scholarly journals Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 23
Author(s):  
Oxana Khapilina ◽  
Ainur Turzhanova ◽  
Alevtina Danilova ◽  
Asem Tumenbayeva ◽  
Vladislav Shevtsov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endemic Species ◽  
Biological Diversity ◽  
Natural Populations ◽  
Subsequent Development ◽  
Dna Profiling ◽  
Primer Binding Site ◽  
Anthropogenic Factors ◽  
Habitat Specificity ◽  
Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

scholarly journals Differential relationships between habitat fragmentation and within-population genetic diversity of three forest-dwelling birds

2014 ◽  
Author(s):  
Benjamin Zuckerberg ◽  
Matt Carling ◽  
Roi Dor ◽  
Elise Ferree ◽  
Garth Spellman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Forest Fragmentation ◽  
Habitat Loss ◽  
Population Genetic ◽  
Biological Diversity ◽  
Haplotype Diversity ◽  
Habitat Specificity ◽  
Fragmented Landscapes ◽  
Population Genetic Diversity

Habitat fragmentation is a major driver of environmental change affecting wildlife populations across multiple levels of biological diversity. Much of the recent research in landscape genetics has focused on quantifying the influence of fragmentation on genetic variation among populations, but questions remain as to how habitat loss and configuration influences within-population genetic diversity. Habitat loss and fragmentation might lead to decreases in genetic diversity within populations, which might have implications for population persistence over multiple generations. We used genetic data collected from populations of three species occupying forested landscapes across a broad geographic region: Mountain Chickadee (Poecile gambeli; 22 populations), White-breasted Nuthatch (Sitta carolinensis; 13 populations) and Pygmy Nuthatch (Sitta pygmaea; 19 populations) to quantify patterns of haplotype and nucleotide diversity across a range of forest fragmentation. We predicted that fragmentation effects on genetic diversity would vary depending on dispersal capabilities and habitat specificity of the species. Forest aggregation and the variability in forest patch area were the two strongest landscape predictors of genetic diversity. We found higher haplotype diversity in populations of P. gambeli and S. carolinensis inhabiting landscapes characterized by lower levels of forest fragmentation. Conversely, S. pygmaea demonstrated the opposite pattern of higher genetic diversity in fragmented landscapes. For two of the three species, we found support for the prediction that highly fragmented landscapes sustain genetically less diverse populations. We suggest, however, that future studies should focus on species of varying life-history traits inhabiting independent landscapes to better understand how habitat fragmentation influences within-population genetic diversity.

scholarly journals DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10674
Author(s):  
Oxana Khapilina ◽  
Olesya Raiser ◽  
Alevtina Danilova ◽  
Vladislav Shevtsov ◽  
Ainur Turzhanova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Biological Diversity ◽  
Vegetative Reproduction ◽  
Natural Populations ◽  
Mobile Genetic Elements ◽  
Ice Age ◽  
Conservation Strategy ◽  
Relict Species ◽  
Genetic Elements

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

scholarly journals iPBS polymorphism of rare relict and endangered Allium species growing on the territory of Kazakhstan Altai

2020 ◽  
Vol 200 (9) ◽  
pp. 63-73
Author(s):  
Olesya Rayzer ◽  
Oksana Hapilina
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Dna Amplification ◽  
Practical Significance ◽  
Primer Binding Site ◽  
Natural Habitats ◽  
Allium Species ◽  
Different Populations ◽  
High Level

