Conservation Genetics - Science topic
Conservation genetics is an interdisciplinary science that aims to apply genetic methods to the conservation and restoration of biodiversity. Researchers involved in conservation genetics come from a variety of fields including population genetics, molecular ecology, biology, evolutionary biology, and systematics. Genetic diversity is one of the three fundamental levels of biodiversity, so it is directly important in conservation of biodiversity, though genetic factors are also important in the conservation of species and ecosystem diversity. Conservation of genetic variability is important to the overall health of populations because decreased genetic variability leads to increased levels of inbreeding, and reduced fitness.
Questions related to Conservation Genetics
I'd like to sequence the genome of the gopher tortoise. The genomes of congeners are ~2.4Gb. I'm trying to decide how much coverage is necessary; we plan to run the sample on a portion of a NovaSeq run, and at least one PacBio SmrtCell. I'm trying to evaluate the benefits of additional sequencing effort: my starting point would be something like 30x coverage for the 2x150 NovaSeq run, and one PacBio SmrtCell (~8x coverage with HiFi reads? Not so sure about this), but i'm wondering how necessary a second PacBio cell, or additional Illumina reads, would be for assembling a nice genome.
We don't have any tissues available for transcriptomics, and the immediate application will be to map whole-genome methylation seq reads to the genome.
I'm pretty new to all of this, so any suggestions or references to guidelines are most welcome! Thanks!
According to PowerMarker V3.0 manual, this software has been specifically designed to analyze SSR and SNP data. However, by literature review we find some publications on ISSR markers that used PowerMarker for data analysis. I would be grateful if you could kindly upload a sample input file of 0/1 data for this software.
I recently became aware of a published proposal to reintroduce African cheetahs in India by US scientists.
Apart from scientific considerations - I have much to disagree on this proposal - my question is: should it be proposed if the last Asiatic cheetahs lived in Israel or Jordan rather than in Iran, as it is the case? I believe that global organizations should try to support local and national conservation initiatives, not totally disvalue work in Iran that is really critical for the conservation of Asiatic cheetah.
I calculated an AMOVA using Arlequin (10.000 bt) on a microsatellite dataset (12 sats). There are 4 more or less differentiated subpopulations. The data is fine, I did vast checks and a lot of other analyses.
In my AMOVA however, I end up with the following percentage of variance explained:
Among subpops: 1.69 (significant)
Among inds within subpop: -2.43 (not significant)
Within inds: 100.73 (not significant)
I realise this is a strong indicator for good admixture, and no real subpop strcuture. Yet I am a little confused about the negative value:
- Is this totally fine, an artefact of computation?
- Or does it indicate some problems with the AMOVA?
Thank you for your help!
Have you ever measured root exudates to soil?
Would you please mention some techniques?
Thanks in advance, with the best regards,
Dr. José Carlos Lorenzo Feijoo
Head, Lab for Plant Breeding and Conservation of Genetic Resources,
Bioplant Centre, University of Ciego de Avila, 69450, Cuba.
Tel. 53 33 225768/212719 www.bioplantas.cu
My colleagues and I are investigating the population structure of ruffed lemurs throughout their known distribution. We've already run both a structure analysis and a principal coordinate analysis & it's looking like we've got K=2 populations/genetic clusters. Based on these analyses, it seems as though a large river is likely acting as a dispersal barrier; however, we'd like to be able to test this hypothesis. We've tried SAMOVA and Geneland, but have been unable to get the dataset formatted appropriately (or some other issue -- hard to tell, but we can't get either of the programs working). Can anybody help?! Example input files and/or suggestions for appropriate tests would be extremely helpful! We've got two weeks before the revision is due!
Has anyone run into a problem with micro checker? I have loaded one genepop data set micro checker and it was successfully loaded. But when I try to load another genepop file that has much more data, micro checker refuses to load, despite the fact that this second file run successfully in genepop.
