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Phylogenetics - Science topic

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Any details (Books , courses, slides, articles) can help me. what are the difference between botanical and phylogenetic classification? Thank for your response
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Botanical classification was designed by Linnaeus. Phylogenetic classification deals with the relationship amongst the organisms. Based on the characteristic features of the ancestors, species can be classified. There are many books, journal, power point presentation available online related to your query.
To enhance skill: (i) Regular interaction with plant species (ii) Information of different plant groups (iii) Knowing plant species of your surrounding (common name, botanical names, habit & their importance) (iv) Kitchen gardening (v) Field visits to documentation and photography of plant species (vi) Visit to the herbaria (vii) Reading updated literature (viii) Botany related short projects (ix) Participation in botany related seminar/ symposia/ workshop/ training.
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Hello, I got a question with the units of sequencing products. Most of the phylogenetic study that using ddRAD or other NGS method provided the data size of their analyzed dataset using the unit "loci" or "SNP". While for research using Sanger sequencing and PCR, they used "base pairs" or "nts". If I would like to compare the molecular data size between these researches, is there a transforming algorithms to do it? Or could I just simply use these number to compare (e.g. 1400 bps v.s. 7000 SNPs)? Thanks!
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Why do you want to "compare" the size of markers? I think the absolute size of bp is incomparable between a sequence and SNPs among genome, cause all nucleotides in a sequence are linked and not all of them are polymorphic; while SNPs are polymorphic loci scattered on different positions of a genome, which may be less linked to other SNPs. Also, sequence and SNP provide different aspects of evolutionary information, so I think comparing a single sequence to a RAD-seq data could not provide you some useful information
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I will appreciate any of the professors who can shed additional lights on two basic problems, I have recently faced with:
1. why two accessions belonging to one species with exact bases show a low posterior probabilities in phylogenetic analyses (bayesian, maximum likelihood, etc.). Alignments are the same, then we predict the high clade credibility, but why do they show the poor supports. What is the reason?
2. I am studying on two close species. I am sure that they are not the same due to distinct morphological differences and difference in their alignments. Which software (s) can help me to indicate that they are still separated not the same? I have tested SplitTree, RDP, Haplotype and different phylogenetic analyses, but still I need to find much precise software. Any suggestion will deeply appreciated.
Best Regards
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Dear Atena,
at best we have a ZOOM meeting and have a direct look on your alignment and data.
Low node support is of course due to poor (relative) support of low numbers of SNPs and/or homoplastic features of those.
But finally, a genetic distance based on a cladogram (and maybe few genes ?) is very often not a good argument to separate closely related species. Microevolutionary process have different dimensions compared to macroevolutionary (often cladogenetic) perspectives.
Cheers and best
Marcus
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Dear all, in the lab I currently work in we intented to sequence entire mtDNA of selected mammalian species, that had not yet been annotated or deposited into GenBank. However, one stumbles upon a question, whether or not this is trully a prudent thing to do. The advent of NGS in the last decade has enabled mtDNA to be sequenced in entirety as a by-product of WGS/shotgun sequencing. Judging by complex evolutionary patterns (eg. reticulate evolution), using only mtDNA can also hardly be justified as a base for larger and well-supported phylogenetic studies, since nDNA is a must in such casses. The question therefore is, whether or not annotating single mitochondrial DNA's from a single individual of a species is still a sound final objective of a research project?
I look forward to receiving Your opinions.
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Mitochondrial DNA is marvelous for phylogenies. For one thing it is not subject to the confusion of recombination so what you see is similarity by descent alone.The protein coding genes are really quite tidy and phylogenetically informative for a range of ancient (COI, 1st and 2nd positions) and recent divergences (e.g. ND2, COI 3rd position) and very fast changes (control region). mtDNA alone might be somewhat biased since it is maternally inherited and the genes are all involved with respiration and metabolism. So one must also use a few messier nuclear gene to offset the bias that could result from using only mtDNA. Also the mtDNA is inherited as a single marker so represents a very nice long seuquence compared to any nuclear gene which Is subject to recombination. The best analyses will estimate a species tree from mitochondrial and well-chosen nuclear genes that will likely have slightly different gene trees from one another. Model the mitochondrial genes with a different model of sequence evolution from the the nuclear genes with using coalescent methods to coax the gene trees into a single species tree.
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While working with some stratigraphically significant extinct larger foraminiferal species, I noticed signatures of ‘plastogamy’ and other ‘sexual reproduction’ in some specimens (Journal of Foraminiferal Research, v. 37(1), pp. 41-45, 2007). Since ‘interbreeding’ and ‘sexual reproduction’ are some essential parameters of a biological species, the specimens representing the morphospecies are different in possessing crucial traits of a biological species. Being part of phylogenetic species, these may serve as a bond between paleontological and biological species and help in establishing gene flow and genetic classification in paleontology. Such forms may be grouped separately in paleontological species.
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I am sorry, I am a geomorphologist, not the least skill in foraminifera!
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Hello,
This is for an undergrad paper I need to complete.
I am comparing the R^2 from a regression of 3 biodiversity measures: phylogenetic, functional and species richness to see which one is the best predictor of primary production.. Phylogenetic had a r2 of 0.28 and species richness had a r2 of 0.21, while functional diversity 0.077.
I was wondering if I could state from the r2 values that phylogenetic diversity was the best predictor? Since species richness had a r2 of 0.21, is it too similar to say phylogenetic is better than species richness?
Thanks
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Kindly go through the following link, I hope all doubts regarding R^2 shall be cleared.
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Does anyone know of a recent review or meta-analysis of molecular vs. morphological phylogenies? That is, has there been a recent analysis of how often the two lead to statistically indistinguishable phylogenetic hypotheses for the same sets of taxa (across many clades) and how often they significantly differ?
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Dear Matthew, many thanks for asking this very interesting technical question on RG. Apparently the problem is finding a recent review article on this topic. The latest review I found dates back to the year 2016 which is not really recent any more:
Morphological and molecular convergences in mammalian phylogenetics
This paper has been published Open Access so that it is freely accessible as full text (please see attached pdf file).
