206 ◽

2020 ◽

Vol 26 (4) ◽

pp. 211-216

Author(s):

Alma Molytė ◽

Alina Urnikytė ◽

Vaidutis Kučinskas

Keyword(s):

Comparative Analysis ◽

Genetic Structure ◽

Multidimensional Scaling ◽

Population Genetic ◽

Venous Blood ◽

Principal Component ◽

Principal Coordinates Analysis ◽

Data Set ◽

Background Population ◽

Principal Coordinates

Background. Population genetic structure is one of the most important population genetic parameters revealing its demographic features. The aim of this study was to evaluate the homogeneity of the Lithuanian population on the basis of the genome-wide genotyping data. The comparative analysis of three methods – multidimensional scaling, principal components, and principal coordinates analysis – to visualize multidimensional genetics data was performed. The results of visualization (mapping images) are also presented. Materials and methods. The data set consisted of 425 samples from six ethnolinguistic groups of the Lithuanian population. Genomic DNA was extracted from whole venous blood using either the phenol-chloroform extraction method or the automated DNA extraction platform TECAN Freedom EVO. Genotyping was performed at the Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Lithuania, with the Illumina HumanOmniExpress-12 v1.1 and the Infinium OmniExpress-24. For the estimation of homogeneity of the Lithuanian population, PLINK data file was obtained using PLINK v1.07 program. The Past3 software was used to visualize the genotype data with multidimensional scaling and principal coordinates methods. The SmartPCA from EIGENSOFT 7.2.1 program was used in the principal component analysis to determine the population structure. Conclusions. Methods of multidimensional scaling, principal coordinate, and principal component for the genetic structure of the Lithuanian population were investigated and compared. The principal coordinate and principal component methods can be used for genotyping data visualization, since any essential differences in the results obtained were not observed and compared to multidimensional scaling. The Lithuanian population is homogenous whereas the points are strongly close when we use the principal coordinates or principal component methods.

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From Catastrophe to Recovery: Stories of Fishery Management Success

From Catastrophe to Recovery: Stories of Fishery Management Success ◽

10.47886/9781934874554.ch2 ◽

2019 ◽

Keyword(s):

Rainbow Trout ◽

Brook Trout ◽

Salmo Trutta ◽

Fishery Management ◽

Species Conservation ◽

Livestock Grazing ◽

Genetic Introgression ◽

Genetic Management ◽

Chemical Treatments ◽

Management Actions

Abstract.Ã¢â‚¬â€Native golden trout of CaliforniaÃ¢â‚¬â„¢s upper Kern River basin have inspired anglers and scientists alike with their beauty, ecology, and evolutionary history. Three Rainbow Trout Oncorhynchus mykiss subspecies comprise the golden trout complex: California Golden Trout O. m. aguabonita, Little Kern Golden Trout O. m. whitei, and Kern River Rainbow Trout O. m. gilberti. This chapter focuses on restoration and management of the first two subspecies, California Golden Trout and Little Kern Golden Trout. Agency biologists, other scientists, and citizens have all worked for more than 100 years to protect and save these subspecies from a range of threats, some of fishery managersÃ¢â‚¬â„¢ own making and some threats evolving over time. Major problems have included overharvest by anglers, overgrazing of habitat by livestock, competition and predation by nonnative Brown Trout Salmo trutta and Brook Trout Salvelinus fontinalis, and hybridization with introduced nonnative forms of Rainbow Trout subspecies; these factors drove both species perilously close to extinction by the late 1960s. Little Kern Golden Trout were listed as threatened in 1978 under the U.S. Federal Endangered Species Act. That same year, the federal government designated large portions of California Golden Trout and Little Kern Golden Trout native watersheds as the Golden Trout Wilderness. Management actions to prevent extinction and conserve these subspecies have included angling regulations, livestock grazing restrictions, barrier construction, chemical treatments to remove nonnative trout, and research to identify and quantify genetic introgression of nonnative Rainbow Trout genes into native golden trout populations. Restoration efforts have, thus far, averted extinction, allowed populations to rebound, and provided several important lessons on genetic management of closely related subspecies, including pitfalls of a zero-introgression target for conservation, the potential need to continue management indefinitely, being responsive to emerging threats, recognizing that barriers to upstream fish movement can be useful, the caveats of using hatcheries for conservation, the potential role of native trout donor populations to facilitate restoration, and the need to harness public and stakeholder understanding and support for species conservation.

