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Genetic Diversity - Science topic

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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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Parmeshwar K. Sahu : If you can convert your data into BINARY format (0 and 1), then you might be able to use DARWin Software from CIRAD. The phylogenetic tree outputs generated using DARWin software may be displayed in rectangular or radial formats.
DARWin is free software anyone can download and use. Here is the link to download DARWin software: https://darwin.cirad.fr/
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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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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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Thanks for your answer. I would agree, perhaps the key thing is that you need to use the same set of SNPs? But what if you use different SNPs for different populations / regions - then is the comparison more robust if you remove the monomorphic loci?
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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)
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#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 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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Hi
Please have a look at my answer to this question here:
If you have any questions just let me know.
kind regards
Stephan
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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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I'm looking for a software tool that may help me in the analysis of genetic diversity and population structure. 
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After sequencing of the specific region from different populations of insects the sequences were edited and aligned using software like Bioedit and CLUSTAL. The aligned file of sequences can be used for construction of phylogenetic studies by using distance matrices, maximum parsimony method, neighbour joining, branch-and-bound parsimony method, bootstrapping with the help of programmes like MEGA7, PAUP, PHYLIP. The softwares like DnaSP are very useful for haplotype diversity analysis. The evolutionary and geographical relationships among haplotypes, a median-joining (MJ) haplotype network was constructed with Propart software. The neutrality tests like Fu and Li’s D_test and F_test and Tajima’s D tests and genetic differentiation help for finding demographic history information can be performed using DnaSP software for detecting the range of population expansions. The software’s like Arlequin and DnaSP are used to know pairwise genetic distance (FST) calculate the genetic variation between and within different populations
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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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In checking for genetic diversity parameters such as the proportion of polymorphic loci (P), the average number of alleles per locus (Ap), the average number of effective alleles per locus (Ae), The mean expected heterozygosity per locus (He) for each primer combination, the Nei's genetic distance I scored my SRAP markers (0/1) for presence and absence. however these markers have mult loci. I’ve tried some softwares and I have not gotten result. I used GenAlEx and the percentage of polymorphism was 100% for every marker I try . I used PowerMarker and I could not continue because of the multiple alleles. Can anyone help me ?
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Kwadwo Gyapong Agyenim-Boateng , can you please provide me with your input data file for PopGene? I try to calculate genetic diversity parameters, but the program give me result for the each loci in the SRAP-primer combination. How did you organize your data?
Thank you in advance!
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Hi, I would like to know if there is a -fairly easy- way of quantifying the variability of a gene, at both the nucleotide and protein level, within different strains of a specific virus. My goal is to compare the variability of different genes and determine which of them is the most conserved.
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Yes, there are dozens of tools for this. One is the DataMonkey adaptive evolution server: http://www.datamonkey.org/
Another is Stuart Ray's SimPlot which plots the similarity of one virus to all of the others in your alignment, across the genome (or aligned region of the genome).
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I'm studying the polymorphism of a microsatellite related productive performance in 4 goat breeds and I would like to represent the distances between them according to its polymorphism (alleles and genotypes), which method is the most appropriate: PCoA, dendrogram,...? . Thank you in advance
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For me both are fine. As you want to show distance based on polymorphism, so you must show results in both graphs. It would be very nice presentation.
But I will prefer PCA over dendrogram, if you want to choose one of them.
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Hi everyone!
How comparable are the expected heterozygosity (He) values obtained from the assessment of different kinds of molecular makers?
For example, if I have a He=0.5 from a study based on SSRs, and a He=0.1 from another research that used RAD markers, is it correct to conclude that the population studied with SSRs has a higher genetic diversity than the population studied with RAD?
Thank you for your help!
best,
DU
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My opinion: absolutely not. Measures of heterozygosity are not directly comparable between different marker types due to their inherent properties. RAD (and SNPs in general) tend to have lower He than SSRs. It's just the product of the higher allelic diversity observed with SSRs.
Hope this helps.
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Routinely Mahalanobis D2 statistics is used to assess the genetic diversity pattern in crop plants. Principal component analysis is also used for the same. Is there any paper comparing the efficiency of these two methods in genetic diversity analysis? What are the major difference between two? Which method is more suited for genetic diversity analysis?
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Linear regression model or logistic models
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I have several SNPs with a frequency greater than 95% and they ask me not to consider them in the study of genetic diversity in Theobroma cacao.