Abstract. The purpose of the study. The estimation of genetic polymorphism of Kazakhstan populations of rare relict and endemic Allium species. The novelty of the research is the use of the modern molecular genetic iPBS (Inter- Primer Binding Site Polymorphism) method of DNA amplification to assess the genetic diversity of different populations of Allium sp., collected in their natural habitats in the Kazakhstan Altai. Methods. Samples of medicinal relict and endangered species A. ledebourianum, A. altaicum, A. microdiction were collected in the places of their natural growth in the territory of the Kazakhstan Altai. DNA was isolated from 3–5 day sterile seedlings using lysis STAB buffer with RNaseA. PBS primers were used to assess the genetic diversity of different populations of Allium spp. The amplification results obtained using different PBS primers were evaluated in the GenAlex 6.5 macro program for Excel. Results. The polymorphism of 16 genotypes of the rare relict and endangered Allium sp. was analyzed using 7 PBS primers. Clearly distinguishable amplicons were obtained, the number of which varied depending on the primer used. The dendrogram, based on UPGMA analysis, grouped the studied genotypes into 2 main clusters, one of which included samples from the A. altaicum population, and the second cluster included samples from the A. ledebourianum population. A. microdiction represented by one sample did not enter any cluster, and formed a basal branch in the dendrogram. The results of the study have revealed a high degree of iPBS polymorphism and genetic diversity in rare relict and endangered Allium sp. Practical significance. The use of the molecular genetic iPBS method allows to identify a high level of polymorphism, which can serve as a basis for the identification of various genotypes of the Allium sp., which will significantly supplement traditional preservation methods of natural populations of this genus.

scholarly journals Developing a monitoring program of genetic diversity: what do stakeholders say?

2021 ◽  
Author(s):  
Rea Pärli ◽  
Eva Lieberherr ◽  
Rolf Holderegger ◽  
Felix Gugerli ◽  
Alex Widmer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Online Survey ◽  
Biological Diversity ◽  
Stakeholder Analysis ◽  
Natural Populations ◽  
Monitoring Program ◽  
Convention On Biological Diversity ◽  
Term Survival ◽  
Network Analyses ◽  
National Monitoring

AbstractGenetic diversity is a fundamental component of biological diversity, and its conservation is considered key to ensure the long-term survival of natural populations and species. National and international legislation increasingly mandates a monitoring of genetic diversity. Examples are the United Nation’s Convention on Biological Diversity (CBD) Aichi target 13 and the current post-2020 negotiations to specify a new target for maintaining genetic diversity. To date, only a few pilot projects have been launched that systematically monitor genetic diversity over time in natural populations of a broad variety of wild species. The Swiss Federal Office for the Environment mandated a feasibility study in 2019 for implementing a national monitoring of genetic diversity in natural populations. To obtain information on whether stakeholders are interested in such a systematic monitoring, what they would expect from such a monitoring and where they see respective caveats, we conducted an online survey, which 138 (42% of those surveyed) Swiss stakeholders answered. We find that Swiss stakeholders are generally aware of the lacking evidence regarding the status of genetic diversity in wild populations and species. Accordingly, most stakeholders are interested in a monitoring of genetic diversity and see opportunities for the application of its results in their work. Nevertheless, stakeholders also expressed concerns regarding financial resources and that the results of a genetic diversity monitoring program would not benefit conservation practice. Our findings highlight the importance of stakeholder engagement and demonstrate the value of a detailed stakeholder analysis prior to developing and implementing a genetic diversity monitoring program. A powerful tool for examining the constellation and interactions of the different stakeholders are social network analyses (SNAs). Finally, it is particularly important to communicate transparently about the possibilities and limitations of a genetic diversity monitoring program as well as to closely involve stakeholders from the beginning to increase the acceptance of genetic diversity monitoring and facilitate its implementation.

scholarly journals Influence of forest technical measures on the reproduction of rare phytorification in forest ecosystems of the Forest Steppe of Ukraine

2021 ◽  
Author(s):  
V Shevchyk ◽  
I. Tymochko ◽  
І. Solomakha
Keyword(s):  
Forest Ecosystems ◽  
Biological Diversity ◽  
Negative Impact ◽  
Subsequent Development ◽  
Steppe Zone ◽  
Anthropogenic Factors ◽  
Forest Steppe ◽  
Forest Plantations ◽  
The Creation ◽  
Protective Forest

