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Genetic Diversity - Science topic

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Does natural selection cause adaptation and can mutation increase genetic variation and relationship among evolutionary mechanisms and genetic diversity?
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Dr Loubna Youssar thank you for your contribution to the discussion
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How does population density affect organisms in an ecosystem and does a large population preserve genetic diversity more than a small population?
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When a population reaches a high density, there are more individuals trying to use the same quantity of resources. This can lead to competition for food, water, shelter, mates, light, and other resources needed for survival and reproduction.The increase in population increases the density, leading to scarcity of resources. This leads to competition in the ecosystem, which impacts survival and reproduction. If one animal's population increases, the population of animals that eat that animal might also increase. Increases in population aren't always good. Sometimes a population will grow too large for the environment to support. Other changes in limiting factors can cause a population to decrease. Human population growth impacts the Earth system in a variety of ways, including: Increasing the extraction of resources from the environment. These resources include fossil fuels, minerals, trees, water, and wildlife, especially in the oceans. Individuals make up a population; populations make up a species; multiple species and their interactions make up a community; and multiple species and their interactions make up ecosystems when you include the abiotic factors. Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction.Distribution is one way that genetic variation can be preserved in large populations over wide physical ranges, as different forces will shift relative allele frequencies in different ways at either end. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes, faster generation times and high rates of gene flow with other populations. Maintaining high genetic diversity allows species to adapt to future environmental changes and avoid inbreeding. Inbreeding, which happens when there are small, isolated populations, can reduce a species' ability to survive and reproduce.
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As above, I'm wondering what is the justification for removing monomorphic SNP loci for genetic diversity analysis?
Using a genome wide association study, I am analysing SNP data for a wide ranging animal species from multiple regions and want to be able compare diversity between regions.
Screening for monomorphic SNPS results in loss of up to 20% SNPs for some regions and <5% for others - is it reasonable to compare these data with monomorphs excluded?
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Hi Elisabeth,
I'm also thinking about this, I reckon that after filtering for monomorphic SNPs in the entire database, it makes sense to me to report the unique monomorphic SNPs per region/population/etc. For downstream analysis, I tried removing unique monom per region and only keeping the common polymorphic SNPs, but it feels like I'm "forcing" something here and losing valuable differences. Still not sure as I can't find much info about this.
Best,
Laura
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With the increasing need for sustainable agriculture and climate change resilience, how can plant breeders effectively incorporate complex traits such as drought tolerance, disease resistance, and high yield into crop varieties while maintaining genetic diversity?
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By computer modelling those parameters and observing yield in response to varying combinations of traits :)
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I am a post graduate student in a NIgerian University. My project is on the genetic diversity of the pathogen responsible for decay in Cassava. Since the study is pretty new to me, i need guide on the right methodology for the research.
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Gbolabo Olaitan Onasanya thank you very much for this answer, this will be considered. again, thank you.
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Pre breeding is essential for linking genetic diversity arising from wild relatives and other unimproved materials to utilization in crop improvement. It is the main link between the germplasm conservation and its use in plant breeding for developing new varieties.
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Pre-breeding aims to isolate desired genetic traits (e.g. disease resistance) from unadapted material like CWR and introduce them into breeding lines that are more readily crossable with modern, elite varieties. Pre-breeding broadens the elite genepool by re-capturing lost beneficial genetic diversity. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this.
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Pre breeding is essential for linking genetic diversity arising from wild relatives and other unimproved materials to utilization. It is the main link between the germplasm conservation and its use in plant breeding. The major challenges of pre-breeding are lack of characterization, evaluation of genetic diversity, documentation of data; inter species relationship and strong breeding program and funding sources.
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Prebreeding has become quintessential in the present world of breeders. The improved lines have either been utilised to full extent or exhausted due to non conservation of the germplasm. Morphological diversity is to be used for developing mitigating new challenges.
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Inbreeding depression occurs when closely related individuals are bred together over multiple generations, leading to a decline in the overall fitness and performance of the offspring. In plant breeding, inbreeding depression is a concern because it can result in reduced vigor, lower yields, increased susceptibility to diseases, and other undesirable traits. To counteract inbreeding depression, breeders often employ techniques like selective outcrossing or hybridization to introduce genetic diversity and restore vigor to the breeding population.
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The concept of inbreeding depression refers to the decline in the overall fitness and performance of offspring when closely related individuals, such as siblings or parent-offspring, are bred together over multiple generations. Inbreeding depression occurs due to the increased expression of harmful or deleterious recessive alleles that are normally masked in genetically diverse populations.
In plant breeding, inbreeding depression has significant implications. When plants are bred within a small, genetically similar population, the frequency of homozygous genotypes increases. Homozygosity can expose recessive alleles that may be associated with reduced vigor, impaired growth, lower fertility, susceptibility to diseases, or other undesirable traits. As a result, inbred plants often exhibit decreased overall fitness and performance compared to their genetically diverse counterparts.
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How does genetic diversity occur and why is it important and genetic variation important to a population?
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Dear Susanta Roy thank you for your contribution to the discussion
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How does genetic variability support the importance of the role of genetic diversity and why is genetic variation important in living things?
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Dear Susanta Roy thank you for your contribution to the discussion
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Why is genetic diversity important and how and why do we measure biodiversity?
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Genetic diversity can be measured directly by looking at genes and chromosomes or indirectly by looking at physical features of the organisms and assuming they have a genetic basis. Using the genetic code is arguably the strongest method of measuring biodiversity as it is looking at the building blocks of life. All the biological data and variation that makes life on our planet work is encoded in DNA. This is known as genetic diversity. It strengthens the ability of species and populations to resist diseases, pests, changes in climate and other stresses. Hence, due to genetic diversity, the varieties that are susceptible, die and the ones who can adapt to changes will survive. Genetic diversity is important for a healthy population by maintaining different varieties of genes that might be resistant to pests, diseases or other conditions. Genetic Diversity refers to the range of different inherited traits within a species. In a species with high genetic diversity, there would be many individuals with a wide variety of different traits. Genetic diversity is critical for a population to adapt to changing environments. Biodiversity is increased by genetic change which increases a species' ability to adapt. Conversely, a population cannot evolve to adapt to environmental change without genetic diversity
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Can we measure biodiversity and how is genetic diversity a measure of biodiversity?