I'm trying an analysis on HIERFSTAT for the first time using a subset of my data. I have some formatting issue that I can not put my finger on because when attempting to run basic.stats and other analyses I get the message
Error in dimnames(x) <- dn :
length of 'dimnames'  not equal to array extent
To get a feel for the program I'm only using a subset of my data for now (one locus). Can anyone advise? I added the file I'm trying to use.
I analysed my samples for isolation-by-distance using a mantel test in Adegenet package. I am not sure if the histogram below shows that my samples has a clear isolation by distance pattern.
Below is the summary of result from the adegenet.
Summary of results
Call: mantel.randtest(m1 = Dgen, m2 = Dgeo)
Based on 999 replicates
Simulated p-value: 0.009
Alternative hypothesis: greater
Also, for the second plot I am not really sure if it is a normal result and I am a bit confused how to interpret it. I hope anyone can help me interpret these plots.
Thank you so much.
I've been out of the game for a few years and I have a lot to catch up on. I'm working on a wild animal population that is currently crashing (>60% decline over the past two decades). Given the situation, is it appropriate to use a program like Bottleneck to look for previous reductions in the effective population size? Or will the current situation mask previous events? Have there been recent developments in detecting these patterns that I should be aware of? Thank you for your time. :)
I am aware of the pedigree and kinship2 libraries in R, but functionality is limited. Programs like EASYPOP can save pedigree information but are not focused on simulation of pedigree parameters specifically. I am interested in looking at e.g. the impact of founder inbreeding levels (usually assumed to be zero) on kinship estimates in subsequent generations.
I am just asking before trying to do something from scratch. :)
So far we’ve been doing microsatellite analyses with a capillary sequencer. The machine is getting old and we need to replace it. Since we’re regularly using MiSeq or HiSeq for other approaches (DNA metabarcoding, Rad-seq, Genotyping By sequencing, …), it seems logical to us to switch completely to a high throughput sequencing platform.
We do work a lot on protected and endangered species, often small critters, as a result of which our DNA-sampling needs to be non-lethal and minimally invasive. This means we often have low quantity and low quality DNA.
RAD-sequencing or other reduced representation genome sequencing is often not possible on these types of samples. I am aware of SNP-methods requiring low amounts of DNA (Fluidigm chips for example), but this still requires other hardware.
Microsatellite genotyping is still very useful to us because the information content per locus is about ten times higher than with SNPs. For a lot of our purposes, we don’t need more than 25 microsatellite loci to get the information we need, and with the small amounts of DNA we have at our disposal this works fine.
I’m looking for people who directly sequence microsat loci via high throughput sequencing, and would like to know their first-hand experiences on feasibility, bottlenecks, bio-informatic pipelines, do’s and don’ts.
A fundamental problem with the effective conservation of (plant) genetic resources is that their natural distribution does in most cases not follow administrative and political borders, they might follow geographical borders, at best. For the development of effective conservation strategies and for the subsequent monitoring procedures we ideally should have a good oversight over and understanding of the distribution of the genetic diversity of the genepool in question and this would require a close collaboration with those countries that are part of the distribution area. Unfortunately, such close collaboration is frequently hindered by political an other constraints. Thus, the question is how we would still be able to develop sound conservation strategies, to implement these and to conduct any monitoring activities in cases collaboration with the identified countries is limited or not existing?
I would like to use the coancestry-based method to assess some population contributions to overall genetic diversity, as developed by Caballero & Toro (Conservation Genetics 3: 289–299, 2002) and implemented in the software MolKin by Guttiérez (Journal of Heredity 96, Issue 6, 2005)
The only problem is that MolKin only runs under Windows 95/98/200/TN/XP. Before loading a virtual machine to make it work, I was wondering if you would know about another soft or, even better, a R package that would help to implement the Caballero & Toro approach? I don't feel quite confident yet to implement this on my own... better check!