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Hi, Mercedes. Are you referring to Major Allele Frequency or Minor Allele Frequency? Looking at your question, I assume it is Major Allele Frequency. Basically, SNPs with MAF >95% are highly homozygous in an assayed population, thus these markers do not provide enough power to differentiate populations, and informative enough for diversity assessment. We sometimes still include these markers when using SNP arrays. You either can re-customize to smaller array or just drop these markers if PCR-based genotyping method is used. For your extra information, hapmap researchers would prefer Minor Allele Frequency. The reason is simple, because their focus is mainly on the common alleles based on Minor Allele Frequencies >0.05 that affect the target traits (mainly disease tolerance in humans). Hope I answer your question, Mercedes.
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  • I want to do my research on underutilized edible aquatic plants but don't have any idea about the application of molecular techniques in my research work. For analyzing genetic diversity and generating genetic diversity, RAPD and ISSR techniques are used.(Eg. plants with same genus).But for analyzing plants with different genus and species, what will be the best molecular techniques?
  • I would love to get your expert's valuable suggestions.Thank you.
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Hi everyone,
I am working in cowpea genetic diversity and I have an issue with DNA extraction, I always get a bad quality of DNA with a lot of contamination.I am looking for a best protocol to purify it.
Thank you for your help,
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Extract it manual using CTAB ....protocol
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I'm working on analysis of genetic diversity of P. vivax in Thailand by DNA sequencing using Illumina Miseq. Gene targets are polymorphic regions of PvMSP-1, PvAMA-1, PvCSP, and PvDBP (4 markers). The problem is how I can estimate the number of samples or isolates as a good representative of certain population. Are there any similar previous works I can look for? Thank you in advance.
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The sample size depends on the type of your population, is it finite population or infinite population.
In the case of finite population, you can use the Slovin formula:
n= N / ( 1+ N * e^2 )
But in the case of an infinite population:
The sample size for any study depends on the standard deviation of the variable ( from previous studies ) and the margin of error you decided. The formula:
n= ( Z^2 * S^2) / E^2
where : Z ( 1.96 for 0.05 and 2.58 for 0.01 )
S = standard deviation from previous studies or pilot study
E = significant level
Also, you can use software to calculate sample size ( SPSS , Minitab , G*power )
My advice to use G*Power . G*Power software is effective tool to calculate sample size for many ranges of experiments. Also, you can determine effect size and power of the test, G*Power is free to download and easy to use after reading the manual, the download link:
The link to download G*Power manual:
I hope that be useful for you.
Good Luck
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I am conducting a research project for "investigating the genetic diversity of Palestinian date palm local cultivars".
I am looking for list of primers for PCR reactions, which are proper for my project.
With thanks
Walid
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I want to analyse genetic diversity (PIC, heterozygosity, allele frequency etc. using power marker software.
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Download the software chnge date of ur system to 1 january 2005 and then u can find convert ur ssr data with respect to demonstration files with in the powermarker. Then run the analysis for ur respective need compare your results with previous studies. Remeber me if u need assistance through out ur manuscript.
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I am planning for development of microsatellite markers for assessment of genetic diversity. But which markers are better (plastid or nuclear) for analysis??
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Definitely nuclear markers will provide higher levels of genetic diversity, i.e. more resolution for studies at the population level
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How genetic diversity in a plant species can be corelated with molecular marker
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A nice example from narrow-leafed lupins can be found in the recent literature, which shows molecular markers are associated with collection site data and demographics in the Mediterranean region. Mousavi-Derazmahalleh et al TAG 131:887 (2018) attached.
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Genomic DNA can be isolated from most parts of the plant. However if I want to analyze the genetic diversity existing among a certain genus/species which part is more preferable?
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The majority of existing DNA extraction methods rely on long incubation and multiple precipitations or commercially available kits to produce contaminant-free high molecular weight DNA.
The extraction of good quality DNA with a high yield is a limiting factor in plants’ genetic analysis. DNA quality from each line should be consistent to allow a proper genetic analysis from several plant individuals. High quality of DNA is characterized by predominantly high molecular weight fragments with an A260/280 ratio between 1.8 and 2.0 and the lack of contaminating substances, such as polysaccharides and phenols
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I would like to perform gene diversity analysis to study their ecological role and function from the bacterial whole genome data sets. This will be comparative study of different bacterial genomes will be published as a research review article.So, can I download and use genome data sets submitted by some one else in the GenBank? Can it be legal to use those genome data sets to use for my analysis?
Valuable suggestions and comments are welcome.
Thanks in advance.
Siva
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the reference used in the database for the dataset must be noted in your text (GSExxxxx for exemple if it's taken from GEO/NCBI).
fred
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i am doing molecular characterization of citrus germplasm, Presently ihave started using some of the SSR markers published in Citrus sinesis genome paper. Presently i evaluating the PCR products on 4% metaphor gels. i am getting bands of different sizes and in some cases present and absent type of bands. SInce i am amateur in scoring molecular markers. i want to know is there any article published explaining how to score a SSR marker for further analysis. thank you 
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While using NTSYS Pc software for divergence analysis, the SSR data scored on the basis of presence and absence as well as molecular size difference have to be arranged into binary matrix. So each allelic variant recognized on the basis of molecular size difference is considered as marker and scored for its presence and absence and then subjected to divergence analysis.