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Animals, plants and ecosystems, we have well established measures of biodiversity, such as the Living Planet Index, which are used in large periodic reports of the state of life on Earth, such as the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) Global Assessment. Genetic diversity can be measured directly by looking at genes and chromosomes or indirectly by looking at physical features of the organisms and assuming they have a genetic basis. Using the genetic code is arguably the strongest method of measuring biodiversity as it is looking at the building blocks of life.
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How the loss of genetic diversity affects the environment andgenetic variation important for a population's success in an environment?
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Genetic variation describes naturally occurring genetic differences among individuals of the same species. This variation permits flexibility and survival of a population in the face of changing environmental circumstances. Sometimes the environment changes a gene either its DNA sequence or its activity level. Either of these effects can change the proteins that are made from a gene, which in turn affects traits. Some harmful environmental factors can change a gene's nucleotide sequence. For example, UV radiation can break DNA strands. All the biological data and variation that makes life on our planet work is encoded in DNA. This is known as genetic diversity. It strengthens the ability of species and populations to resist diseases, pests, changes in climate and other stresses. Genetic variations that alter gene activity or protein function can introduce different traits in an organism. If a trait is advantageous and helps the individual survive and reproduce, the genetic variation is more likely to be passed to the next generation. Individuals in a population are naturally variable, meaning that they are all different in some ways. This variation means that some individuals have traits better suited to the environment than others. Individuals with adaptive traits that give them some advantage are more likely to survive and reproduce. Major causes of variation include mutations, gene flow, and sexual reproduction. DNA mutation causes genetic variation by altering the genes of individuals in a population. Gene flow leads to genetic variation as new individuals with different gene combinations migrate into a population. The genetic diversity of a species is always changing. No matter how many variants of a gene are present in a population today, only the variants that survive in the next generation can contribute to species diversity in the future. Once gene variants are lost, they cannot be recovered. Genetic variation is maintained in most populations through the periodic introduction of new alleles or new allele frequencies from outside the population. If genetic diversity gets too low, species can go extinct and be lost forever. This is due to the combined effects of inbreeding depression and failure to adapt to change. In such cases, the introduction of new alleles can save a population. Maintaining high genetic diversity allows species to adapt to future environmental changes and avoid inbreeding. Inbreeding, which happens when there are small, isolated populations, can reduce a species' ability to survive and reproduce.Without genetic diversity, a population cannot evolve, and it cannot adapt to environmental change. Environmental change is now occurring on a global scale because of human activities, and many species will have to adapt to this change or experience an ever-increasing chance of extinction.
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Can inherited genetic variations be caused by environmental factors only & environmental factors could influence natural selection & increase genetic diversity?
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The genetic variability created by the mutation will be tested by natural selection, which determines what characteristics are inherited in a population over time. Environmental factors such as soil nutrients, temperature, water availability and light intensity influence the genetic and chemical diversity of plant populations. These environmental conditions can exert strong selection pressures; they could even determine the evolutionary course of plant populations. A number of environmental factors can impact natural selection. Climate, habitat type, available food, and a habitat's predators can all impact which traits will be selected. Sometimes the environment changes a gene either its DNA sequence or its activity level. Either of these effects can change the proteins that are made from a gene, which in turn affects traits. Some harmful environmental factors can change a gene's nucleotide sequence. For example, UV radiation can break DNA strands. Beneficial mutations are passed on and harmful mutations are eliminated as organisms adapt to changing environmental conditions and evolve. Genetic diversity is influenced by four events controlling evolution: mutation, genetic drift, gene flow, and natural selection. The environment creates selective pressure that is one of the driving factors in natural selection. Changes in the environment allow for some organisms to survive better than others within a species. Environmental factors, as related to genetics, refer to exposures to substances where we live or work behaviors that can increase an individual's risk of disease or stressful situations. Genetic variations that alter gene activity or protein function can introduce different traits in an organism. If a trait is advantageous and helps the individual survive and reproduce, the genetic variation is more likely to be passed to the next generation. As conditions change, natural selection favors one allele or genetic variant over another. Genes that can facilitate a range of different forms under different environments can also help an organism adapt to changing conditions. If the environment changes rapidly, some species may not be able to adapt fast enough through natural selection. Through studying the fossil record, we know that many of the organisms that once lived on Earth are now extinct. It strengthens the ability of species and populations to resist diseases, pests, changes in climate and other stresses. Gene variations underpin their capacity to evolve and their flexibility to adapt. In addition to demographic processes, ecological and environmental factors can also play a role in shaping genetic diversity patterns. Organisms are born with specific traits inherited from their parents, but the environment can influence them. In cases where food is limited, a typically massive animal may be skinny, or shade over a plant may cause it to be stunted in growth. Instead, most diseases are complex and stem from an interaction between your genes and your environment. Factors in your environment can range from chemicals in air or water pollution, mold, pesticides, diet choices, or grooming products.
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Does genetic diversity reduce extinction and genetically diverse populations more likely to survive changing environments?