Thank you all and a great year 2018,
Considering the fact that crops and their traditional varieties and landraces are widely spread and in most cases do not follow national boundaries it is a given that effective and efficient conservation can only be done through collaboration with neighboring countries. The same applies to the conservation of entire genepools, they typically are widely distributed across farmers' fields, disturbed and natural habitats. Thus, there is a need to involve nature conservationists, genebank curators, botanic gardens, NGOS and farmers that aim at the conservation of genetic resources in farmers' fields, scientists. policy-makers and others to achieve effective approaches. Therefore, networking among all those involved and/or that should be involved seems to be essential to make the efforts sustainable and long-lasting. same applies to the involvement of all stakeholders in the conservation activities, they should have a say in the planning and implementation of the conservation operations.
I´m including P. orbignyi in a population analysis for conservation genetic study. In GenBank are a few sequences; but, into them, there is not any sequence from Brazil, where was originally described the distribution of this stingray. And it is important in order to used as a start or reference point f genetic analysis.
While calculating the evolutionary divergence as computing pairwise distance, (using p-distance methods and Maximum Composite Likelihood model), the values ranged between 0.002-0.138 (p-distance) and 0.001-0.109 (ML) for between individuals of the same species, and for different species. I have got these value as distance matrix table using MEGA 7 software by inserting the nucleotide sequence of COI gene of 661 bp length. Can somebody tell me what are the actual threshold values of the evolutionary divergence calculated by the above said methods to delimit the distinct species? I mean at which values of these distances we would say that these two species/individuals are of distinct species?
I'm using dominant genetic markers to measure genetic differentiation among populations and genetic diversity within populations. Since I'm using dominant markers, I had to calculate allelic frequencies using a bayesian method (Zhivotovsky 1999). There are a lot of measures In the literature (eg. FST; F'ST; GST; G'ST; PhiST; Phi'ST; D) and I want to know which must I choose. I want compare my results with published works with similar species too.
P.S. Sorry for my bad english
Is there anyone who knows a program to estimate the new measures of genetic differentiation described in Jost 2008, Hedrick 2005 and Meirmans et al (2011) (or standardized genetic differentiation measures) for DNA sequence data (mitochondrial or nuclear sequences)?
Hedrick 2005 proposes a new standardized method of comparing the indices of population subdivision when we are using different molecular markers (reviewed by Meirmans et al. 2011 for AMOVAs). In this standardized genetic differentiation measure, the magnitude of its value is the proportion of the maximum differentiation possible for the level of subpopulation homozygosity observed. Perceptibly, when using highly polymorphic markers that make the level of homozygosity low, then the maximum GST value must also be greatly reduced. Mainly care must be taken when we are comparing population differentiation indexes using different markers like microsatellites and SNPs, for instance (i.e. highly variable markers). However, I have not found any program that works on sequence data (e.g. mitochondrial DNA).
As was suggested by Meirmans et al. (2011), sequence data are of a different nature than allelic data as they contain information on the evolutionary relationships between haplotypes, and these population differentiation indexes do not take this information into account so their calculation is difﬁcult for sequence data. I think, programs for calculating these parameters (GenoDive, SMOGD, SPADE, RecodeData) cannot be used to calculate these new measures of genetic differentiation for sequence data.
Briefly, is there any researcher who has estimated these indices from DNA sequences using these or other programs? Have you proceeded in any particular way?
Thanks so much
When I try to collect the earthworm specimens in each spot, I found it's really hard to get enough objective samples in some plots, maybe 1 or 2 or 3 specimens in a plot. However, limited specimens mean pretty limited genetic variation, and actually, the number of samples has a strong relationship with genetic diversity.
Could somebody tell me something about your experience?
I use 15 specimens from 3 different islands separated by the sea using 17 microsatellite loci. If I can not use the data to assess the genetic diversity, then what can I discuss from data?
I did RAPD method of one sample. I used 10 primer for that. now I have one image of that result, how can I calculate and interpret result using polymorphism phylogenetic mapping? is there any software?
I am doing research on Alpine Musk Deer (Moschus chrysogaster) from Nepal to study genetic diversity and individual identification (later is for latrine site use). I tried to find out the microsatellite markers this for a particular species (Moschus chrysaster) but could do so. However, I have found 15 novel microsatellite markers developed for Forest musk deer (Moschus berezovoskii). Now, I would like to know possibilities of Microsatellite Marker of Moschus berezovoskii for Moschus chrysogaster.