An interesting aspect is the issue of acquiring natural features by artificially created tree plantations on the territory of the forest steppe zone of Ukraine. This paper analyzes the conditions of emergence and formation of new habitats rare plant species populations in different types of artificial trees and shrubs of the Forest Steppe of Ukraine. Complexes of natural and anthropogenic factors of necessary conditions creation for realization of this process are defined. The peculiarities of the negative impact of various economic measures on the reduction of the number of individuals of sozophyte plants and even the disappearance of some of their populations are reflected. The peculiarities of the negative impact of various economic measures on the reduction of the sozophyte plants individuals’ number and even the disappearance of some of their populations are reflected. To improve the protection of sozophytes in the forests of the forest steppe zone, it is advisable to review the implementation of certain methods of forest management measures. In particular, it is necessary to completely ban continuous felling in forests of natural origin and the allocation of biofields for natural reforestation. To improve the condition of forest coenoses of protective plantations, including field protective forest strips, it is necessary to conduct a series of experiments with the subsequent development of technology for their coenotic correction in order to increase the general ecological, including phytososological, significance. The implementation of a set of phytomeliorative measures in the creation of protective forest plantations to some extent will help prevent possible climate change, local disasters and will have a positive impact on the processes of crop formation. The creation of sustainable forest plantations will allow the application of environmental protection measures using the regulatory and protective functions of forest ecosystems. Compliance with all these conditions will contribute to the manifestation of various environmental measures for the development and conservation of biological diversity.

scholarly journals Genetic Diversity of Plant Species in Glacier National Park: Implications for Management

1990 ◽  
Vol 14 ◽  
pp. 55-58
Author(s):  
Thomas Mitchell-Olds
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
National Park ◽  
Biological Diversity ◽  
Management Strategies ◽  
Natural Populations ◽  
Glacier National Park ◽  
Isozyme Electrophoresis ◽  
Quantitative Genetic ◽  
Local Environments

Glacier National Park (GNP) is responsible for the management and preservation of biological diversity in the natural populations of plants and animals occurring within its boundaries. Information on existing levels of genetic variation within and among populations is a prerequisite for developing management strategies to maintain genetic diversity and to perform revegetation activities. We are using two methods to assess levels of genetic diversity and differentiation among populations: quantitative genetic analysis and isozyme (electrophoresis) analysis. To examine whether patterns of genetic variation and adaptation to local environments require that sites be revegetated with plants collected from nearby natural populations, or alternatively, whether transplants could be obtained from other sources; we are focussing on three experimental areas: 1. quantitative genetics; 2. electrophoresis, and 3. natural selection.

Urbanization of fauna on the example of marsh frog (Pelophylax ridibundus)

2015 ◽  
Vol 26 (3-4) ◽  
pp. 116-123
Author(s):  
A. P. Korzh ◽  
T. V. Zahovalko
Keyword(s):  
Urban Areas ◽  
Cognitive Modeling ◽  
Negative Impact ◽  
Natural Populations ◽  
Cellular Level ◽  
Anthropogenic Factors ◽  
Migration Routes ◽  
Corrective Effect ◽  
The Impact ◽  
The City