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A species is more likely to survive if it is genetically diverse, because it has a variety of different possible adaptations. Genetic variation describes naturally occurring genetic differences among individuals of the same species. This variation permits flexibility and survival of a population in the face of changing environmental circumstances. Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. Genetic Diversity refers to the range of different inherited traits within a species. In a species with high genetic diversity, there would be many individuals with a wide variety of different traits. Genetic diversity is critical for a population to adapt to changing environments.The greater the genetic diversity within a species, the greater is the chance of that species to survive. Conversely, the lower the genetic diversity within a species, the lower is the chance of survival. This is because unfavorable traits, such as inherited diseases, may become widespread within a population. Populations with low genetic diversity may not be able to adapt to challenges such as changing environmental conditions, shrinking habitats or new diseases, which could put them at risk of disappearing. Genetic diversity of plants, animals and other living organisms is what enables them to survive and thrive in this world. The capacity of species to adapt to new circumstances, whether this is resource scarcity, a changing environment or other disturbances to their natural environment, depends on genetic diversity.
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We're performing genetic diversity studies using SSR and RAPD markers and we're done with the experiments, but we're finding it difficult to get this software for the data analysis.
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Dear Professor,
I think it is not available as open access. I can suggest another application if you, please reveal the purpose.
Thank You
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What is genetic diversity in an ecosystem and genetic diversity a measure of biodiversity and genetic diversity a level of biodiversity?
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Biodiversity is the variety of plants and animals inhabiting in an ecosystem. It includes species diversity, genetic diversity and ecosystem diversity. Genetic diversity is defined as genetic variability present within species. Genetic diversity can be measured directly by looking at genes and chromosomes or indirectly by looking at physical features of the organisms and assuming they have a genetic basis. Using the genetic code is arguably the strongest method of measuring biodiversity as it is looking at the building blocks of life. Biodiversity is usually explored at three levels - genetic diversity, species diversity and ecosystem diversity. These three levels work together to create the complexity of life on Earth. Genetic Diversity is the diversity of genetic characteristics within a species. All the biological data and variation that makes life on our planet work is encoded in DNA. This is known as genetic diversity. It strengthens the ability of species and populations to resist diseases, pests, changes in climate and other stresses. Genetic diversity is important because it gives species a better chance of survival. However, genetic diversity can be lost when populations get smaller and isolated, which decreases a species' ability to adapt and survive. Genetic diversity is the biological variation that occurs within species. It makes it possible for species to adapt when the environment changes. Genetic diversity is particularly important under rapid environmental change. Genetic diversity can be measured directly by looking at genes and chromosomes or indirectly by looking at physical features of the organisms and assuming they have a genetic basis. Using the genetic code is arguably the strongest method of measuring biodiversity as it is looking at the building blocks of life.
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Can ecosystem with a high degree of genetic biodiversity able to adapt to environmental changes & relationship between genetic diversity & ecosystem resilience?
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Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. Loss of genetic diversity could drive widespread loss of physiological versatility and ecological resilience, with flow-on effects cascading through to critical and potentially irreversible, changes to ecosystem structure and functioning.
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I need to determine genetic diversity of different fish populations and subpopulations
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It looks like you have many clearly differentiated populations. I'm not sure what you'd like interpreted and I'd need more context to comment properly. What is the data and what is your question?
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I have done the scoring, but still confused to how to initiate the next step? I have used RAPD and ISSR markers. Please let me know how to do it?
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For RAPD markers, the genetic background is not always known, so if you want to calculate some similarity index from gel images, I suggest scoring the bands as present or absent. The resulting data can be used to calculate e.g. a Jaccard index. If you need software support, I recommend MolMarker.
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CWR are important to assess genetic diversity and agro-biodiversity to better understand how this diversity is distributed across the regions.
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Crop wild relatives (CWR) provide genetic diversity that may not be available in current cultivated varieties. The novel genetic diversity within these wild species may be the building blocks that breeders need to improve productivity and quality of agricultural products. Crop wild relatives provide the opportunity to improve the productivity and resilience of agriculture. However, in the coming century, as population increases to over 9 billion and climate change intensifies, exacerbating the spread of crop pests and diseases, they may become indispensable. CWRs are gene pools; they have a variety of traits which can help in more efficient agriculture practices and more healthy production. They have trait diversity like drought tolerance, pest resistance that farmers and breeders can cross with domesticated crops to produce new varieties.
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Good evening.
I am doing my final project on grapefruit genetic diversity and constructing a phylogenetic tree by comparing two samples of c.maxima, 10 Citrus genus (NCBI results), and outgroups. The outgroup I chose was Zanthoxylum sp or Severinia buxifolia based on the references I had read.
I am doing phylogenetic tree construction using neighborhood joining and maximum likelihood methods with MEGA X. The results shown are different where the outgroup can be seen clearly separated from the ingroup with the Neighborhood joining method. Meanwhile, the out group was included in the in group when using the Maximum Likelihood method. Is this result reasonable? Or should I change the outgroup so that there is a possibility that the results of the two phylogenetic trees are the same?
Please advise.
Thank in advance
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Including an outgroup in phylogenetic tree construction is important because it helps to root the tree and determine the direction of evolution. The outgroup is chosen based on its evolutionary distance from the ingroup, meaning it is a taxon that is closely related to the ingroup but not a member of it. The inclusion of the outgroup can affect the placement of the other taxa in the tree, including its position within or outside of the ingroup.
The difference in results between the two methods you used, neighborhood joining and maximum likelihood, could be due to the different algorithms and assumptions used in each method. It is not uncommon for the placement of the outgroup to affect the position of the ingroup in the tree, and the results from each method should be evaluated and compared to each other and to the available literature to determine the most reasonable placement of the taxa.
If you are concerned about the placement of the outgroup and its effect on the results, you could try using a different outgroup that is more distantly related to the ingroup or choose a different method that may be less affected by the outgroup. However, it is important to keep in mind that the choice of outgroup and method should be based on sound evolutionary and statistical principles.
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Hi all! I performed an AMOVA analysis with SSR markers in poppr R-package with three fungal pops (n=60, 30 and 21). My stratification levels are region (continent) and origin (Countries). DAPC, MSN and Differentiation index (Djost) showed clear differentiation at a region and origin levels although AMOVA is not significant at region level. Any information will be helpfull! Thanks!