You can find and access other potentially useful articles when you search the "Publications" section of RG for the term "Molecular versus morphological phylogeny":
I hope this helps. Good luck with your work and best wishes, Frank Edelmann
P.S. Lucky you live Hawaii! 🤟
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Experiencing slight difference in the results of tress obtained from BEAST and Maximum Likelihood...
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I will suggest to delete the insertion deletion from the alignments. The analysis based on the alignment may provide similar results.
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Hello everyone !!! Currently, I am working on the structure, engineering, and bioinformatics of industrially important enzymes. I am looking for collaborators, having an experience of working in protein bioinformatics, are welcome to working with enzyme bioinformatics projects from phylogenetics to molecular docking, molecular dynamics, simulation, intermolecular interaction, etc. Interested scientists are welcome to contact me on:
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Please have look on our(Eminent Biosciences (EMBS)) collaborations.. and let me know if interested to associate with us
Our recent publications In collaborations with industries and academia in India and world wide. EMBS publication In association with Universidad Tecnológica Metropolitana, Santiago, Chile. Publication Link: https://pubmed.ncbi.nlm.nih.gov/33397265/ EMBS publication In association with Moscow State University , Russia. Publication Link: https://pubmed.ncbi.nlm.nih.gov/32967475/ EMBS publication In association with  Icahn Institute of Genomics and Multiscale Biology,, Mount Sinai Health System, Manhattan, NY, USA. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/29199918 EMBS publication In association with  University of Missouri, St. Louis, MO, USA. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30457050 EMBS publication In association with  Virginia Commonwealth University, Richmond, Virginia, USA. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27852211 EMBS publication In association with  ICMR- NIN(National Institute of Nutrition), Hyderabad Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/23030611 EMBS publication In association with  University of Minnesota Duluth, Duluth MN 55811 USA. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27852211 EMBS publication In association with  University of Yaounde I, PO Box 812, Yaoundé, Cameroon. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30950335
EMBS publication In association with  Federal University of Paraíba, João Pessoa, PB, Brazil. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30693065 Eminent Biosciences(EMBS) and  University of Yaoundé I, Yaoundé, Cameroon. Publication Link: https://pubmed.ncbi.nlm.nih.gov/31210847/ Eminent Biosciences(EMBS) and  University of the Basque Country  UPV/EHU, 48080, Leioa, Spain. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27852204 Eminent Biosciences(EMBS) and  King Saud University, Riyadh, Saudi Arabia. Publication Link: http://www.eurekaselect.com/135585 Eminent Biosciences(EMBS) and  NIPER , Hyderabad, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/29053759 Eminent Biosciences(EMBS) and  Alagappa University, Tamil Nadu, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30950335 Eminent Biosciences(EMBS) and  Jawaharlal Nehru Technological University,  Hyderabad , India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/28472910 Eminent Biosciences(EMBS) and  C.S.I.R – CRISAT, Karaikudi, Tamil Nadu, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30237676 Eminent Biosciences(EMBS) and  Karpagam academy of higher education, Eachinary, Coimbatore , Tamil Nadu, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30237672 Eminent Biosciences(EMBS) and  Ballets Olaeta Kalea, 4, 48014 Bilbao, Bizkaia, Spain. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/29199918 Eminent Biosciences(EMBS) and  Hospital for Genetic Diseases, Osmania University, Hyderabad - 500 016, Telangana, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/28472910 Eminent Biosciences(EMBS) and  School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Panangad-682 506, Cochin, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27964704 Eminent Biosciences(EMBS) and  CODEWEL Nireekshana-ACET, Hyderabad, Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/26770024 Eminent Biosciences(EMBS) and  Bharathiyar University, Coimbatore-641046, Tamilnadu, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27919211 Eminent Biosciences(EMBS) and  LPU University, Phagwara, Punjab, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/31030499 Eminent Biosciences(EMBS) and  Department of Bioinformatics, Kerala University, Kerala. Publication Link: http://www.eurekaselect.com/135585 Eminent Biosciences(EMBS) and  Gandhi Medical College and Osmania Medical College, Hyderabad 500 038, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27450915 Eminent Biosciences(EMBS) and  National College (Affiliated to Bharathidasan University), Tiruchirapalli, 620 001 Tamil Nadu, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/27266485 Eminent Biosciences(EMBS) and  University of Calicut - 673635, Kerala, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/23030611 Eminent Biosciences(EMBS) and  NIPER, Hyderabad, India. ) Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/29053759 Eminent Biosciences(EMBS) and  King George's Medical University, (Erstwhile C.S.M. Medical University), Lucknow-226 003, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/25579575 Eminent Biosciences(EMBS) and  School of Chemical & Biotechnology, SASTRA University, Thanjavur, India Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/25579569 Eminent Biosciences(EMBS) and  Safi center for scientific research, Malappuram, Kerala, India. Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/30237672 Eminent Biosciences(EMBS) and  Dept of Genetics, Osmania University, Hyderabad Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/25248957 EMBS publication In association with  Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/26229292
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Hi everyone,
I am looking for phylogeny of pollinators and ants to construct a phylogenetic correlation matrix. Something similar to what can be found in verlife.
Any ideas?
Thanks in advance!
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I have worked on a phylogenetic analysis based on morphological and molecular characters and the review of a genus of Cicadas. As the research results, we will describe a new genus and 20 new species. I am facing trouble searching for a zoological journal that accepts papers with this amount of taxonomic information. The MS has around 80 pages.
Do you have suggestions of biological/zoological journals that commonly publish large papers that include taxonomy?
For now, I have in mind Zootaxa and Zoological Journal of Linnean Society.
I really appreciate any help you can provide.
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the European Journal of Taxonomy is a 'diamond' open access journal, meaning that you don't pay to publish and nobody pays for reading.
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I would like to add a data matrix of morphological data, assembled in the software Mesquite, to a manuscript. I would either add an electronic supplement (MS Excel format) or a table as *.txt or *.dic file. Anyone with experience around? I find Mesquite to be a bit user-unfriendly with this regard.
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you can just copy paste the selected range using ctrl+v and ctrl+v as long as the selected range is selected on the mesquite matrix. So for example, if you want to copy a range of 3 rows and 3 columns from the excel, you have to copy that range and go to the mesquite matrix and select 3 rows and 3 columns then paste it.
