Phylogeography of Baryancistrus xanthellus (Siluriformes: Loricariidae), a rheophilic catfish endemic to the Xingu River basin in eastern Amazonia

Baryancistrus xanthellus (Loricariidae) is an endemic fish species from the Xingu River basin with its life history in the shallow rapid waters flowing over bedrock substrates. In order to investigate the genetic diversity and demographic history of B. xanthellus we analyzed sequence data for one mitochondrial gene (Cyt b) and introns 1 and 5 of nuclear genes Prolactin (Prl) and Ribosomal Protein L3 (RPL3). The analyses contain 358 specimens of B. xanthellus from 39 localities distributed throughout its range. The number of genetically diverged groups was estimated using Bayesian inference on Cyt b haplotypes. Haplotype networks, AMOVA and pairwise fixation index was used to evaluate population structure and gene flow. Historical demography was inferred through neutrality tests and the Extended Bayesian Skyline Plot (EBSP) method. Five longitudinally distributed Cyt b haplogroups for B. xanthellus were identified in the Xingu River and its major tributaries, the Bacajá and Iriri. The demographic analysis suggests that rapids habitats have expanded in the Iriri and Lower Xingu rivers since 200 ka (thousand years) ago. This expansion is possibly related to an increase in water discharge as a consequence of higher rainfall across eastern Amazonia. Conversely, this climate shift also would have promoted zones of sediment trapping and reduction of rocky habitats in the Xingu River channel upstream of the Iriri River mouth. Populations of B. xanthellus showed strong genetic structure along the free-flowing river channels of the Xingu and its major tributaries, the Bacajá and Iriri. The recent impoundment of the Middle Xingu channel for the Belo Monte hydroelectric dam may isolate populations at the downstream limit of the species distribution. Therefore, future conservation plans must consider the genetic diversity of B. xanthellus throughout its range.

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220 Mitochondrial DNA polymorphism as a measure of genetic diversity in African tilapia fish

Journal of Animal Science ◽

10.1093/jas/skz258.094 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 47-48

Author(s):

Ekei Ikpeme ◽

Ekerette Ekerette ◽

Michael Ozoje

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Cytochrome B ◽

Fixation Index ◽

Cyt B ◽

Important Species ◽

Loop Region ◽

South West ◽

D Loop ◽

Two Populations

Abstract This study focused on the assessment of genetic diversity in African tilapia fish (Oreochromis niloticus) obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome B region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop region was sequenced for all samples from the two populations, while cytochrome b (cyt b) region of mtDNA was only sequenced for samples from South-South population Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. There were 176, 162 and 144 polymorphic sites for D-loop of South-South, South-West and cyt b of South-South populations, respectively. Haplotype diversities (Hd) were 1.00 ± 0.024 and 1.00 ± 0.030 while nucleotide diversities were 0.168 ± 0.086 and 0.161 ± 0.084 for D-loop of South-South and South-West populations, respectively. For the cyt b, haplotype and nucleotide diversities were 0.91 ± 0.003 and 0.051 ± 0.016. The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Phylogenetic analysis grouped the samples into two clusters based on population. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (P < 0.05). The findings of this study revealed high level of genetic diversity among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.

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Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Diversity ◽

10.3390/d11040062 ◽

2019 ◽

Vol 11 (4) ◽

pp. 62 ◽

Cited By ~ 12

Author(s):

Yasmin G. S. Carvalho ◽

Luciana C. Vitorino ◽

Ueric J. B. de Souza ◽

Layara A. Bessa

Keyword(s):

Genetic Diversity ◽

Life History ◽

Plant Species ◽

Life History Traits ◽

Demographic History ◽

Haplotype Diversity ◽

Molecular Techniques ◽

Fixation Index ◽

Relative Contribution ◽

Recent Trends

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Genetic Investigation of Four Beluga Sturgeon (Huso huso, L.) Broodstocks for its Reintroduction in the Po River Basin

Environments ◽

10.3390/environments8040025 ◽

2021 ◽

Vol 8 (4) ◽

pp. 25

Author(s):

Caterina M. Antognazza ◽

Isabella Vanetti ◽

Vanessa De Santis ◽

Adriano Bellani ◽

Monica Di Francesco ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Genetic Variability ◽