Ignacio
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Absolutely delighted to do so. Let me know if you have any other questions.
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I'm interested in exploring the bottleneck history of an endangered population whose genetics has been previously sampled using nuclear and mtDNA. However, this population has extremely low genetic diversity, with 2 haplotypes between 36 sampled individuals. I've been unable to find results using such samples alone through coalescent modeling (i.e. Bayesian Skyline) likely due to the homogeny. As a work-around to give models some diversity to work with, would it be possible to add samples of an outgroup population that's closely related to my study population (likely diverged ~1 million years ago or less) to find any meaningful bottleneck information?
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You can't do much with two haplotypes and another species as an outgroup; you should consider looking up old museum and archaeological materials on your animal of study to genotype them and learn how variability has changed over time.
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i am trying to do genetic diversity analysis (allele frequency, PIC, Nei genetic diversity and shanon information index etc..). in my data some locus have 1 alleles other have 2, 3 and 4 alleles per locus. when i used Genalex it analyze only Binary and data have locus with two alleles only.
Thank you all!
Best Regards,
Haftom
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please let me know if u solved the issue
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I have done genotyping by sequencing on phythopathogenic fungi. I would like to calculate the genetic diversity indices (diversity index (h), unbiased diversity index (uh), and Shannon’s information index (I)) . However, I have more than 8,000 SNPs, which does not allow me to use GeneAlEx 6.41 . Do you know of any other software that I can use to make my calculations from my VCF files?
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I am not sure if it will calculate the exact indices you mentioned, but I have used vcftools (https://vcftools.github.io/index.html) to calculate measures of genetic diversity for that many SNPs before.
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I am just wondering since markers are usually used to measure genetic diversity.
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It depends on the level and what you mean by genetic diversity. Within a single organism? No. Within a population? No. Within a species? Normally not. Between species - yes, but that would be genetic diversity in the sense of species diversity.
Cheers
Konrad
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I would like to interpret the molecular diversity using the parameter nucleotide diversity (pi). The lowest value of Pi that I have is 0.00099 and the highest one is 0.02292. However, I have no reference to interpret these values whether it was considered as low, moderate, or high diversity? Do you know how to interpret these values?
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It surely depends on what type and range of organisms you are studying. The diversity we observe in HIV-1 in one single infected individual over ten years is greater than the diversity we observe between different species of insects or mammals over millions of years. The diversity between viruses today in the global SARS-CoV-2 pandemic varies with time, depending on whether two major lineages such as Delta and Omicron are co-circulating or Omicron has taken over and delta died out.
The diversity in insect or birds or shellfish is different than the diversity in mammals. You should compare the values you have in your organism to the values from other similar organisms.
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Recently, I have worked on genetic diversity analysis in mango genotypes using SSR markers. I can do it well as it is diploid. However, I have a question in my mind. If I worked on the triploid or tetraploid organism for genetic diversity analysis using SSR markers, how I count allele bands in gel image and make input files for GeneAlex, Darwin and other statistical software.?
If anybody worked with the triploid and more allelic organisms, please help me.
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don't get confused with ploidy level and multiple allele. traits exhibition depends on allelomorph of candidate gene not on its ploidy level.
solution for your confusion is go for binary coding (presence or absence) in Darwin.
ex. for scoring
sample Primer 1 Primer 2
210 220 250 310 320 350
1 1 0 1 1 1 1
2 1 1 1 1 1 1
3 1 1 1 0 1 1
similarly in case GenAlEx (based on band weightage)
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I am wondering are there are any papers comparing the genetic diversity open pollinated cultivar vs an inbred lines, in naturally cross pollinating crop species such as corn and onions?
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Dear Brandon,
I hope this article will be of help for you. Best regards,
Noemi
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I'm working on the genetic diversity of livestock populations. I have used the Molkin software in my research, and I would like to use it again. Unfortunately, I can't download it from this website:
I need it urgently.
Thank you in advance for your cooperation.
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Hello everybody, im currently writing my bachelor degree project, and im working with DNA polimorfism on plume moths (Pterophoridae) with two genera, theta, pi, hd, and S, my question is, how can i know where those values, for instance for tetha pi and hd are high or low? which crireria do i have to know? is there teoric fundament that explains a scale between 0-1?
my values for pi are : 0.015 and 0.08
for theta are: 0.015 and 0.029
and hd are : 0.833 and 0.892
i have read a lot of papers and they catalogue those values as low, but dont know with which criteria.
thank you so much for helping.
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Thank you so much for your answer Professor
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Which software we can use to prepare circular dendrogram from Phenotypic Data (Morphological Data)? Please give your comments with name and link of software, if possible. I shall be thankful to you.
Regards
Parmeshwar
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See if the attached screenshot paper is of help to you. Best wishes, David Booth
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Good day everyone, I am currently carrying out my final year project about the analysis of genetic diversity status of Malin sheep. However, I am facing some problems when using the Powermarker software. The result I get when using Powermarker software is the PIC of each individual instead of each marker. I have no idea in how to modify my data as an input to run in Powermarker software in order to get the PIC for each marker. Would anyone mind to do me a favor in correcting my format? It would really help me out in my final year project.
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Dear shi
You should be using Arlequin program Pop gene program to calculate PIC
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Hello Community,
Regarding total heterozygosity, I'm thinking 0.1 means moderate to higher genetic diversity?
I think I understand my Fst results ranging from 0.05 - 0.08, meaning low to moderate differentiation/structure between populations. Its just that all of my p-values are 0.001. Does this mean I have an insufficient amount of heterozygotes in my sample size?
PLEASE help me!