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Evaluating the Predictive Power of Ordination Methods in Ecological Context

Mathematics ◽

10.3390/math6120295 ◽

2018 ◽

Vol 6 (12) ◽

pp. 295 ◽

Cited By ~ 2

Author(s):

Otto Wildi

Keyword(s):

Goodness Of Fit ◽

Optimal Choice ◽

Alternative Methods ◽

Site Factors ◽

Real World Data ◽

Principal Coordinates Analysis ◽

Data Set ◽

Ordination Methods ◽

Principal Coordinates ◽

Almost All

When striving for the ordination methods best predicting independently measured site factors, the following questions arise: does the optimal choice depend on the kind of biological community analysed? Are there different ordination methods needed to address different site factors? Simultaneously, I explore alternative similarity approaches of entire ordinations, as well as the role of the transformations applied to the scale used in measuring species performance. The combination of methods and data transformations results in 96 alternative solutions for any one data set. These are compared by a graphical display, that is, an ordination of ordinations. The goodness-of-fit of independently measured site factors is assessed by two alternative methods. The resulting 96 performance values serve as independent variables in trend surfaces overlaid to the ordination of ordinations. The results from two real-world data sets indicate that some ordination methods greatly vary with data transformation. Scores close to a binary scale perform best in almost all ordination methods. Methods that intrinsically constrain the range of species scores, such as principal components analysis based on correlation, correspondence analysis (including its detrended version), nonmetric multidimensional scaling, as well as principal coordinates analysis based on the Bray-Curtis distance, always figure among the most successful methods, irrespective of data used.

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Genetic relationships and variation among ecotypes of seashore paspalum (Paspalum vaginatum) determined by random amplified polymorphic DNA markers

Genome ◽

10.1139/g94-143 ◽

1994 ◽

Vol 37 (6) ◽

pp. 1011-1017 ◽

Cited By ~ 37

Author(s):

Zhao-Wei Liu ◽

Robert L. Jarret ◽

Ronny R. Duncan ◽

Stephen Kresovich

Keyword(s):

Rapd Markers ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

The United States ◽

Principal Coordinates Analysis ◽

Data Set ◽

Seashore Paspalum ◽

Principal Coordinates ◽

Paspalum Vaginatum ◽

High Level

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic relationships and variation among ecotypes of the turfgrass seashore paspalum (Paspalum vaginatum Swartz). Vegetative tissues or seeds of 46 seashore paspalum ecotypes were obtained from various locations in the United States, Argentina, and South Africa. Leaf DNA extracts were screened for RAPD markers using 34 10-mer random primers. A total of 195 reproducible RAPD fragments were observed, with an average of six fragments per primer. One hundred and sixty-nine fragments (87% of the total observed) were polymorphic, among which 27 fragments (16%) were present in three or less ecotypes, indicating the occurrence of a high level of genetic variation among the examined accessions of this species. Cluster analysis (UPGMA) and principal coordinates analysis were performed on the RAPD data set. The results illustrate genetic relationships among the 46 ecotypes, and between ecotypes and their geographical origins. Ecotypes from southern Africa could be differentiated from the U.S. and most of the Argentinean ecotypes. With a few exceptions, ecotypes collected from Argentina, Hawaii, Florida, and Texas were separated into distinct clusters.Key words: RAPDs, polymerase chain reaction, genetic diversity, phenetic analysis.

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Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters

Scientific Reports ◽

10.1038/s41598-021-94257-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kean Chong Lim ◽

Amy Yee-Hui Then ◽

Alison Kim Shan Wee ◽

Ahemad Sade ◽

Richard Rumpet ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Population Structure ◽

Genetic Structure ◽

Genetic Differentiation ◽

Fishery Management ◽

Peninsular Malaysia ◽

Fine Scale ◽

Nadh Dehydrogenase Subunit 2 ◽

Bamboo Shark

AbstractThe demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.