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As the title says, I have performed multiple ILD tests on PAUP with different settings and all of them reflect congruence between chloroplastic genes and ITS sequences (P > 0.1). I was wondering what would the implications be for these sequences or the taxa involved? Does this mean that the rate of change in nuclear and plastidial sequences are comparable? What does the congruence tell me about the history of the genes?
I was not able to find many papers in plants where they have performed phylogenetic analyses with plastidial and nuclear sequences concatenated, so any suggestion would be highly appreciated. Thanks in advance for your response
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Si el análisis te da congruencia entre particiones (nuclear y plastidial) significa que dichas particiones están contando la misma historia, reflejan la misma hipótesis filogenética. El ILD es para todo el árbol, pero vos visualmente podes verificar si los clados que se forman en ambas particiones son los mismos, y si agrupan los mismos taxones. Si las particiones fueran incongruentes, y además los clados están bien soportados, entonces podrías sospechar que ocurrieron eventos de hibridación e introgresión, captura de cloroplasto, o sorteo incompleto de linajes, considerando que los genes nucleares se heredan por ambas vías, y los plastidiales por una sola vía. La congruencia entre particiones te permite poder concatenar tu dataset plastidial y nuclear y analizarlo como uno, para encontrar el árbol de especies; si hubiera incongruencia, es mejor analizar los árboles de genes por separado. Espero que esto te haya servido un poco!
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Hello! I'm a new observer on the iNaturalist system, and I mostly post insect macro photos ( https://www.inaturalist.org/observations?place_id=any&user_id=cback&verifiable=any ).
I find that Mecoptera, in spite of their relative abundance, diversity and phylogenetic interest, are an orphan group in terms of systematics references, at least for North America. I read your comment on BugGuide about the non-availability of Penny's monograph. Has anyone managed to secure a copy of this document? It would be a starting point in order to provide high quality photos of specimens with a verifiable ID. Grateful if you can spare the time for a reply,
Regards,
Christian Back
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Thanks Leo for your kind efforts. I never thought of looking for the monograph this way. I will try to dig and hopefully retrieve a copy of it. I think it is a pity that the years of work of Dr. Penny represented by this work are not available. Regards, Christian
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I am doing a phylogenetic analyses of two sets of proteins (A and B) that are functionally very closely related and share a "large degree" of sequence similarity. I have identified from various species protein sequences I want to include in the analyses (for both proteins). Each separate sequence was included based on their similarity / BLAST results to the known and characterized (functionally) proteins (A and B) in Arabidopsis. I am worried that some of the species included might however represent paralogs and not orthologs. Is there any analyses where I can "plug and play" the data that I have and see whether it comes out as orthologs (hypothetically then an orthologous group for protein A and one for protein B). I do not want to do an analyses where I search a database for orthologs, I want to ID it in the sequences I already have in my dataset (which were included obviously based on certain pre selected criteria). Not all the species / sequences we include might be from completed sequenced and annotated genomes.
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Hi Rouvay,
If I understand this question correctly, one way to proceed could be to evaluate, by mutual alignments of your n protein datasets, on your n assembled genomes.
Synteny could possibly be used to identify/differentiate orthologs from paralogs. However, tandem duplication could be a problem...
Another way could be to use dedicated tools: orthomcl, OMA...
Romain.
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CIPRES is charging non-US users, and I need to find another external server to run some phylogenetic analyses.
It is a large dataset for some Andean plants, NTAX=214 NCHAR=5849, 40 million of generation.
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I saw that some papers use both cpDNA and nrDNA in a single phylogenetic study. Why not just choose one? What are the functions of each type of DNA? What is the benefit of using both?
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In the most of green plants, chloroplast (DNA) transmits , usually, to the progenies through the maternal gamete. Then, we can determine the (cytoplasmic) maternal plant (by the cp DNA haplotype) in the hybrids when both parents have the different cpDNA haplotypes. Nuclear DNA transmits to the progenies from both parents. We can determine, luckily, the both parents of the hybrids and the direction of crossings when you examine both the cpDNA & nrDNA.
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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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Better means it gives faster results and higher likelihood!
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Well...I guess depends of your type of data and the type of analysis you want to do. For example, for bayesian inference analyses the softwareBEAST is well known: https://www.beast2.org/
And RaxmL for Maximum likelihood you can use RAxML
Also, if you have a problem with the time of the analyses, I suggest to use a web server like CIPRES https://www.phylo.org/portal2/login!input.action
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Dear All
I am trying to applying a phylogenetic correction to an MCMC model, but I have problems in making the inverse matrix. I can visualise the treeplot very well, but when I use the script:
inv.phylo<-inverseA(phylo_ultra,nodes="TIPS",scale=TRUE)
R tells me that there is an error:
Error in pedigree[, 2] : incorrect number of dimensions
In addition: Warning message:
In if (attr(pedigree, "class") == "phylo") { :
Do you have any experience with this? I couldn't find a solution so far
Thanks in advance
David
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Hi Wilson
there were actually a few misspelled names, but R still tells me 'some levels of animal do not have a row entry in ginverse' Might there be another reason for that? cheers d
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Can anyone help e to interpret my phylogenetic network?
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Dear Reem,
Could you explain your problem? Exactly what kind of help do you need?
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I have a set of trees and am using Blomberg's K to detect phylogenetic signal. I am finding that for several of them, my values for K are close to 0 (in the region of K = 0.001 - 0.004) which would suggest no phylogenetic signal. However, the P values are high significant (p = 0.001), which suggests these results are different from a random distribution of traits.
Does this suggest that there is significant signal, but it is extremely weak?
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Well, Blomberg's K is a two-tailed test. Your result indicates an opposite of trait conservatism. It is called a significant trait convergence. Closely related species are the most distinct. See for instance what is called 'anti-signal' in this paper: Pei et al. (2011; https://doi.org/10.1371/journal.pone.0021273). I will give you another example: Take a look in this paper: Jombart et al. (2010; doi:10.1016/j.jtbi.2010.03.038), what is called "local structure", or "negative phylogenetic autocorrelation". They say: "A local structure would be observed whenever closely related taxa tend to be more different with respect to a given trait than randomly chosen taxa. (...)". OK, but you have more tools to investigate this, like the "Root/tips skewness test (two sided)" of Pavoine et al. (2010; Ecological Monographs, 80(3): 485–507).