Statistic Value Std.Dev. c.i.2.5% c.i.97.5% Description
Num 1.950 0.007 1.935 1.963 Number of alleles
Eff_num 1.153 0.007 1.139 1.169 Effective number of alleles
Ho 0.109 0.005 0.099 0.119 Observed Heterozygosity
Hs 0.108 0.004 0.100 0.117 Heterozygosity Within Populations
Ht 0.115 0.005 0.106 0.124 Total Heterozygosity
H't 0.117 0.005 0.108 0.126 Corrected total Heterozygosity
Gis -0.001 0.018 -0.036 0.034 Inbreeding coefficient
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Heterozygosity is a measure of variability (diversity). Under no dominance situation, a population has maximum variability for a biallelic gene if the gene frequency is 0.5 (heterozygosity=0.5). In your case, heterozygosity is extremely low, and therefore, the diversity is very low.
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I have to study the genetic diversity among the accessions of millets using SSR markers, so can I use the boiling lysis method for DNA extraction instead of CTAB.
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Anoop Singh This is a method that we used for 20 years. Sorry, there is no reference for it.
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Which new/modern softwares are being used for SSR analysis ? i mean for genetic diversity, to estimate inbreeding or out breeding guess of population in plants
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All of what colleagues wrote from the programs are effective and good at parsing SSR
And I think the best modern software is STRUCTURE
Mega and Power Marker
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Hi, I am not really sure if this question is valid nor makes any sense.
But for example we have a single (imaginary) species, let's say Pikapika pii, and determined its genetic diversity. PCA and STRUCTURE clustering showed three groups, GRP1, GRP2, and GRP3.
My question is, can I treat these three groups as "separate species" and use it to run a multispecies SDM, or run an ensemble of single species SDM, or this is not valid/possible at all.
I would appreciate any help/correction with this thought. If possible, you can also refer publications that I can read, or experts that I can directly consult/talk with.
Thank you so much for your time and help.
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John Paul Manamtam Payopay : Yes, if you prepare data.
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I am looking for a laboratory, either a research facility or a commercial lab which can undertake Y chromosome analysis.
I am in New Zealand. I have hair samples. Some of the 'subjects' are dead so blood from these stallions is not possible.
This is for a wider project which is looking at genetic diversity within a minority breed.
Thank you.
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I am developing a phylogeography workflow and I need PERMUT cpSSR to compute NST and GST for mitochondrial Cytochrome c Oxidase (COI) haplotypes so that I can test for genetic differentiation between populations. Unfortunately, I haven't found any functional Linux OS link to this tool. The links i have tried include those found here:
Even a GAP package - https://www.gap-system.org/Manuals/pkg/permut-2.0.3/doc/chap0.html - which is not a good option.
(III) https://prodinra.inra.fr/?locale=en#!ConsultNotice:255707 - works but only a .exe file is available.
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Hi Hernan,
How you prepared the input file for PERMUT? do you have any example file?
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I am working on genetic diversity by RAPD. Can someone please provide me any manual/tutorial to analyze the RAPD binary data using POPGENE software?
Thank you very much!
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Thank you very much, I have sent you some queries.
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Hello everyone,
I am interested to use mitochondrial marker cytochrome b to assess the fish diversity. Can this marker be used if I am interested to assess the interspecific variations among different fish species?
Thank you!
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Whether this gene (or any gene) is appropriate for your study must be determined empirically and tends to be taxon-specific: for example, there is little variation within populations in the North American darters (Percidae), but fixed differences are common between populations; conversely, there is enough variation in many of the cyprinid species I have worked with. Note that Cytochrome b was (and is still) used intensively in North American Ichthyology since the early 1990s - and this literature would provide a very useful set of references to put your data in context. The more prominent studies using cytb were phylogeographic in nature (differences among conspecific populations), although some (including myself) have used cytb for intrapopulational work when appropriate. Note that much of the variation within species will be at the third codon position.
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I am planning to conduct a genetic diversity & population structure study in African zebu cattle. I will use 77k SNP markers to genotype the population. What would be your though about ideal sample size?
Thanks
A. Ali (PhD)
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Genotyping and Quality Control
ORIGINAL RESEARCH article
Front. Genet., 10 October 2018 | https://doi.org/10.3389/fgene.2018.00438
Samples were genotyped at Geneseek (Neogen Corporation, Nebraska, United States) using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array consisting of 150,000 SNPs, while SNPs for the reference breeds had been genotyped with the Illumina HD Bovine (777K SNPs) array. The SNPs in GGP array were optimised for use in dairy cattle having the most informative SNPs from Illumina Bovine 50k and 770k chips and additional variants known to have a large effect on disease susceptibility and performance. Genotype data quality control and cheques were carried out using PLINK v 1.9 (Purcell et al., 2007) and included removal of SNPs with less than 90% call rate, less than 5% minor allele frequency (MAF) and samples with more than 10% missing genotypes. Additional removal of SNPs not mapped to any chromosome left a total of 120,591 SNPs for analysis. Of the 299 animals, 12 failed the above outlined quality cheques and were removed from the analysis. Total genotyping rate in remaining samples was 0.991. The 120,591 SNPs used in the analysis covered 2516.25 Mb with an average distance of 22.67 kb between adjacent SNPs. The mean chromosomal length ranged between 42.8 Mb on BTA 25 and 158.86 Mb on BTA 1. The mean length of adjacent SNPs per chromosome ranged between 18.67 and 23.89 kb on BTA 14 and BTA 29, respectively. The linkage disequilibrium (LD) across the genome averaged 0.41. Private alleles, defined as variants which are segregating in only one population when evaluating multiple populations, were identified using a custom script in R. A total of 143 private variants, most (132) of which originated from the Rwanda cattle population were detected.
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Dear All,
I am interested in analyzing the genetic diversity of fish species using the mitochondrial D-loop region. Can you please suggest to me an article reporting universal primers to be used in different fish species?
Thank you very much.
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Vast literature is available.
Check the following. Good Luck!!
