Genetic analysis of Rhaponticum carthamoides (Asteraceae) during restoration of natural populations in the Altai Republic

Rhaponticum carthamoides (Willd.) Iljin is a rare species for Altai Republic. It possesses medicinal and fodder properties and therefore is considered a valuable resource species. Populations of this species are regularly exposed to anthropogenic impact. The impact factors are harvesting of rhizomes and cattle grazing. We have carried out the restoration of two populations of this species. The seeds for restorative planting were collected from healthy plants in the same populations, at a distance of 10 km or less from the restoration site. The genetic analysis of DNA fragments showed a reliable similarity of genetic diversity in planted and naturally growing individuals in each of the studied populations. Comparison showed that plants in more remote locations, which are less accessible for tourism and economic activities, were characterized by higher genetic diversity.

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Alive and kicking, or, living on borrowed time? – Microsatellite diversity in natural populations of the endangered Ulmus minor Mill. sensu latissimo from Croatia

Acta Botanica Croatica ◽

10.1515/botcro-2016-0007 ◽

2016 ◽

Vol 75 (1) ◽

pp. 53-59 ◽

Cited By ~ 2

Author(s):

Marko Zebec ◽

Marilena Idžojtić ◽

Zlatko Šatović ◽

Igor Poljak ◽

Zlatko Liber

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Genetic Bottleneck ◽

Dutch Elm Disease ◽

Significant Excess ◽

Mediterranean Populations ◽

Ulmus Minor ◽

Study Results ◽

The Impact ◽

Microsatellite Diversity

AbstractThe main objective of this research was to assess the genetic diversity of 5 natural field elm populations in Croatia. The study results suggest that the observed populations are characterized by a satisfactory amount of heterozygosity, and that the impact of the Dutch elm disease on the amount of genetic diversity in the sampled populations is currently negligible. However, one population displayed a significant excess of heterozygosity, implying a genetic bottleneck. The existence of a very clear genetic differentiation between the continental and the Mediterranean populations of Ulmus minor in Croatia was noticed.

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Coalescent Theory of Migration Network Motifs

Molecular Biology and Evolution ◽

10.1093/molbev/msz136 ◽

2019 ◽

Vol 36 (10) ◽

pp. 2358-2374

Author(s):

Nicolas Alcala ◽

Amy Goldberg ◽

Uma Ramakrishnan ◽

Noah A Rosenberg

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Nucleotide Diversity ◽

Natural Populations ◽

Node Degree ◽

Small Subset ◽

Network Motifs ◽

Coalescent Theory ◽

Migration Networks ◽

The Impact

Abstract Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets—sky island birds of genus Sholicola and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.

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Coalescent theory of migration network motifs

10.1101/190249 ◽

2017 ◽

Author(s):

Nicolas Alcala ◽

Amy Goldberg ◽

Uma Ramakrishnan ◽

Noah A. Rosenberg

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Nucleotide Diversity ◽

Natural Populations ◽

Node Degree ◽

Small Subset ◽

Network Motifs ◽

Coalescent Theory ◽

Migration Networks ◽

The Impact

ABSTRACTNatural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a large mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with small density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into several disconnected components. We illustrate our results using two example datasets—sky island birds of genus Brachypteryx and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity and for designing strategies to alter population migration networks to maximize genetic variation in the context of conservation of endangered species.

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Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration

Scientific Reports ◽

10.1038/s41598-020-71835-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Selouka Mint Abdelaziz ◽

Leila Medraoui ◽

Mohammed Alami ◽

Ouafae Pakhrou ◽

Meryem Makkaoui ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Inter Simple Sequence Repeat ◽

Resolving Power ◽

Balanites Aegyptiaca ◽

Marker Index ◽

Information Index ◽

Genetic Diversity And Structure ◽

Two Populations ◽

Amova Analysis

Abstract Drought and desertification are the major environmental constraints facing the Sahelian agro-ecosystems for decades. Assessing genetic diversity of native tree species is critical to assist ecosystems restoration efforts. Here we describe genetic diversity and structure of seven Balanites aegyptiaca L. natural populations distributed across the Sahelian-Saharan zone of Mauritania using 16 polymorphic ISSR primers. These generated 505 polymorphic bands. Polymorphism information content (PIC) varied from (0.13–0.29) with an average 0.23, marker index (MI) averaged 7.3 (range 3.3–10.3) and resolving power (RP) ranged from (4.53–14.6) with an average 9.9. The number of observed alleles (Na) ranged from (0.62–1.39), Effective number of alleles (Ne) varied from (1.26–1.37), Shannon’s information index (I) ranged from (0.25–0.36). AMOVA analysis showed that 80% of the genetic variation was fined within populations, which is supported by a low level of genetic differentiation between population (GST = 0.21) and an overall estimate of gene flow among populations (Nm = 1.9). The dendrogram based on Jaccard's similarity coefficient and the structure analysis divided the seven populations into two main clusters in which two populations from the Saharan zone were grouped. Our results provide baseline data for genetic conservation programs of this Sahelian neglected crop and with an important econ-ecological role.