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A preliminary genetic structure study of the non-native weed, common tansy (Tanacetum vulgare)

Canadian Journal of Plant Science ◽

10.4141/cjps10203 ◽

2011 ◽

Vol 91 (4) ◽

pp. 717-723 ◽

Cited By ~ 1

Author(s):

Benjamin Clasen ◽

Nicole Moss ◽

Monika Chandler ◽

Alan Smith

Keyword(s):

Genetic Structure ◽

North America ◽

Small Variation ◽

Structure Study ◽

Inter Simple Sequence Repeat ◽

Principal Coordinates Analysis ◽

Tanacetum Vulgare ◽

Pair Group ◽

Principal Coordinates ◽

Disturbed Areas

Clasen, B. M., Moss, N. G., Chandler, M. A. and Smith, A. G. 2011. A preliminary genetic structure study of the non-native weed, common tansy (Tanacetum vulgare). Can. J. Plant Sci. 91: 717–723. Common tansy is an herbaceous perennial member of the Asteraceae and is considered a weed in North America. Common tansy was introduced deliberately for use as a funerary herb, medicine, preservative, and animal and insect repellent. It is known to escape cultivation and invade disturbed areas, spreading both sexually and asexually. This paper reports a preliminary analysis of the genetic structure of 10 invasive common tansy populations in Minnesota and Montana, USA, and Alberta, Canada. Ninety polymorphic loci were found using six inter simple sequence repeat (ISSR) primers used to amplify DNA from 40 individuals from 10 discrete populations. The diversity within and among populations was assessed using the Dice coefficient of similarity and AMOVA. The AMOVA showed that diversity within populations was generally high and that there was relatively small variation among populations. An unweighted pair-group with arithmetic mean (UPGMA) dendrogram was constructed based on the distance between populations, and demonstrated substantial and distinct clustering of a population from Ramsey County, Minnesota. A principal coordinates analysis clustered all individuals from Ramsey County distinctly from other individuals, indicating a possible limited gene flow among this population and the other populations sampled in this study. Understanding genetic diversity and the distribution of diversity within and among populations may help predict the potential for successful management of common tansy populations in North America.

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Spatial Genetic Structure and Population Dynamics of Gummy Stem Blight Fungi Within and Among Watermelon Fields in the Southeastern United States

Phytopathology ◽

10.1094/phyto-01-16-0006-r ◽

2016 ◽

Vol 106 (8) ◽

pp. 900-908 ◽

Cited By ~ 18

Author(s):

Hao-Xi Li ◽

Marin Talbot Brewer

Keyword(s):

United States ◽

Population Structure ◽

Genetic Structure ◽

Spatial Genetic Structure ◽

Southeastern United States ◽

Principal Coordinates Analysis ◽

Stem Blight ◽

Gummy Stem Blight ◽

Principal Coordinates ◽

Regional Population

The epidemiology of gummy stem blight (GSB) of cucurbits, particularly the sources of inoculum for epidemics, and the regional population genetic structure of the causal fungi Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), S. citrulli, and S. caricae are not well understood. Our goal was to better understand the population structure and fine-scale spatial genetic structure of Stagonosporopsis spp. in the southeastern United States. Overall, 528 isolates collected from nine fields in 2012, 2013, and 2014 were genotyped with 16 microsatellite markers. In 2013, S. caricae was first detected in the southeastern United States; however, S. citrulli remained the dominant species, representing 96.4% of the isolates. Principal coordinates analysis, discriminant analysis of principle components, and analysis of molecular variance indicated that most populations of S. citrulli were genotypically diverse, yet dominated by widely distributed clones that contributed to regional population structure. Spatial genetic structure resulting from aggregation of clonal genotypes at distances of less than 10 meters was detected within two of three fields in which isolate location was recorded. Studies on the epidemiological and fitness differences between S. citrulli and S. caricae and of prevalent and widespread clones will provide insight into the population structure and species dynamics observed in GSB epidemics.

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Geographical description and molecular characterization of genetic structure and diversity using a 6K SNP array in Turkish oat germplasm

Canadian Journal of Plant Science ◽

10.1139/cjps-2017-0293 ◽

2019 ◽

Vol 99 (1) ◽

pp. 12-21

Author(s):

Gönül Cömertpay ◽

Ephrem Habyarimana ◽

Faheem Shehzad Baloch ◽

Hüseyin Güngör ◽

Tevrican Dokuyucu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Snp Array ◽