Universal Primers for Amplification of the Complete Mitochondrial
Control Region in Marine Fish Species
Length variation and sequence divergence in mitochondrial control region of Schizothoracine (Teleostei: Cyperinidae) species
Genetic diversity of mitochondrial control region (D-Loop) polymorphisms in Coilia ectenes taihuensis inhabiting Taihu Lake, China
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The project's budget is 12,000$ does not include buying any equipments except (for example) a genotyping analysis kit, I did a project for analyzing genetic diversity and selection signatures in four endangered cattle breeds using Illumina BovineHD kit but it was not satisfying, any suggestions? it is very important and crucial for my career.
Thanks in advance,
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You can also choose to study the diversity, evolutionary phylogenetics or domestication of a species. Large stractural varitions on genetic disease is also a choice.
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I am interested in assessing the inter- and intra-specific variations in fish using genetic markers. RAPD, cytochrome b, COI, microsatellites are mostly used for the evaluation of genetic variations. Can you please recommend me the best marker to be used.
Thank you.
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Good, definitely you can see variation exists. But need to check with different Primers as some of the primers do not show any variation.
Probably you might have started screening.
Good Luck!
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According to the http://popgen.net/soft/lositan/, I can't open the website. If someone knows how to download the LOSITAN software, a software of population genetic diversity.
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Dear Santos
Many thanks for your help, but I don't how to install lositan.
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Most of the literature used partial cytochrome b gene sequences for animal phylogenetic studies instead of the complete sequence. What is the reason behind this where full or complete cytochrome b gene sequence could explain more details?
Thank you very much!
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Hi!
You got the answer.
Simply to show/prove populations are phylogenetically distant from other species three regions of mtDNA viz. cytochrome b, 16S RNA and and D-loop regions will be used.
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Hii, please give me a complete guide or any material to analyse the Experimental data of RBD, CRD etc. to a find Genetic diversity, Character association, Path analysis & other Plant Breeding related experiments by using IBM SPSS
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Dear @Rajasekhar Chowdary Duddukur As suggested by @Suyash Bhimgonda Patil, I also suggest you to access online portal of OP Stat for analysis of genetic diversity, character association, path coefficient analysis and other plant breeding experimental data. It is useful, and I have used it several times.
Best wishes, AKC
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Iam currently working on my paper regarding the genetic diversity. I want to visualize my distance matrix data on a heat map, and I think it will be good as it is new for me. Is there anyone here can suggest me a software or online tools that I can use to generate a heat map to visualize distance matrix?
Thank you
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Thank you Ashraf M. T. Elewa , your suggestion help me a lot
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Hello everyone:
I'm looking for any method which allows to represent (or measure) spatially the genetic diversity in a given landscape (interpolation maybe). I ran EEMS (Petkova 2017) which infers patterns of gene flow among localities and I tried to ran AIS (Miller 2005) and despite this last one works well with microsats (13 loci) the program just crashed with DNA sequences (1500 bp) and SNP's (6000 biallelic), it seems this method was put aside and support for this is not longer available. Thanks in advance
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I conducted an SDS PAGE electrophoresis on wheat wild varieties to separate their glutenins and measure the genetic diversity of my sample. I only ran one electrophoresis. Can a genetic drift explain this low value ? The samples of T. monococcum I used are from different geographical origins and the heterozygosity found is still very low compared to other studies like the
Alvarez et al, in 2006 where they analysed 22 samples all originated from a small area in Spain ( He=0.252). How can I explain it ?
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Thank you so much ! Mauro Santos
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Hello, I have been looking for information regarding the declining use of the genetic diversity in the heirloom apples. Based on the work by Dr D. A. Noiton the majority of apple cultivars are at least partial derived from 5 cultivars. I am wondering what factors led to this to situation. Does anyone around know of any papers on this subject? I have been having trouble finding such information.
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Thank you Dr Brandon Singhfor this important question about the causes of loss of apple diversity.
In a 2010 report, the FAO estimated that three quarters of crop diversity had been lost between 1900 and 2000, stressing that "the genetic diversity of the plants we grow and consume - and related wild species - could be lost forever, thus compromising future food security ”.
In the specific case of apple and according to Kathrin Strohm (2013),
of the 30,000 apple varieties found all over the world only 30 are used and traded commercially. In the case of United States, it is clear that the biodiversity of apples has declined since the rise of industrial agriculture confirmed Rossi Anastropoulo (2014). Like any commercial industry, the focus in apple production remained fixed on profit. Therefore, in order to increase their crop yields, apple growers began to emphasize traits that would produce a good harvest and make transportation more feasible. These traits include disease resistance, hardiness, and durability, and the high importance placed on these characteristics slowly began to replace any focus on taste. The apple industry did not focus on selling apples that would taste best or even function well in the kitchen, but instead focused on varieties that would make the most money in the marketplace, added Anastropoulo (2014).
The same author mentionned that the apples have unique genetic codes, and once they have disappeared, they are gone forever, if not saved by apple detectives.
Despite the fact thant apple is the favorite fruit of Europeans, the number of commercial varieties collapsed in the 20th century. According to Kathrin Strohm (2013), only 13 apple varieties covered nearly 72 % of the entire European apple acreage in 2007.
In the special case of France, several causes mean that the diversity of apples has decreased. For example, it is said that "all misshapen, dull or stained apples are prohibited for sale". Thus, according to a president of a French association working to save local apples, France imports apples, beautiful and colorful, ruling out a large available local panel, not falling within these standards.
On the other hand, and still in the case of France, it is said that even if local varieties of apples appeal to consumers, tree growers are hardly interested in these old varieties. They want to tonnage, with apples sized, trees planted tightly, treated, suitable for irrigation, chemical thinning, conservation, and which produce every year.
These links could help you to take some informations that you need. Good luck.
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I am currently studying genetic diversity in a single population that consisted from different families (terms in tree improvement). But I assumed that I cannot use Nei's distance since I only use single population. The data was codominant markers and I use Shorea leprosula as species, kindly help.