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In case of cyanobacterial taxonomy, what is the final status of the organism which forms phylogenetically distinct clade but are not distinguishable by any of the morphological feature? Can we conclude it as a novel taxon? If no, then how can we report them in a publication?
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If it were a taxon of the animal or plant kingdom, the answer is that it is a new taxon. In Monera I don't know that. I attach an example of a work on a cryptic species in sea urchins just in case it is of interest to you:
Bronstein, O., Kroh, A., Tautscher, B., Liggins, L & Haring, E. 2017. Cryptic speciation in pan-tropical sea urchins: a case study of an edge-of-range population of Tripneustes from the Kermadec Islands. Scientific Reports, 7: 5948. DOI:10.1038/s41598-017-06183-2.
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Rather than using sequence alignment data, I wanted to have phylogenetic tree from distance matrix and bootstrap as part of statistical analysis. Anyone to tell me how to execute this analysis?
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Dear all,
I have been working with MEGA and distance matrix. I am attching a mini-tutorial to compute UPGMA dendrograms.
I have tried with MEGA-X and it perfectly works.
#############################
1-Calculate your distance matrix with your favourite software (e.g. in ".xls" format)
2-Prepare the matrix as explained by MEGA developers (Figure 1) in a ".txt" file. I show my own datafile (Figure 2). Warning: Keep the structure, including blanks.
3-Save this file as ".meg" file. It will be ready to use in MEGA.
4-Open ".meg" file with MEGA, select Pairwise distance > Lower left matrix > OK
5-Check data in the file read by MEGA. The matrix should be identical that your previous one (".xls" or similar; Step 1)
6-Select data and click "Phylogeny". You could compute UPGMA tree
7-MEGA offers a good variety of options to customize your tree
Good luck!
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Dear experts,
In technical articles, we see lots of statements telling us "indels" are useful in phylogenetic reconstruction because they play a major role in genomic evolution.
** I am dealing with 14bp deletion at several sequences of a non-coding gene, and I have two ambiguities as follows in my interpretations:
1- Taking into account that "non-synonymous" refer to frame-shifted mutations which alter amino-acid or protein in "protein-coding" genes, is it correct to name 14bp deletion in a "non-coding" gene as non-synonymous in my dataset?
2- In routine phylogenetic reconstruction using RaxML or MrBayes (when deletions are considered as gaps), strains with the same deletion did not cluster closely, as I expected, do I have to do something specific while making phylogeny with these data?
Thanks a lot for your answers,
Ahmad
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Insertions or deletions in non-coding regions should not be considered "nonsynonymous" they are not coding for any protein. Even in known structural RNA genes such as ribosomal RNA genes or transfer RNA genes, the terms synonymous and nonsnonymous really do not apply.
A major problem with insertions and deletions in estimating phylogenies, is that there are many types of insertions and deletions and the size of an insertion or deletion does not correlate with genetic "distance" or the importance of the in/del. For example gain or loss of an intron, or gain or loss of a transposable element is a large change but of lesser phylogenetic importance than many other types of smaller insertions/deletions. Gain or loss of a number of repeat elements in repetitive sequences is also of low importance. So "scoring" insertions and deletions is problematic.
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For my master thesis I am conducting a phylogenetic research and for this I'm using tools like MEGA, IQTREE, FigTree, etc to make a phylogenetic tree. I wanted to know if IQTREE integrates the evolutionary placement algorithm (EPA) when it calculates a phylogenetic tree
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The EPA is used by raxml. I don't think iqtree uses it
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Hi all,
Considering that one has the whole genome sequence (annotated) of a bacterium and wants to know if it has the potential to cause human diseases, what steps would you recommend (insilico)?
I noticed that one of my novel species falls into the phylogenetic cluster of Pseudomonas aeruginosa and is closely related to P. alcaligenes (which was isolated from human blood samples and is also responsible for bioremediation purposes) based on genome tree.
Does this affiliation can be trusted with respect to the pathogenecity tendency?
Thanks,
Timsy
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I have been working on a study trying to estimate body mass in mammals using a skeletal proxy in R. My dataset has high phylogenetic signal (Pagel's Lambda = 0.9) and I am interested in removing the effects of phylogenetic signal to produce more accurate estimates of body mass.
I had tried to do this using PGLS, but PGLS ended up producing higher error rates than the same data under OLS despite the high phylogenetic signal. Part of this appears to be because there are several particular clades with long branches (e.g., Monotremata) that form regression lines above or below the line of best fit, and their phylogenetic position distorts the resulting best-fit line. I had thought PGLS took phylogenetic covariance into account when estimating values, but it looks as though it only uses phylogenetic signal into account to minimize the residuals of the best fit line. It does not put the phylogenetic covariance back into the estimation of the y-value.
I.e., the function does not go: "Taxon X is positioned as sister to Monotremata. Therefore it should deviate above or below the regression line to a degree similar to its phylogenetic distance and the mass estimate should be adjusted accordingly?"
Given this, is there any way to use a topology to estimate a value that considers phylogenetic covariance and the phylogenetic postion of the unknown taxon when estimating this value, rather than just using it to minimize the residuals when calculating the best fit line?
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Agreed. PVR R-package is all you need to run your analysis.
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I have a question, when I used the picante function to analyze the phylogenetic community structure and phylogenetic signals in R, it appeared an error:"'phylo' is not rooted and fully dichotomous", I don't understand what's the problem, the attached file is my phylogenetic information, please check it, I am sorry to trouble you all, but I really want to solve this problem, thanks a lot.
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Yes, i think too
*The unrooted tree should be transformed into rooted tree. Try this code, phy=multi2di(phy1), where phy1 is the unrooted tree.
Thanks Wenjie Wan
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I am an undergraduate and I would like to broaden my knowledge on this subject, beginning by its principles. Maybe it would help that purpose to broaden my knowledge on Phylogenetics as well. Thanks all of you in advance.