River Basin ◽

Captive Breeding ◽

Conservation Strategies ◽

Huso Huso ◽

Po River ◽

Beluga Sturgeon ◽

Po River Basin

The reintroduction of the extinct beluga sturgeon (Huso huso L.), an anadromous species with economic and traditional relevance, is a priority in next conservation strategies in Northern Italy. The EU-LIFE NATURA project aims to reintroduce the beluga sturgeon in the Po River basin through a captive breeding program. Critical requirements for the success of the program are river connectivity and knowledge of genetic diversity of the selected broodstocks to ensure self-sustainability of reintroduced populations. Here, the four broodstocks used for the reintroduction of beluga sturgeon have been genetically screened, genotyping 13 loci and sequencing mitochondrial DNA cytochrome b (Cyt b) gene and the entire mitochondrial DNA control region (D-Loop). The four broodstocks showed a medium-high level of nuclear genetic variability and the presence of two sub-populations, evidencing a total level of inbreeding coefficients able to sustain the good potential as future breeders. Mitochondrial analyses showed a genetic variability comparable to wild populations, further strengthening the positive potential of the investigated broodstock. Therefore, this study, showed how the degree of genetic diversity found within the four broodstocks used for H. huso reintroduction in the Po River basin could be suitable to ensure the success of the program, avoiding the inbreeding depression associated with founder effect and captive breeding.

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Trends in climate extreme indices assessed in the Xingu river basin - Brazilian Amazon

Weather and Climate Extremes ◽

10.1016/j.wace.2021.100306 ◽

2021 ◽

Vol 31 ◽

pp. 100306

Author(s):

Edmundo Wallace Monteiro Lucas ◽

Francisco de Assis Salviano de Sousa ◽

Fabrício Daniel dos Santos Silva ◽

Rodrigo Lins da Rocha Júnior ◽

David Duarte Cavalcante Pinto ◽

...

Keyword(s):

River Basin ◽

Brazilian Amazon ◽

Climate Extreme ◽

Xingu River ◽

Extreme Indices

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Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis

Malaria Journal ◽

10.1186/s12936-021-03664-8 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Li-Yun Lin ◽

Hui-Ying Huang ◽

Xue-Yan Liang ◽

Dong-De Xie ◽

Jiang-Tao Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Natural Selection ◽

Protein Structure ◽

Transmembrane Protein ◽

Fixation Index ◽

Bioko Island ◽

Adhesive Protein ◽

Trap Gene ◽

Selection Of

Abstract Background Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As a potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was described. Methods 153 blood spot samples from Bioko malaria patients were collected during 2016–2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools. Results A total of 119 Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN–dS (6.2231, p < 0.05) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst > 0.15, p < 0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG > 1) indicated a destabilization of protein structure. Conclusions Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes), which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations have been shown to be detrimental to the protein structure or function and deserve further study and continuous monitoring.

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Using HEM surveys to evaluate disposal of by-product water from CBNG development in the Powder River Basin, Wyoming

Geophysics ◽

10.1190/1.2901200 ◽

2008 ◽

Vol 73 (3) ◽

pp. B77-B84 ◽

Cited By ~ 14

Author(s):

Brian A. Lipinski ◽

James I. Sams ◽

Bruce D. Smith ◽

William Harbert

Keyword(s):

River Basin ◽

Produced Water ◽

Water Discharge ◽

Geophysical Methods ◽

Powder River Basin ◽

Coal Bed ◽

Coal Beds ◽

Occam’S Inversion ◽

Product Water ◽

Location Strategies

Production of methane from thick, extensive coal beds in the Powder River Basin of Wyoming has created water management issues. Since development began in 1997, more than 650 billion liters of water have been produced from approximately 22,000 wells. Infiltration impoundments are used widely to dispose of by-product water from coal bed natural gas (CBNG) production, but their hydrogeologic effects are poorly understood. Helicopter electromagnetic surveys (HEM) were completed in July 2003 and July 2004 to characterize the hydrogeology of an alluvial aquifer along the Powder River. The aquifer is receiving CBNG produced water discharge from infiltration impoundments. HEM data were subjected to Occam’s inversion algorithms to determine the aquifer bulk conductivity, which was then correlated towater salinity using site-specific sampling results. The HEM data provided high-resolution images of salinity levels in the aquifer, a result not attainable using traditional sampling methods. Interpretation of these images reveals clearly the produced water influence on aquifer water quality. Potential shortfalls to this method occur where there is no significant contrast in aquifer salinity and infiltrating produced water salinity and where there might be significant changes in aquifer lithology. Despite these limitations, airborne geophysical methods can provide a broadscale (watershed-scale) tool to evaluate CBNG water disposal, especially in areas where field-based investigations are logistically prohibitive. This research has implications for design and location strategies of future CBNG water surface disposal facilities within the Powder River Basin.

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Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Plant Genetic Resources ◽

10.1017/s1479262121000034 ◽

2021 ◽

Vol 19 (1) ◽

pp. 20-28

Author(s):

Abush Tesfaye Abebe ◽

Adesike Oladoyin Kolawole ◽

Nnanna Unachukwu ◽

Godfree Chigeza ◽

Hailu Tefera ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Glycine Max ◽

Snp Markers ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Lines ◽

Soybean Germplasm ◽

Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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