We had already started a research, based on landscape genetics for a resistance animal species. In this study, we used SSR markers for genetic distance parameters such as Fst, Nei distance etc,. Now, is it logic using OWA scenarios to determine habitat suitability between two centroid of animal population?
Protecting the right of the local community/country to use their own genetic resources available in a particular area is an important element of environmental and biodiversity conservation. However, one of the biggest biodiversity conservation challenges faced by southern peripheral countries is biopiracy and related issues. I am doing some research works regarding that. Could you pleases help me to fin out suitable research works based on that
I'm looking for publically available datasets which have genes for which the coalescence times are either known, or have been estimated with a sufficient degree of confidence using one or several coalescence time estimation methods? I'm looking for the data and any accompanying publications, especially those for which the genes, and the times are easily accessible.
I've run Structure to detect population structure in 20 populations of a Mediterranean shrub. I used 6 runs fro each K, with a burn in of 100000 and 1000000 iterations. I then used Structure Harvester to implement the Evanno method and obtained the results observed in the attached graphs.
I wonder whether anyone has any insight regarding the large Delta K obtained. I've never seen anything like this in the literature. Also, if K=2 is the true K, this does not match with the relatively high values of Fst between populations (values up to 0.25).
Any hints or recommendations?
I was wondering if there was a package that helps with RAPD data, specifically population genetics. I heard about "poppr" but I am not sure if it works for this type of marker, it says it works for dominant data but it never specifies.
For studying the genetic diversity of the species within and between its populations, microsatellite or SSR markers is used in different groups of a multiplex. For bin setting and data analysis of the geneMapper report, what is the available software can be used?
with all the best,
Prediction capability of Species Distribution Models are generally measured through ‘Area Under Curve (AUC)’ using training data sets. I have developed four distribution models of my study species. All models are in raster format. Training data sets are exact GPS locations of the species. Can anyone help me! How to create AUC using R commands? Which R package can be used? Please share your R codes if available!
I am interested to undertake a study on determination of level of inbreeding in elephant population in an isolated habitat. The nature of study area is thick forest, hence collection of fecal samples is the relevant approach to study Genetics of elephants. Anybody who is familiar and experienced in designing protocol of collection and analysis of DNA Fecal Samples. The population is not well known, population number is approximated 102 elephants. Thanks
I have a list of rat genomic regions. I have liftovered them to human orthologous regions. For the rat regions that can be successfully converted to human orthologs, I want to find out if the matched rat-human regions are conserved. I can use the phastCons score or phyloP score to evaluate the level of conservation, but these values are based on multiple-species alignment (46 species). What I am really interested in is the conservation between human and rat. I wonder how I can obtain that value? using blastn or fasta or something else?
I am working on conservation genetics of some alpine medicinal plants. I have used some dominant markers and co-dominant markers. I am unable to construct network tree by using Splitstree.
Can anybody please help me to construct the input matrix for "Splitstree" or "Neighbournet" using binary data matrix (1,0).
I'm trying to use the Samova software, but on the site there is only the example file to DNA sequence.
Someone would have a example file for multi loci microsatellite?
I tried to generate the file by GenAlEx but was not compatible.
I'm working on a fish species with populations distributed across a river network, using microsatellite markers to investigate population genetics and landscape genetics in a conservation context. I would like to:
1) Tease apart which landscape-based distance variables (distance between, elevation change, count of anthropogenic structures, etc.) are contributing most to fragmentation of identified populations; and
2) If the top contributing types of features are anthropogenic (e.g., dams or road crossings), I would like to identify the individual features within that type that are functioning as the most restrictive barriers.
Any ideas of potentially useful programs, analyses, or references would be appreciated. Thank you.
I work on an ancient protein family that exists in both eukaryotes and prokaryotes and my interest is in elucidating its deeper branches. When I pull down the data from NCBI I get about 6000 sequences. If I use an algorithm to help me cluster similar proteins (e.g. 80% similar) it gets reduced, and if I do my clustering with 50% similarity I get about 550.