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The official rules for animal nomenclature are available at https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/ This gives the rules for using names, not the systematic and phylogenetic question of which names are biologically useful. The Treatise on Invertebrate Paleontology volumes (http://paleo.ku.edu/treatise2/treatise.html) have some useful guidelines on taxonomy and taxonomic usage.
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I have a regression equation in which I am curious if the amount of scatter around the regression line is driven by phylogeny. I know there is a lot of phylogenetic signal because Pascal's lambda is very high, but I am more interested in seeing how much it affects the strength of the relationship between X and Y. I had thought about trying to calculate phylogenetic independent contrasts and using those to see if the spread about the regression line was less under phylogenetic independent contrasts than data that does not take phylogeny into account, but in thinking about it I realized that I haven't seen phylogenetic contrasts done in biology in what seems like ages. Everyone seems to be doing Phylogenetic Generalized Least Squares now, and if I recall right I remember someone like Revell (2010) mentioning that PGLS and independent contrasts are functionally identical.
My question is, do people still use phylogenetic independent contrasts in biology and if so would this be an appropriate use of them to investigate my data.
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Yes Sir .
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Hi all,
I am interested to do a comparative genome analysis using EDGAR comparitive genomic tool. I have a novel bacteria whose genome sequence was obtained by us and now I was to do compare this novel strain´s genome to it´s phylogenetically closely related neighjbours. This bacterium belongs to the genus of Paracoccus.
I notice that EDGAR allowed to select the genomes which are already provided in their database but does not allow to add a sequence of any genome (may be I missed?). Could you please suggest me how can I do a genome comparison using thsi tool or if you can suggest some other tools (in case EDGAR does not allow to add new WGS to their database for comparison)?
I know about BRIG but that is not as cool as EDGAR since it provides Venn diagrams and many other results for better interpretation.
Thank you and Regards,
Timsy
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Hello, I think you need to register to EDGAR and create a new project.
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Hi all,
A tree is binary if every interior vertex has degree three. So, I just want to find some methods like recursive algorithm to construct all phylogenetic binary trees. The running result is like these:
n=3
Input:Sklu,Scer,Spar
Output:(Sklu,Scer,Spar);
n=4
Input:Sklu,Scer,Spar,Calb
Output:((Sklu,Calb),Scer,Spar);
Output:(Sklu,(Scer,Calb),Spar);
Output:(Sklu,Scer,(Spar,Calb));
n=5
Input:Sklu,Scer,Spar,Calb,Smik
Output:(((Sklu,Smik),Calb),Scer,Spar);
Output:((Sklu,(Smik,Calb)),Scer,Spar);
Output:(((Sklu,Calb),Smik),Scer,Spar);
Output:((Sklu,Calb),(Smik,Scer),Spar);
Output:((Sklu,Calb),Scer,(Smik,Spar));
Output:((Sklu,Smik),(Scer,Calb),Spar);
Output:(Sklu,((Scer,Smik),Calb),Spar);
Output:(Sklu,(Scer,(Calb,Smik)),Spar);
Output:(Sklu,((Scer,Calb),Smik),Spar);
Output:(Sklu,(Scer,Calb),(Spar,Smik));
Output:((Sklu,Smik),Scer,(Spar,Calb));
Output:(Sklu,(Scer,Smik),(Spar,Calb));
Output:(Sklu,Scer,((Spar,Smik),Calb));
Output:(Sklu,Scer,(Spar,(Calb,Smik)));
Output:(Sklu,Scer,((Spar,Calb),Smik));
b(n)=(2*n-5)!! b(3)=1!! b(4)=3!!=1×3 b(5)=5!!=1×3×5
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Hi Qiyun,
The function allFurcTrees in the R package phytools can generate all bi- and multifurcating unrooted trees.
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Need a detailed tutorial on XLSTAT ( Input type format, output file, drawing conclusions etc) Unable to find online.
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As Csaba mentions, I believe there isn't any tool for this. However, if you want to analyze genetic data via Excel, I recommend you GenAlEx: https://biology-assets.anu.edu.au/GenAlEx/Welcome.html Another user-friendly tool that can parse with Excel look-alike genetic data is Genodive: http://www.patrickmeirmans.com/software/GenoDive.html And here are some online tools specifically for phylogenetics: https://ngphylogeny.fr/tools/ www.atgc-montpellier.fr/phyml/
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I have a set of 16 species of nematodes, i build a mitochondrial and nuclear phylogeny with them, and i found discordance between the two phylogenetic hypothesis. One of the common reasons for this discordance is incomplete lineage sorting and introgression, i want to test for this phenomena as the cause of the discordance in my set of species. Is there a software or way you could recommend to test for this two causes?
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Hi Guillermo. I'm not sure if you're still looking for answers to this question, but if you are then MSCquartets might be of interest to you. MSCquartets is an R package developed by myself and coauthors that tests the MSC. It tests either a specific species tree topology specified by the user or any species tree topology, with gene trees arising under the MSC as the null hypothesis. The tests are exhaustive, so rejection of the null hypothesis could be due to introgression or other factors. To use MSCquartets you need gene tree ``data'' (technically not data because they will be inferred gene trees). Let me know if you want more information.
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Dear fellow researchers,
Our team is still developing SARS CoV-2 culture for a foundation of various testing, however as we known that besides established culture it is needed to precisely identified the virus that are present in our culture. PCR based methods is our choice based on availability to confirm SARS Cov-2 existence qualitatively.
Besides confirmation, we think that phylogenetic study is still needed. However our facility does not have next gene sequencer for whole genome sequencing, therefore we think that partial genome sequence could offer a rapid results and information about virus origin based on phylogenetic study.
We would ask, is there any primer for specific sequence in SARS CoV-2 genome that could be used for phylogenetic study (partial sequence)? And what software or tools that fellow researchers could suggest for us?
Thank you
Best Regards
Andi YW
Faculty of Medicine
Airlangga University, Surabaya, Indonesia
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Interesting question
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Dear community,
I am rather new to phylogenetic comparative methods and seek your advice.
I want to compare a continuous trait (dependent) between species belonging to either groupA and groupB (groupA and groupB are two states of a categorical binary trait in this case). Using traditional statistics, a Mann-Whitney U test lets me reject the null hypothesis, as clearly the trait values of groupA tend to be greater than the trait values of groupB (see attached plot).