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Low genetic diversity and inbreeding depression in Queensland Koalas

Wildlife Research ◽

10.1071/wr9930177 ◽

1993 ◽

Vol 20 (2) ◽

pp. 177 ◽

Cited By ~ 29

Author(s):

JMW Wilmer ◽

A Melzer ◽

F Carrick ◽

C Moritz

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Inbreeding Depression ◽

Natural Populations ◽

Small Population ◽

Phascolarctos Cinereus ◽

Low Genetic Diversity ◽

History Of ◽

Biased Sex Ratio ◽

Two Populations

The amount of genetic variation in two natural populations of Queensland koalas (Phascolarctos cinereus adustus) was assessed by analysis of mitochondrial DNA. Levels and any adverse effects of inbreeding (inbreeding depression) were estimated from the pedigree of a well-characterised captive colony. Genetic diversity of mitochondrial DNA was found to be exceedingly low both within and between the two populations, but the variation detected was found to be strongly structured geographically. Inbreeding levels in the captive colony were moderate to high yet the only apparent evidence of inbreeding depression was a male-biased sex ratio. There was no evidence for decreased juvenile survivorship or growth rate with inbreeding. Because of the limited data it would be premature to conclude that koalas are relatively resistant to the effects of inbreeding. However, we suggest the hypothesis that koalas have a history of small population size, resulting in reduced susceptibility to inbreeding depression.

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GENETIC ANALYSIS GERMAN SHEPHERD BREED DOGS USING MICROSATELLITE DNA MARKERS

Animal Breeding and Genetics ◽

10.31073/abg.52.21 ◽

2016 ◽

Vol 52 ◽

pp. 166-171

Author(s):

V. V. Dzitsiuk ◽

S. G. Kruhlyk ◽

V. G. Spyrydonov

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Microsatellite Markers ◽

Dna Markers ◽

Microsatellite Loci ◽

Genetic Evaluation ◽

German Shepherd ◽

Genetic Characteristics ◽

Expected Heterozygosity ◽

The Impact

Modern methods of breeding dogs are based on getting of stable phenotypic uniformity by using close inbreeding or breeding by one line, but such strategy leads to a loss of genetic diversity, and as a result there are genetic defects in breeds which have no external manifestations or manifest in adulthood of dogs and are transmitted from generation to generation. Therefore, to prevent use of dogs with genetic abnormalities in breeding, and to develop standards for a breed and make an accurate pedigree, must carry out the genetic evaluation of animals. One of the modern tools for dogs’ genetic evaluation is DNA-testing using microsatellite loci permitting to match the parental couple effectively, identify (to certify) animals, undertake a comprehensive assessment for heterozygous and homozygous genotypes in populations, permitted for use in the selection process, and illustrate clearly the impact of artificial selection on the genetic characteristics of breeds. The study was conducted in Ukrainian Laboratory of Quality and Safety of Agricultural Products in Department of Molecular Biology Research. For the genetic analysis 42 German Shepherd dogs, used for breeding in kennels of Ukrainian Kennel Union (UKU), were selected. The material for the research was DNA isolated from dogs’ buccal epithelium cells and blood. Genomic DNA was extracted using a standard set of reagents for DNA isolation. Level of theoretically expected heterozygosity (Hexp) varied between 0.385 (PEZ1) to 0.835 (PEZ8). On average theoretically expected heterozygosity with coefficient of 0.657 had not significant advantage over value of actual heterozygosity (0.629), it also shows that the status of the sample of dogs is close to balance. The same is observed in actual and expected heterozygosity for PEZ 6 (0.629) and PEZ 8 (0.657) loci, which also shows the balance. For FHC2010 loci actual heterozygosity is higher than expected, indicating increasing the number of heterozygous individuals. For FHC2054 locus, by contrast, theoretically expected heterozygosity (0.670) dominates the actual (0.429), indicating the lack of heterozygous genotypes in this micropopulation. The value of PIC (polymorphism information content) of the analysed loci ranged from 0.325 to 0.740 with average value 0.574. PEZ6, PEZ8, FHC 2010 and FHC 2054 loci optimally meets their suitability for genetic certification of genotypes because their frequency varies from 0.587 to 0.740. The reduced average index of polymorphism for PEZ1 locus with coefficient of 0.325 confirmed the insufficient level of its polymorphism for full genetic evaluation of the micropopulation of German Shepherd dogs (PIC < 0.500), as confirmed by Chinese researcher J.-H. Ye, according to his data PIC value for PEZ1 locus was 0,320, which correlates with our results. And PIC value for PEZ8 locus was 0.740 in our studies, whereas according to J.-H. Ye – 0,720, which, by contrast, indicates high polymorphism and confirms the effectiveness of its use in genotyping of dogs. Probability of exclusion of accidental allele coincidence (PE), which is 0.675 on average, indicates a lack of the number and informativeness of the selected microsatellite markers for German Shepherd as in this case a combined probability (CPE) of accidental allele coincidence is 0.933886 or 93.3%. The chosen microsatellite loci to study the genetic structure of the German Shepherd dog population, show a sufficiently high informativeness of chosen system of molecular genetic DNA markers. However, there is the need for using additional microsatellite markers which will increase the combined probability of accidental allele coincidence (CPE) from 93.3% to 99.9%. The analysis of heterozygosity is important in studying the dynamics of genetic processes in populations, because heterozygosity has an effect on many factors, including mutations, selection, non-random mating, genetic drift, etc., so continuous monitoring of genetic diversity is required for their timely identification and development of measures to improve breeding work on biodiversity in different dog breeds.