The question is, in your experience, which one would you choose:
- use the smaller dataset (or even smaller) and do the most sophisticated, yet computationally intensive, analyses you can hoping that if there is a signal, these analyses would pick it up and thus the deeper branches get better support.
- use a lot of data and hope that then the intermediate evolutionary steps could be inferred more easily and the deeper branches get more support?
I have microsat data for 7 loci and overwhelmingly I see a pattern of homozygote excess in all populations. My microsats were developed using this species and these pops so it is unlikely that the pattern is due to null alleles. As much as possible I have eliminated likely clones as these are flatworms connected to a host and I have only selected one individual per host.
I am finding some research that has found homozygote excess in non-selfing hermaphroditic species but not much to explain the mechanism of it. I was just curious as your thoughts on why exactly this is occurring?
I have demonstrated a project, assessing the genetic diversity of breeds of an animal using SSR markers. I've got the allelic data from GeneMapperv.3.7 but i have no idea how to plot the dendrogram to show the genetic distance and what is the software through which I can calculate the Cophenetic Coefficient for my data? Can anyone guide me through this?
I have also attached an excel file containing the allelic data.
I want to check the clonal fidelity of a medicinal orchid propagated from the mother plant using axillary branching.Now cross verify the robustness of the protocol I want to use molecular markers to verify its stability. Our lab dont have any MASAP/SSAP or SNP infrastructure. I came through this paper which has applied the identical approach http://www.sciencedirect.com/science/article/pii/S0378111914000493
I need a software that calculates bias-corrected Nei’s genetic distance (Nei 1978) matrices and perform a Ward’s cluster analysis on the data together with bootstraps.
I have a question concerning the time scale (x-axis) of Bayesian Skyline Plot (BSP) analysis as implemented in BEAST. I am not very familiar with the model underlying this analysis.
I run BSP analyses on three different dataset (one each population) for the mitochondrial COI (537bp). The first population included 97 sequences, the second population 167 sequences, and the third population 48 sequences. The programs (Beauti + BEAST + Tracer) produced 3 BSPs with different time scales: the first population, 0 to 450 Kya; second population, 0 to 1800 Kya; and third population 0 to 350 Kya. My question is “how the more ancient value of x-axis is obtained? It seems related to the number of sequences in the original dataset, does it? If so, which is the relation between the number of sequences and the length of x-axis (time) of the BSP?
Any suggestion will be greatly appreciated.
The coulour variants of many species have in recent years being bred as a separate group or individuals. This is either a a result of their easthetic value or economic gain. Whether the separate or exclusive breeding has an impact on the natural population genetics is the question?
I used DNeasy (Qiagen) and invitrogen DNA mini extraction kits with digestion modification, but I am not getting DNA's. So please anyone can give me the protocol or kit to extract DNA from 50 to 100 years old museum preserved/dried bird samples. Thanking you.
What is the best marker/technique (microsatellite loci, RAPD etc) to investigate the maternal and paternal origin of captive chelonians? Also, is the same marker valuable for addressing genetic inbreeding on captive animals? Is there an optimal number of markers to use?
when I am doing linkage mapping including distorted marker, such distorted marker are coming in different groups. is it needed to remove such markers or need to add to same linkage group?
I'm studying the population genetics of an intestinal nematode (raccoon roundworm) using microsatellites. An analysis using GenePop shows significant LD in 20 out of 28 possible comparisons between loci (!). Is this a reflection of how highly partitioned the worm populations are between hosts, or an indication that the loci are somehow problematic vis-a-vis making population genetic inferences?
More broadly, what does finding (or not finding) LD tell us in the context of a PopGen analysis? Seems like checking for LD is almost a ritual feature in the MM of articles, but I'm unclear on its purpose. As a newcomer to the field, any insights would be welcomed. --Thanks
I have a long list of human proteins. Is there an online tool or resource material that can be used to determine the conservation of these proteins across the eukaryotic phylogenetic tree?