However, how can I implement a phylogenetic correction into the above analysis? I have already performed a PGLS and calculated phyogenetic signal for the regression using Pagel's lambda in ape/nlme (lambda-0.98). I have found that the traits evolve according to the phylogeny, as after performing a likelihood ratio test I found that the calculated lambda is not different than lambda=1.
My question is how do i go on from that point to test whether the trait values are different between groupA and groupB, taking into account the phylogenetic nonindepednence of the traits?
I understand that if the lambda of the regression would not be significantly different compared to lambda = 0, then I could just treat the trait values of each species as independent data points, but I do not understand how to compare trait values between the two groups if 0<lambda<1 or if lambda=1 (which is the case in this example).
Thank you for your time and your patience!
P.S. What do I do if instead of just groupA and groupB I have an additional 2 groups (groupC and groupD).
I have understood that using software like mcmcPGLMM might be a good idea for doing what I want, but I seem to hardly understand anything from the documentation
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Interesting question. Following the discussion.
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In this case we have two phylogenetically species, but they do not differ morphologically. We are treating it as a cryptic species and we want to formally describe it, using only molecular data (ITS nucleotide bases differences).
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It seems most of the new researchers have forgotten that the molecular phylogenetic data are secondary and morphological characteristics are primary.
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I would like to analyse fish gut bacteria by the Functional analysis by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). How is this analysis done?
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see
The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences
A.D. Miller, C.M. AustinJournal:Molecular Phylogenetics and Evolution
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I am trying to infer both maximum likelihood and bayesian phylogenetic trees using RADseq reads. I have already created my sets of radtags using Ipyrad which also I used to export the consesus sequence for all of my samples both in a concatenated sequences phylip file and as a SNPs-only phylip file.
Should I be using the whole sequences for my phylogenetic reconstructions or only the snps?
Also, I know that a best-fit nucleotide substitution model should be chosen before trying to build a phylogenetic tree. However, I have not seen any consensus on published papers of how this is done with RADseq data. Some articles choose a nucleotide substitution model without explaining how they chose it, others use a software as IQ_Tree to estimate a single model for their whole data set, while others use software as PartitionFinder to split their data and estimate a substitution model for each partition.
Which would it be the best approach? Specially considering that my data sets have high amounts of missing data (around 60%). And, if a model-test should be done, which is a good program to work with these large files?
Any help will be kindly appreciated!
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¡Hola Rodrigo!
Espero te encuentres muy bien,
¿Tienes un outgroup para enraizar tu árbol? ¿Has usado CIPRES?
Te recomiendo construir tu árbol con RAxML. Considerando el origen de tus datos, yo utilizaría jModelTest2 para encontrar el modelo de sustitución más adecuado (que en general va a ser GTR+G+I, aunque también puedes considerar correrlo solamente como GTR+I, porque RAxML corre mejor con ese). Utiliza solamente los sitios variables.
Una opción muy versatil para correr análisis preliminares, es subir tu archivo en .phy a http://www.atgc-montpellier.fr/phyml/, poner todo en automático y con base en los resultados ahora sí correrlo largo en RAxML.
Te comparto un consejo que me salvó la vida: a veces las señales de las relaciones filogenéticas entre individuos es más clara si solamente analizas los árboles con marcadores neutrales. Puede que no pase en todos los casos, solamente que en la experiencia personal, fue hasta que removí los outliers que mis muestras encontraron su sitio en una monofilia congruente con los análisis de estructura.
Ya por último, no te preocupes por el missing data. Te comparto un artículo que habla de eso:
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I am working on phylogenetic beta diversity in microbial assemblages across biomes, and interested in calculating betaNTI through the null distribution of betaMNTD by randomizing OTUs across the phylogeny and recalculating bMNTD 999 times. Does anyone have a script for this?
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The easiest way is to follow Stegen et al. 2013 ISMEJ:
An Updated Raup-Crick script is here
If you are to use the script by Franz Krah, please cite (sorry for the self -advertisment)
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Which is one is better in between 16S rRNA and microsatellite phylogentic study?
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16s rRNA study
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I am doing a study on phylogeography. An average pairwise difference and Nei's distance matrix was generated in Arlequin. I am having a hard time interpreting the results. As far as I know, higher values would mean higher pairwise difference.
(1) What if I get a negative Nei's distance? (2) What do they mean by "corrected" average pairwise difference? 
Hope someone could help. Thank you.
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Nei's DA is only applicable to frequencies, which inherently have values 0 < p <= 1.
For example, if the value x=12 occurs 30 times among all the loci values in a dataset of 120 profiles, then x has a Loci frequency of 30/120.
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I have a small data set consisting of 16 sequences, 919bp each. I am trying to determine the phylogenetic relationship among the individuals. I am wondering if the neighbor-joining method, maximum likelihood or bayesian analysis works best for small data sets like mine. Thank you.
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MrBayes will give you robust results, it's just about finding the best running parameters. And for ML, researches tend to go for RaxML, maybe you could try it and see what happens with the bootstrap values of the output.
Cipres server has various online versions: http://www.phylo.org/
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I have four whole genomes sequencing of E. coli isolates , and I wanna to classify in phylogenetics groups.
Whats is the best ways?
Thanks.
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Dear Andres,
The pan-genome of each phylogroup procured from the pan-genome of the species is noteworthy to be read. Moreover, Identification of the nodes corresponding to the most recent common ancestor (MRCA) for each phylogroup from the rooted species tree using the findMRCA function from the phytools v.0.6.44 R package.
I hope the attached article will be helpful.
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I want to learn R Programming for phylogenetics, phylogeography, and biodiversity studies. I hope it will be free and online! Or Introduce the best books for self studying
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I may suggest you to look for "Cookbooks" for the specific objectives you are trying to solve. As the name says, it's more like a recipe, where you can read workflows that will guide you through every step. (Other tip may be googling for "subject/software tutorial".