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You might build a dendrogram/network based on allele shared distances (across codominant loci) for this single population. Maybe check the documentation of the R package "poppr" if this measurement for genetic distance is covered, it's nicely documented by the authors: https://grunwaldlab.github.io/Population_Genetics_in_R/index.html
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Copy number variations (CNVs) are the gains or losses of genomic regions which range from 500 bases upwards in size. Whole-genome studies have revealed the presence of large numbers of CNV regions in human and a broad range of genetic diversity among the general population. CNVs have been the focus of many recent studies because of their roles in human genetic disorders.
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CNVs are usually detected by techniques like chromosomal microarray and MLPA. But nowadays, advanced NGS technologies enable also CNV detection along with SNV detection. The Read depth and Pair end mapping/End-pair mapping are usual algorithms used for CNV detection using several statistical models or clustering approach. Markov model is also used. CNVs can affect 15% of the human genome and lengths can vary from 50 bp to 1 Mbp. They can also be intragenic. Decrease in copy at particular locus is deletion and increase in copy can be duplication or triplication..
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Dear all,
I would appreciate your help in getting the script on R with regards to count the private alleles number and frequency per location. I am working on the genetic diversity and population structure of isolates of Zymoseptoria tritici on wheat that were collected from different locations in Tunisia.
Thank you,
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thank you so much
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I am new to the research topic related to genetic diversity.
As I know, genetic diversity of a population can be quantified by haplotype diversity, nucleotides diversity, ... But, for example, I have two population one has haplotype diversity = 0.15 and another has haplotype diversity = 0.18, how can I compare this two populations in terms of genetic diversity level statistically?
Thanks in advance,
Linh
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Hi guys, Thanks for your concerns!
Even though this problem seems only happened to me due to my shallow knowledge in this field. But in case someone looking for the answer to a similar question. Below is my solution.
First, I calculated the haplotype diversity (and nucleotide diversity as well) for two of my populations (by using dnaSP). Then I got the mean values of Hd and their standard deviation values. Now, I can compare these two means by using tsum.test function in "BSDA" R package (t-test based on summary data). Below is the R code.
-----
install.packages("BSDA") #install package BSDA from CRAN
library(BSDA) #load package BSDA
tsum.test(mean.x = NULL, s.x = NULL, n.x = NULL, mean.y = NULL, s.y = NULL,
n.y = NULL, alternative = "two.sided", mu = 0, var.equal = FALSE,
conf.level = 0.95)
------
#Now, just put my values into the code line and RUN.
#mean.x = single number representing the mean of x population
# a single number representing the sample standard deviation for x
#n.x = a single number representing the sample size for x
# mean.y= a single number representing the sample mean of y
#s.y = a single number representing the sample standard deviation for y
#n.y = a single number representing the sample size for y
You can also do ANOVA based on summary data using (ind.oneway.second) function in ‘rpsychi’
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Which conservation strategy is more suitable for such a condition? Is it possible to change the IUCN status from endangered to lower risk?
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  • By following the IUCN guidelines mixing with local ethical values of that area.
  • By creating awareness and capacity building of the target population groups.
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Q is i m working on genetic diversity on a particular plant using issr markers. From genetic distance generated from genealex i have to use mega software to generate dendrogram but problem is while trying to open the saved mega file it doesnt work. Where is the error?is it regarding the way mega file is saved?or something else
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I'm certain I answered this question yesterday... You can use a GenAlEx genetic distance Tri-matrix file which needs to be converted to a MEGA file and saved as a *.meg file. Otherwise, MEGA will not open it...Try that Aijaz..
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Q is i m working on genetic diversity on a particular plant using issr markers. From genetic distance generated from genealex i have to use mega software to generate dendrogram but problem is while trying to open the saved mega file it doesnt work. Where is the error?is it regarding the way mega file is saved?or something else
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So you have a genetic distance file, (tri matrix or sq matrix?). Tick the Tri-matrix option then export as a MEGA file. You need to save it as a '.meg' file? If not, MEGA won't open it.. When selecting which tree to open, tick the genetic distance, Tri matrix option...
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Dear All,
I'm still relatively new to genetic diversity analysis of plant pathogens. I'd like to ask for suggestions on how to produce a dendrogram consisting of a combination of several genetic markers using the NTSYS software.
I'm using SSR and ISSR markers to analyse the diversity of various isolates of Fusarium wilt pathogen. I'm confident of generating a data matrix using a single genetic marker (using binary codes) and then producing a dendrogram. However, I'm not entirely sure how the data matrix would look like when more than one genetic markers are used.
May I ask for your suggestions on how a data matrix consisting of more than one genetic markers would look like?
Also, is it necessary to test the combinability of data sets from different genetic markers using partition homogeneity test using PAUP software? Does anyone have any experience in handling such test using this software?
Thank you in advance.
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Binary data matrix of two different markers has to be combined into one input file. Genelyx software is much easier to analyse. After getting result of Nei's genetic diversity of populations, u can transfer the data to mega for dendrogram construction.
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I am trying to establish a genetic monitoring program for an endangered fish species. The genetic diversity baseline was set 5 years ago. My study is a follow-up looking at impacts of a changing environment on the diversity of the species. I was wanting to run an AMOVA to look for any evidence of molecular variance explained by a temporal aspect.
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Hi. there,
I can suggest you to calculate the genetic variability within each locality or environmental condition, and then perform CCA. (Canonical correspondence analysis), which gives you an idea that how genetic diversity changes towards environmental conditions. CCA can be done by PAST software.
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I 'm working on genetic diversity analysis of crop plants with variable ploidy level using SSR markers. I suppose calculation of heterozygous frequencies and allelic dosage etc would be difficult for polyploids.So,is there any way to find Linkage disequilibrium for SSR markers.
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I might try this: This was developed at my university. It might help.