S. apetala germinates and grows several inches but then cann't survive in the planted forest. Its natural regeneration is a worldwide problem. I have worked on soil physico-chemical properties, now focusing on genetic diversity of the sp. Any more suggestion?
This kind of comparison seems tricky and polemic, however, still very necessary!
I am working on identifying the origin of an invasive anuran using mtDNA genetic markers and have found only two similar papers. These are the phylogeography of Bufo marinus (=Rhinella marina) (Slade and Moritz 1998) and a more recent paper by Kuraishi et al 2009 looking at the origin of Polypedates leucostymax in Japan. Does anyone know of similar studies on other invasive anurans such as Lithobates catesbeianus or Eleutherodactylus coqui?
I am trying to amplify seven SSR loci, that I used to genotype my study species individuals, in 2 out-group species (within same genus and within same family). I am getting amplification for 2 loci in individuals belonging to the same family using the same protocol that I optimize before but other 5 loci are not amplifying. Also, no loci amplified in individuals belonging to the same genus. DNA concentration for out-group individuals within the same genus = 5ng/ul and within same family = 3 ng/ul. I would appreciate it if anyone could suggest anything about this problem.
Note: I have already tried touchdown PCR annealing temperature variable
Hi everyone I am running Structure programme smoothly. I scored data as o and 1and perform analysis but in the result files are empty at the end of the simulation. I tried both window 7 and 8 for running structure version 2.3.3 and 2.3.4 but the problem is still there. The data file I prepared as a binary matrix and species is assumed haploid input format is when uploaded with structure and programme were set with length of burning period 20000 and number of MCMC100000, using Admixture model with correlated allele frequency assuming set of population of 10. I set K=2 to K=10 the programme run smoothly but I could not get result file even after so many change. One more thing want to share that I am getting the value of Ln Like= --- and Ln PD = 0 is this the reason of no results. and if this the reason then how I can remove it Kindly suggest what is needed to be done exactly
I am considering to design species specific primers to identify species from fecal samples. Would you like to suggest me which software is the best ?
Can you suggest a best protocol to bombard a gene on soft petal (such as Lilies)? What is the best shooting pressure and distance? Also, I have a problem with tissues browning and eventually cell death happened after bombardment. Any suggestion? Thank you.
Can anyone provide reliable information on species pairs (fishes are preferable) that have clear differences in morphological characters but show a little or no difference on the DNA level?
Species names in Latin would be nice.
References would be great.
I did a genomic DNA extraction of fungal tissue using a CTAB/phenol based automated extraction. To my knowledge the samples were not treated with prot K or RNAase during the process.
When I look at the genomic DNA on a gel, I see unexplained smeared bands below 50bp, with additional smearing below that. I ran the attached gel in attached image too long, and the smear bled into the wells below. The 1.5% gel was stained with GelRed, and run at 100v for 40min.
Does anyone know what this low molecular weight band and smearing could be?
We are looking for a neuropeptide in ants and we need to do slides of 10-12µm for MALDY and inmunohistochemistry. I froze the animal and try to get the slides, but the results are very poor. Does anyone know what we can do next?
In the study several genetic sex determination methodologies were investigated, compared, and discussed.
Thank you so much!
I am interested in studying the phylogenetic relations of a C. elgans enzyme that is conserved from yeast to mammals. I have generated a phylogentic tree representing over 100 eukaryotes and found the C. elegans enzyme at the base of the tree. It seems as though there are not enough sequences of species between yeast and C. elegans , i.e. I found no homologous sequences in Cnidaria, Porifera, Placozoa and other lower eukaryotes. I wonder if my enzyme is situated at the base of the tree due to the lack of annotation of early eukaryotes. Is this a known problem in phylogeny?
Thanks for your help!
I have been trying and did set data as well, but Arlequin shows error/warning message. I am using mtDNA D-loop marker.
High haplotype diversity could be driven by large population sizes and gene exchange with larval admixture from different genetic pools. I would like to know some proposed explanations for genetic diversity hotspots in marine species.