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In term of bolting garlic may be three types non-bolting, incomplete bolting and complete bolting. In case of complete bolting it may be used for genetic exchange (crop improvement) but what is practical use non-bolting and incomplete bolting garlic genotype genetic diversity study.
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The other two types of garlic may contain transgressive traits that will also be useful to improvement of your trait of interest. As Suzuki correctly and succinctly stated, "There are no qualitative traits". Some loci explain much more of the genetic variation in a given trait than other loci, but every trait has multiple loci that impinge upon the final phenotype. Also, without the comparators of the other two classes of garlic, how would you know if allelic uniformity at a suspected beneficial locus was significant or not? One needs to include as much phenotypic diversity as possible in breeding programs. You will inevitably narrow the pool down later after understanding what you have to work with.
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Hello there,
I'm trying to get some useful results for my thesis using STRUCTURE Software.
I'm soing researches on the genetic diversity of Gentiana germanica within a population as well as between different Populations.
So far I've generated Results using the PCR-ISSR method.
And I got a file with 6 markers and in total 101 bands.
If the band is present it's 1 and if not it's 0.
Now I was wondering which parameters I have to set in structure to get a result, so far I didn't get anything useful, I tried the no admixture modell and the admixture model.
Can anyone help me please!
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Dear Nora,
In my experience, most researchers failed to conduct Structure analysis with dominant marker due to incorrect input format/setting.
First you should create new project in Structure and set the ploidy of your data as "1" because your ISSR data is dominant (not codominant as SSR).
Second, you should define code of recessive (0 in your case) in first line of your input data and carefully check whether you click the right option during constructing project in Structure.
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I want to study genetic diversity of Uropathogenic E. coli  .I  DNA extraction methods for E.coli by boiling.but i don't band in elektroforez.
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Dear Zeynab Faraji and everyone with the particular interest,
The RAPD is a very demanding technique, as it requires a lot of precision and the right PCR conditions to be maintained. Firstly, if the RAPD is failing, I would suggest to perform the gradient PCR. I had assessed RAPD with DNA extracted by boiling method and the results were really great, of course, after performing the gradient reaction and finding the best conditions.
In addition, another cheap, repeatable and more reliable method for the genetic diversity of UPEC is ERIC-PCR.
Good luck.
Rūta
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What are the Tajima's D and Fu and Li's D and F statistics value means?
I am analyzing a set of 30 sequences of a gene using DnaSP and getting the Tajima's D (1.005) and Fu and Li's D (-0.950)  and F  (-0.349) statistic P values being not  significant.  Can anyone help me in interpreting  of positive value for Tajima and Negative Fu and Li's ?
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There has been some debate on this but if you have population structure you can get false significance and false values (not under every scenario, but there are some ways this can happen and in my option more often then not). In any case this statistic are meant to be ran on within a single population, and violating this is highly advised against.
My suggestion is to:
1) Make a haplotype network (or phylogeny) and see if there is any pattern in the association of geography or phenotype (i.e. is there population structure).
2) If there is a clear pattern of population structure then run Tajima's D and Fu's F (or other statistics you like) on each independent population. If there is no structure then run it as if it is one population.
I should also note that if you are using a low number of samples you can also get bad estimates of Tajima's D and Fu's F. For example, in a similar oddity with these statistics it was later discovered that the research was calculating using two samples, as you would expect this does not work well. I would suggest at least 20-30 samples per population (30 is rule of thumb if the are looking a single genes or small set of loci) and would not trust any values for anything calculated with <10 samples.
Hope this helps,
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Is there a study on the molecular diversity of Lepidium or other Brassicaceae plants using Start Codon Targetted Polymorphism (SCoT) marker?
Can the SCoT primers used for other plants be used for Lepidium?
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Hello,
I do not know any paper on Lepidium sp. in which authors used SCoT markers. However, this is a universal method for DNA fingerprinting (applied so far on many plant species) so I am sure that you can use it in your studies.
Best wishes
Piotr
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I have a dataset of 6 microsats loci from 11 populations of a barnacle. I’d need 100-1000 matrices of pairwise Fst-values, in order to carry out a spatial analysis. Is there any software producing these bootstrapped matrices?
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I had some troubles running diveRsity::writeBoot.
diveRsity::basicStats and diveRsity::diffCalc ran my data. However, I had to make minor adjustments to my data to writeBoot (remove some empty spaces).
Also, parallel argument must be set to TRUE. parallel = FALSE causes problems.