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genetic diversity tool analysis
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Lots of people asking me for a copy, so I uploaded one.
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I have mitochondrial DNA sequences to perform analysis of the genetic diversity and population structure of a fish species. What packages can I use on R? I estimate that I need to generate haplotype networks, PCA and diversity indexes.I thank you in advance for your contribution.
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Hello Sávio Guerreiro , the following article may help to address your question.
Best wishes.
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I would like to do genetic diversity analysis. Kindly suggest the name of important and free softwares for attractive NJ tree, dendrogram and PCA diagram?
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Dear Parmeshwar Sahu
I agree with suggestions given by Jetty Ramadevi. Moreover, you can also access Google; you may find what you desire!
Thank you!
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I have a dataset of 12 nuclear markers. Can I conduct population analysis (AMOVA, Fst) using Arlequin by multilocus sequence nuclear data? How can I prepare the input file?
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Hi Larissa
I'm having the same problem as you had, with 5 loci.
I tried to change the Data type: Standard, and use the haplotype data, not the sequence, but I'm not sure if it works the same with the sequence.
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I am investigating the genetic diversity of a few species over geographic distance via IBD. I have my input file in txt format, however, I have troubles specifying populations.
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Thank you so much Jose Alberto Lopez-Aleman for this input. I will surely try those. I was using IBD application. Thanks, again.
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Dear Colleagues,
I would be grateful if anyone could help me.
Our department got some Kitaibelia vitifolia x Kitaibelia balanse hybrid plants seeds to study few years ago. Unfortunately we don't have any pure Kitaibelia balansae line. In order to determine the genetic diversity/ gene pool of the population, i need pure parental line.
Thanking your help in advance.
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Dear Hicham,
I am so happy to see your message. I 'll be very grateful if you could send me some seed of K.balansae. Is it possible? If You interested in the study of the hybrid population, I can send you seeds as vel.
Best wishes!
Erika
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Are there specific packages to do these analyses in R?
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SNPhylo
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Hi everyone I am running Structure version 2.3.4 programme smoothly.But now I am facing problem that in Result folder I am getting only one file although I am setting k=2 to k=10 and iterations 5 with admixture model format. Earlier there was not any problem.
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Thanks a lot, Alberto Fameli and Jose Alberto Lopez-Aleman for valuable suggestions... With Regards
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Why ITS is better than any other technique s to identify genetic diversity In a population?
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Actually, ITS are not very useful for within species population diversity as it reveals mainly variation between species. It is so called barcoding markers used for species discrimination and identification. For population diversity you need more variable markers. They are selected depending on availability of genomic information for the species and costs and time required. If no genomic data available, arbitrary amplification methods like AFLP will work for diversity, but will not give information of genotypes (they are called dominant markers). Microsatellites (SSR, STR) require big work for their development, but if already discovered can be very convenient. Same thing with SNP, however they are best used in huge amounts, so usually require expensive microchip equipment and expendables. And the ultimate solution is whole genome sequencing, which is very expensive and demanding for time, skills and resources, but giving the most comprehensive variation data possible.
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As we can identify what kind of incorporation done by corona virus in host can be studied to imply treatment accordingly.
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Dear Pratik Pusadkar,
Hi,
Identifying the incorporation done in coronavirus genome can be achieved by tracking the epidemic done in the human population engaged on a worldwide scale. It can be able by tracking and comparing the mutation genes that are occurred within and between populations during the illness epidemic. Some molecular techniques such as SNP and NGS which can be able to identify the mutant gene even in only one nucleotide, are efficient for this purpose. The outcome cladogram from the phylogenetic analysis of worldwide populations can guide us to the origin formed diversity of coronavirus. Studying the genome of the virus at the source of diversity can be more effective in better identifying the structure of the virus.
Best,
Saeed
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I would like to know if anyone knows about other software other than Genemapper/Genamarker to visualise peaks, or whether there is any online platform available? Thanks in advance.
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I do agree with mr. Rileys suggestions. Or try to collaborate with a gp that hsa the ABI tools
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How can I explain it:
If genetic diversity within population is high (48%) but the gene flow is very low (0.229)
What is the reason?
could you please help me?
Thanks a lot in advances.
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Nice Contribution Peymaneh Davoodi
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Hello,
I trimmed and assembled (Reverse and Forward) my sequences using CLC Main Workbench software. The trimming I did aims to remove poor quality 3’ and 5’.
I’m going to perform multiple alignment, haplotype diversity and phylogenetic tree, using other software (DnaSP, Arlquin and MEGA).
Those softwares need uniform size of sequences (same length).
I have about 120 COI sequences of different sizes (640-750bp). The expected size was 710 bp.
Is there any software or method to trim sequences at same length: either one by one or both together? Which size do I need to choose for this trimming in my case?
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Please someone help give me a step wise procedure to trim poor quality from nucleotide sequences in either MEGA or Bioedit. Thanks.
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Hi,
I am trying to isolate EMS-associated Vibrio parahaemolyticus using TCBS for whole genome sequencing. However, I notice some green colonies have different shades of green and different textures especially after 48 hours. Anyone who experienced this please advise? Are they all Vibrio parahaemolyticus given their vast genetic diversity? What would be a better way to isolate?
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There ate two greeb colonies on TCBS agar. Aside from Vibrio parahaemolyticus, Vibrio vulnificus also produces green colonies because they do not ferment sucrose.
SOURCE: Mahon Diagnostic Microbiology
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I am looking for an abundance weighted phylogenetic diversity index. Barker (2002; Biological Journal of the Linnean Society, 2002, 76, 165-194) adapted the faith index to incorporate also absolute or relative abundance. However, in my opinion, this index results in some weird artifacts when relative abundance is used.
Does anybody have some tips + preferential suggestions for r-packages to implement other indices?
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Hill number (familly), a = 2; similar to the Simpson diversity, also named effective number of variants.
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