Snp Markers ◽

Gene Banks ◽

Cultivar Development ◽

Principal Coordinates ◽

Secondary Center ◽

Geographical Regions ◽

Genetic Structure And Diversity

Cultivated oat (Avena sativa L. and Avena byzantina Koch) is native to Turkey, a secondary center of oat diversity. Oat breeding has received less attention relative to other cereals. In this work, the diversity of oat landraces collected from different regions of Turkey as well as obtained from different gene banks was investigated using 3293 high quality SNP markers. Expected heterozygosity (Hs), observed heterozygosity (Ho), inbreeding coefficient (Fis), and overall genetic diversity (Ht) of the oat gene pool were 0.22, 0.01, 0.96, and 0.38, respectively. The value of the genetic differentiation (Fst) metric for genetic structure was 0.41 and indicated that kinship was more of a determinant for population structure than the geographical provenance. The populations from different geographical regions shared a great proportion of genetic diversity. Clustering using model-based STRUCTURE, principal coordinates (PCoA), and neighbour-joining (NJ) algorithms were mostly comparable except for five discrepantly clustered accessions in NJ and PCoA relative to STRUCTURE, which can be attributed to the relatively reduced resolution power in the NJ and PCoA approaches. SNP markers partitioned all oat accessions into four main groups (A, B, C, and D) with 10 unclassified accessions. Some landraces were identical based on genetic distance and can represent duplications in gene banks. The data presented in this work represent the initial results on genetic diversity as investigated in Turkish oat, and are an important resource for systematicians, geneticists, and breeders interested in Turkish oat germplasm. These results are expected to open new opportunities for further studies in oat genomics and cultivar development.

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Natural hybridization between Elymus repens and E. hispidus assessed by AFLP analysis

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2007.025 ◽

2011 ◽

Vol 76 (3) ◽

pp. 225-234 ◽

Cited By ~ 11

Author(s):

Magdalena Szczepaniak ◽

Elżbieta Cieślak ◽

Piotr Bednarek

Keyword(s):

Pollen Viability ◽

Vegetative Reproduction ◽

Natural Hybridization ◽

Hybrid Origin ◽

F1 Hybrids ◽

Aflp Analysis ◽

Principal Coordinates Analysis ◽

Data Set ◽

Principal Coordinates ◽

Elymus Repens

Hybrid speciation within the genus Elymus is analyzed and discussed. The supposed hybrid origin of Elymus x mucronatus between Elymus repens and Elymus hispidus was tested. In this aim, pollen viability and AFLP variation of putative progenitors and progenies from two natural populations were studied. Pollen fertility of hybrids ranging from 0 to 91.95% (average 59.50%) indicates the occurrence of F1 hybrids and backcross hybrids. Seven EcoRI/MseI AFLP primer combinations generated a total of 477 AFLP fragments (300 polymorphic) for 48 parental and hybrid individuals. UPGMA and principal coordinates analysis of the AFLP data set show that hybrids are closer to E. hispidus than to E. repens and suggest unidirectional introgression towards E. hispidus. AFLP fragments of the hybrid taxon were additively inherited from the parental species and no hybrid-specific bands were identified. AFLP analysis validates the hybrid status of E. ×mucronatus. Populations in which E. repens, E. hispidus and their hybrids co-occur still progress from early hybridization stages of F1 hybrids to an advanced hybridization stage of a well-established hybrid swarm. E. ×mucronatus is potentially self-sustaining by predominant vegetative reproduction by rhizomes and partial fertility leading to the development of mature seeds. We propose to consider Elymus ×mucronatus as a new species of hybrid origin in the Polish flora.

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Diversity within American cassava germ plasm based on RAPD markers

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000100034 ◽

2000 ◽

Vol 23 (1) ◽

pp. 189-199 ◽

Cited By ~ 32

Author(s):

Carlos Colombo ◽

Gérard Second ◽

André Charrier

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Core Collection ◽

Rapd Markers ◽

Germ Plasm ◽

Sao Paulo ◽

Climatic Data ◽

São Paulo ◽

Principal Coordinates Analysis ◽

Principal Coordinates

This work focuses on the genetic diversity of American cassava through RAPD molecular markers. The 126 genotypes studied were distributed on four geographical levels ranging from local to continental. Samples included ethnocultivars from the Santa Isabel community in the Brazilian Amazon, local cultivars collected in the State of São Paulo, native accessions from very diverse Brazilian regions, and representative accessions from the Centro Internacional de Agricultura Tropical (CIAT) core collection. Eighty-eight polymorphic bands were analyzed. Results revealed the weak genetic structure of the cassava analyzed. The pattern formed by the first two axes of the principal coordinates analysis (PCoA) revealed an overlapping of the São Paulo State genotype, the Brazilian group and the core collection accessions. The Santa Isabel ethnocultures formed a separate group. The weak genetic structure of cassava can be explained by the common practice of exchanging botanical material among small producers as well as by recombinations among genotypes. When the genotypes were analyzed using climatic data, the sample sites were found to be structured according to temperature and precipitation. RAPD markers proved very useful in the genetic diversity study, resulting in important implications for cassava germ plasm collections and genetic breeding.

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