Here are some pages that I believe can help you:
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The recent official publication of PhyloCode has caught my attention, not for new arguments being presented for a system that has already been extensively discussed and, as I see it, whose downsides and problems surpass the envisioned advantages, but surprisingly because of the mediatic coverage it is currently receiving. So many of the major newspapers, which are generally regarded as part of the "mainstream media", are publishing articles and stories praising the "new" PhyloCode as a much-welcome, even necessary, advance to the "terribly outdated" taxonomic classification system currently in use, which "ignores decades of advances in molecular phylogenetics and does not reflect evolutive relationships of organisms". Anyone familiar with the current practices in Systematics is aware that this is malicious disinformation.
In talking with colleagues some have resonated with my impression that, instead of an academic debate, the PhyloCode is becoming a mediatic thing, so that systematists in disagreement with its adoption are branded as "reactionary" and "outdated", not only by the colleagues with whom they disagree but also by the "mainstream media" and possibly the public influenced by it. This type of political interference is negative to Science, and certainly very much unwanted by those endeavouring to advance, improve and refine human understanding of Earth's biodiversity and Natural History.
I think this debate should be kept academic, free as much as possible from this type of political interference. Your thoughts on this topic are very much welcome.
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The success of the Linnean taxonomic system has been its stability. The proof is that the system has persisted for more than two centuries and it is still useful.
Stability was granted because -among other reasons- any change that wanted to be performed on the nomenclatural structure had to be done formally within the academic world.
Paradoxically, it resulted to be a double-edged sword:
1- On the one hand, it enabled communication between researchers, as everybody has to attach to a same nomenclatural framework.
2- But on the other, it really hampered any change, making the Linnean system to look old and rigid.
Turning the ordering of biodiversity in a "matter of opinion" as presented in media is clearly counterproductive. We all must be aware that embracing an unstable phylocode system that tends to name any sister-clades relationship, may have deleterious effect on knowledge transference and mutual understanding.
Now there are a series of journals specialized in fostering formal taxonomic changes. These publications ease taxonomic rearrangements in our raping-changing world, transferring phylogenetic results into manageable taxonomic units, and helping taxonomy to keep up to date.
Let's do not defenestrate what has been achieved over so many years!
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Using IQTREE I received the most optimum models for my data to analyse phylogenetic tree-reconstruction. IQTREE is able to use, aside from the Gamma distribution for heterogeneity across sites also the FreeRate model:
"FreeRate model (Yang, 1995; Soubrier et al., 2012) that generalizes the +G model by relaxing the assumption of Gamma-distributed rates. The number of categories can be specified with e.g. +R6 (default 4 categories if not specified). The FreeRate model typically fits data better than the +G model and is recommended for analysis of large data sets."
Does anyone know if it is possible to use this FreeRate model in MrBayes (or in RevBayes), and if yes, how to I put that in the script?
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Hey Pepijn! I came across this problem too. It seems it's not possible to include FreeRate model in mrbayes. Here's a link to another answer:
There's a cool parameter in IQTRee '-mset mrbayes' that will only include models also available in mrbayes when doing model testing. It only work with nucleotide data though so if you have something like PICS-Ord regions in your alignment you'll get an error.
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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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I want to determine the phylogenetic age of the members of the Lepidoptera (Sphingidae) based on mtDNA, using BEAST software; But I do not have a good indicator. Please what is mutation rate in the mitochondrial genomes of the Lepidoptera (in million years)?
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I would highly recommend to anyone interested in tectonic calibration to read 'Molecular Panbiogeography of the Tropics" (2012) and 'Biogeography of Australasia' (2014) as starting points. These books include hundreds of examples of tectonic correlation with extensive integration of phylogeny for an immense range of animal and plant groups, and also presents a critical account of the issues in molecular calibration. This is just the tip of the iceberg. As for molecular rates of divergence, there seem to be all sorts of models so you take your pick - assuming there is a molecular clock in any meaningful sense. Some have objected to tectonic calibration where it provides ages for a subclade that would then push the larger clade back into e.g. the pre-Cambrian. Of course they never consider that perhaps their clock model is erroneous. Primates provide an excellent example for tectonic correlation with group after group of distributions corresponding to major tectonic events of Mesozoic and Cenozoic time. Some molecular researchers fall back on the mystical 'I can't believe it' when tectonic ages considerably predate the oldest fossil, but other molecular researchers are quite happy when their fossil calibrated estimates considerably predate the oldest fossils. There is a lot of waffle thinking out there, but the fact is that the vast array of modern life shows tectonic correspondence with Mesozoic tectonics. That is the great reality. Fossil-calibrated molecular clocks were widely proclaimed to falsify that, but it was all smoke and mirrors.
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Greetings from Brazil
I've been searching for the most appropriate gene to determine the phylogenetic relationship among Gram-negative bacteriophages and I've found several options, such as "major capsid protein", "helicase" and "terminase large subunit". Does anyone has some personal experience they'd like to share?
Thank you in advance.
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Abhijeet Singh I'll try it right away, thank you very much.
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Hi, I'm new to Phylogenetics. How do i draw interpretations & evaluate the attached Phylogeny tree?
For example,
- what are the types of information that can be derived from this phylogenetic tree?
- what are the interpretations that can be made on the virus isolated from singapore?
- what can i hypothesized about the ancestral strain of this virus?
Thank you.
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It has enormous information, however, What is the question that you are asking? You have to hypothesize first and then analyse not vice-versa.
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I have a 16s rRNA amplicon sequences (next generation sequence), I want to find out the phylogenetic diversity of a geographical region, How can I do that? please tell me the different approaches. thanking in anticipation.
… 
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You can analyse various descriptive statistics of nucleotide variation and population differentiation in DNAsp (Rozas et al, Mol Biol Evol. 2017 Dec 1;34(12):3299-3302). 16s may not be the most informative marker, though.
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I have a phylogeny and two categorical traits (one binary, one multi-state) mapped to its tips. My claim is that there is a correlation in their phylogenetic distribution, i.e. that they evolved in concert, or dependently.
How can I test that formally?
I have tested for phylogenetic signal using Fritz' D (Fritz & Purvis 2010,)
of which there is plenty. But I am stumped on how to show that there is a correlation in presence/absence of one trait and the state of another. I can visualise that in a traitgram/phylomorphospace plot in phytools, but that doesn't give me a number that says "these are not independent".