Recently, the number of published works devoted to the processes of synanthropization of fauna, is growing like an avalanche, which indicates the extreme urgency of this theme. In our view, the process of forming devices to coexist with human and the results of his life reflects the general tandency of the modern nature evolution. Urbanization is characteristic for such a specific group of animals like amphibians, the evidence of which are numerous literature data. Many researchers use this group to assess the bioindicative quality of the environment. For this aim a variety of indicators are used: from the cellular level of life of organization up to the species composition of the group in different territories. At the same time, the interpretation of the results is not always comparable for different areas and often have significantly different interpretations by experts. Urban environment, primarily due to the contamination is extremely aggressive to amphibians. As a consequence, the urban populations of amphibians may be a change in the demographic structure, affecting the reproductive ability of the population, the disappearance of the most sensitive species or individuals, resizing animals, the appearance of abnormalities in the development, etc. At the same time play an important amphibians in the ecosystems of cities, and some species in these conditions even feel relatively comfortable. Therefore, it is interesting to understand the mechanisms of self-sustaining populations of amphibians in urban environments. To assess the impact of natural and anthropogenic factors on the development of amphibian populations were used cognitive modeling using the program Vensim PLE. Cognitive map of the model for urban and suburban habitat conditions were the same. The differences concerned the strength of connections between individual factors (migration, fertility, pollution) and their orientation. In general, factors like pollution, parasites, predators had negative impact on the population, reducing its number. The birth rate, food and migration contributed to raising number of individuals. Some of the factors affected on the strength to of each other as well: the majority of the factors affected the structure of the population, had an influence on the fertility. Thanks to it the model reflects the additive effect of complex of factors on the subsequent status of the population. Proposed and analyzed four scenarios differing strength and duration of exposure. In the first scenario, a one-time contamination occurs and not subsequently repeated. The second and third scenario assumes half board contamination, 1 year (2 scenario) and two years (scenario 3). In the fourth scenario, the pollution affected the population of amphibians constantly. In accordance with the results of simulation, much weaker than the natural populations respond to pollution - have them as an intensive population growth and its disappearance at constant pollution is slow. Changes to other parameters of the model showed that this pollution is the decisive factor -only the constant action leads to a lethal outcome for the populations. All other components of the model have a corrective effect on the population dynamics, without changing its underlying trand. In urban areas due to the heavy impact of pollution maintaining the population is only possible thanks to the migration process – the constant replenishment of diminishing micropopulations of natural reserves. This confirms the assumption that the form of existence metapopulations lake frog in the city. In order to maintain the number of amphibians in urban areas at a high level it is necessary to maintain existing migration routes and the creation of new ones. Insular nature of the placement of suitable habitats in urban areas causes the metapopulation structure of the types of urbanists. Therefore, the process of urbanization is much easier for those species whicht are capable of migration in conditions of city. In the initial stages of settling the city micropopulationis formed by selective mortality of the most susceptible individuals to adverse effects. In future, maintaining the categories of individuals is provided mainly due to migration processes metapopulisation form of the species of existence is supported). It should be noted that the changes in the previous levels are always saved in future. In the case of reorganizations of individuals we of morphology can assume the existence of extremely adverse environmental conditions that threaten the extinction of the micropopulations. 

scholarly journals The Patterns and Puzzles of Genetic Diversity of Endangered Freshwater Mussel Unio crassus Philipsson, 1788 Populations from Vistula and Neman Drainages (Eastern Central Europe)

Life ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 119
Author(s):  
Adrianna Kilikowska ◽  
Monika Mioduchowska ◽  
Anna Wysocka ◽  
Agnieszka Kaczmarczyk-Ziemba ◽  
Joanna Rychlińska ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Scales ◽  
Freshwater Mussel ◽  
Its Region ◽  
Strong Relationship ◽  
Mantel Test ◽  
Freshwater Ecosystems ◽  
Hierarchical Organization ◽  
Anthropogenic Factors

Mussels of the family Unionidae are important components of freshwater ecosystems. Alarmingly, the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species identifies almost 200 unionid species as extinct, endangered, or threatened. Their decline is the result of human impact on freshwater habitats, and the decrease of host fish populations. The Thick Shelled River Mussel Unio crassus Philipsson, 1788 is one of the examples that has been reported to show a dramatic decline of populations. Hierarchical organization of riverine systems is supposed to reflect the genetic structure of populations inhabiting them. The main goal of this study was an assessment of the U. crassus genetic diversity in river ecosystems using hierarchical analysis. Different molecular markers, the nuclear ribosomal internal transcribed spacer ITS region, and mitochondrial DNA genes (cox1 and ndh1), were used to examine the distribution of U. crassus among-population genetic variation at multiple spatial scales (within rivers, among rivers within drainages, and between drainages of the Neman and Vistula rivers). We found high genetic structure between both drainages suggesting that in the case of the analyzed U. crassus populations we were dealing with at least two different genetic units. Only about 4% of the mtDNA variation was due to differences among populations within drainages. However, comparison of population differentiation within drainages for mtDNA also showed some genetic structure among populations within the Vistula drainage. Only one haplotype was shared among all Polish populations whereas the remainder were unique for each population despite the hydrological connection. Interestingly, some haplotypes were present in both drainages. In the case of U. crassus populations under study, the Mantel test revealed a relatively strong relationship between genetic and geographical distances. However, in detail, the pattern of genetic diversity seems to be much more complicated. Therefore, we suggest that the observed pattern of U. crassus genetic diversity distribution is shaped by both historical and current factors i.e. different routes of post glacial colonization and history of drainage systems, historical gene flow, and more recent habitat fragmentation due to anthropogenic factors.

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