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Genetic diversity, structure, and kinship analysis of Trachemys venusta venusta in Wildlife Management Units and wild populations in south Mexico. Implications for conservation and management

10.1101/2020.01.27.920983 ◽

2020 ◽

Author(s):

Elsi B. Recino-Reyes ◽

Julia M. Lesher-Gordillo ◽

Salima Machkour-M’Rabet ◽

Manuel I. Gallardo-Alvárez ◽

Claudia E. Zenteno-Ruiz ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Management Plan ◽

Freshwater Turtle ◽

Freshwater Turtles ◽

Wild Populations ◽

Genetic Management ◽

Kinship Analysis ◽

Management Units ◽

The Impact

AbstractThe Meso-American slider turtle (Trachemys venusta) is a freshwater turtle endemic to Mexico and Central America. Due to the overexploitation of its natural populations, it is in the at risk category formulated by the Official Mexican Standard NOM-059-ECOL-2010. In the state of Tabasco, Management Units for the Conservation of Wildlife (UMA) were created to reduce the impact of overexploitation of freshwater turtles. However, no genetic management plan was considered. This study presents the level of genetic diversity of the founder individuals in order to develop a management plan which will optimize reproduction in the UMA. Genetic diversity was compared between captive (n = 45) and wild (n = 86) individuals using 14 microsatellite molecular markers. Level of genetic diversity could be considered as low (He < 0.6) for a species of turtle and suggests that a higher level of protection is required for this particular species. Furthermore, values were slightly higher for the captive group reflecting the mix of genetic sources (founding individuals from different localities) and demonstrating that the captive population is genetically representative of natural populations. The genetic structure analysis revealed a relationship between captive and wild populations, indicating the influence of the two principal river basins in this region on the population of freshwater turtles. Finally, according to the results obtained from the analysis conducted using Storm and ML-Relate programs, we recommend the use of 19 females and 13 males, generating a potential of 247 dyads with no relationship. These first results of genetic management in a Mexican UMA, demonstrate the importance of molecular approaches at the time of managing and conserving species in captivity.

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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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Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius)

Genes ◽

10.3390/genes12020138 ◽

2021 ◽

Vol 12 (2) ◽

pp. 138

Author(s):

Corey Kirkland ◽

Marta Farré

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Mitochondrial Genome ◽

Captive Breeding ◽

Natural Populations ◽

Water Vole ◽

Captive Population ◽

Arvicola Amphibius ◽

Relationship Of ◽

The Impact

The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species.

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The Impact of Anglicizing Former German-Language Psychology Journals on Authorship and Citation Frequencies

European Psychologist ◽

10.1027/1016-9040/a000074 ◽

2012 ◽

Vol 17 (3) ◽

pp. 190-198 ◽

Cited By ~ 2

Author(s):

Günter Krampen ◽

Thomas Huckert ◽

Gabriel Schui

Keyword(s):

Side Effects ◽

English Language ◽

General Trend ◽

Native Language ◽

Impact Factors ◽

German Language ◽

Journal Articles ◽

Number Of Citations ◽

The Impact ◽

Number Of Authors

Exemplary for other than English-language psychology journals, the impact of recent Anglicization of five former German-language psychology journals on (1) authorship (nationality, i.e., native language, and number of authors, i.e., single or multiple authorships), (2) formal characteristics of the journal (number of articles per volume and length of articles), and (3) number of citations of the articles in other journal articles, the language of the citing publications, and the impact factors (IF) is analyzed. Scientometric data on these variables are gathered for all articles published in the four years before anglicizing and in the four years after anglicizing the same journal. Results reveal rather quick changes: Citations per year since original articles’ publication increase significantly, and the IF of the journals go up markedly. Frequencies of citing in German-language journals decrease, citing in English-language journals increase significantly after the Anglicization of former German-language psychology journals, and there is a general trend of increasing citations in other languages as well. Side effects of anglicizing former German-language psychology journals include the publication of shorter papers, their availability to a more international authorship, and a slight, but significant increase in multiple authorships.

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