In principle, phylogenetic independent contrasts (Felsenstein 1985) could be used to test for correlation, right? But PIC is for continuous characters, not categorical ones.
I have found phylogenetic logistic regression (Ives & Garland 2010, https://academic.oup.com/sysbio/article/59/1/9/1723322), but this is only for binary traits. I have read the "Analysis of Phylogenetics and Evolution in R" (Paradis 2012) and "Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology" (Garamszegi (Ed.) 2014) books and googled myself to perplexion. I hope someone more knowledgeable can help me!
Many thanks in advance.
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Rutger is quite right. You have an 18-parameter model with dependence, and an 8-parameter model without dependence. You can compute the lnL_18 (for the dependence model) and lnL_8 (for the independence model), and use a likelihood ratio test with likelihood ratio chi-square = 2(lnL_18 - lnL_8) with 10 degrees of freedom (for the null hypothesis that the dependence model and the independence model fit the data equally well).
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I have constructed phylogenetic tree in Mega software (attaching snapshot), importing 'FASTA format' data from NCBI. According to editor, Nodes labelling should be in order: Genus, species, strain, Accession No. in brackets.
Please let me know how to edit sequence labels?
Thanks,
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Thanks :)
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I would like to separately perform Genotyping-by-Sequencing (GBS) on individuals from different non-model species. These species have no close phylogenetically species with complete genome sequenced. Therefore, using GBS I will have a set of SNPs genotypes from genomic DNA for each species. Is currently there a method that can allow me to detect and isolate only loci, among those I have retrieved, that are shared and genotyped in both the two species?
Many thanks!
Paolo
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How fortune i am finding this great question and answer.
I am a junior researcher and recently working with rice, just want to know how to retrieve SNP data from one specific gene in many rice cultivar.
What kind of database i should go for this purpose?
Thank you for your responds
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Recently, Christopher Monit, Richard A. Goldstein & Greg J. Towers published an article entitled 'ChromaClade: combined visualisation of phylogenetic and sequence data' in BMC Evolutionary Biology volume 19, Article number: 186 (October, 2019).
In all respects this looks like a very interesting tool to analyze sequence data and phylogenies. Has anyone tried it? Could you comment on the outputs please?
Thanks for your time.
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Brian Thomas Foley, would you mind sharing some of the tools you've employed to visualize amino acid mutations on a phylogenetic tree? I am having trouble running ChromaClade
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I have long been wondering about the following problem.
The regular, conventional theory of evolution states that mutations occur randomly.
The molecular clock states that mutations occur at a relatively constant rate over geological time (thus enabling to establish phylogenetic relationships).
Are not these two statements completely incompatible?
How can random events lead to a regular mechanism?
Albert Jacquard stated that the simplest hypothesis to explain the constant rate of amino-acid substitutions in polypeptides was to postulate that spontaneous mutations occur at a constant rate over time. Is not such an explanation tautological?
How is it possible to establish a logical correlation between random mutations and the molecular clock?
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A way of understanding this is to look at an analagous random process which derives time: radioactive half-life. Radioactive decay of any individual atom is a random event; we can never predict when a single atom might undergo radioactive decay. But if we look at a large number of the radioactive atoms, we can say how much time it will take for half of them to have decayed. For example, polonium-210 has a half-life of 138 days; if we start with a pot of a billion polonium-210 atoms and wait 138 days, 500 million of them will have decayed into different elements. Rhodium-101 has a half life of 3.3 years. It was start with a pot of 100 of them, 3.3 years later we will have around 50 left.
The same principle applies to molecular evolution. Neutral mutations (mutations which do not change the function of the sequence) are incorporated into sequences randomly*. We cannot say when a mutation might occur, but if we look at a lot of them, we can see a generalised rate of mutation. For example it might be 5 substitutions (mutations) per 1,000 sites, per million years. If we look at the same 1,000 nucleotide-long gene from two different species, and there are ten changes between them, we infer that around 2 million years have passed since they shared the same sequence: since they were the same species.
* Just to address a common misunderstanding: mutations can be random (but not always), but natural selection is definitely not random. Most mutations are rejected via natural selection - but the substitutions (=mutations) we use for molecular clocks are not affected by selection (a non-random process). For the molecular clock, the mutations are neutral: in protein coding genes, they make the same protein, despite a change in nucleotide content of the gene sequence. Without going into detail, each nucleotide triplets "word" (codons) which control the production amino acids (the components of proteins) can be "spelled" differently, but have no effect on the phenotype, so have no effect on fitness, and so cannot be subject to selection. (I am over-simplifying here.)
Overview
Kimura - Neutral theory of molecular evolution
Zuckerkandl & Pauling 1965
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During the last years ecological publications lacking in-depth taxonomic analysis of the material in study are published with increasing frequency, even in journals with a high impact index. More and more often there are lists of the most diverse groups, animals and plants, where "Genus Suchus sp.1" appears; "Genus Suchothersus sp. nearby (read: similar. "near" would be equivalent to phylogenetically related!) to guyus As a taxonomist, but above all as a biogeographer, I suggest that authors, reviewers and editors be more demanding about this aspect of their manuscripts. I believe that the correct identification of the species represents an added value for such papers. I’ll be very grateful for all opinion
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Igor (and other disputants): you are of course right as regards the question what and how should be, but your appeals should be addressed not so much "to the authors (during review) and to future authors (during lectures)" but to the publishers, editors, reviewers, funding agencies, general "policy-makers", &c.! Authors themselves "believe that they must prioritize greater number of species included into the analysis rather than the true taxonomic identity of the sample" because they usually must indeed do so: the attempt to prioritize taxonomy would have almost invariably resulted in rejection of their papers from most journals (especially those included in "ISI-lists", of high IF, &c., i.e. just those which, unfortunately, determine a scientist's career...), outright turning down their grant applications, and finally perhaps loss of the job... Unfortunately, under the present conditions most scientists (especially those employed in scientific institutions...), to have a chance to "survive", must "prioritize the act of publishing rather than the true contribution to the scientific community" - but this is not their fault!
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Good days to all the comunity. I'm doing works on trait evolution at interspecific level and I'm having problems with philogenetic tests. I need some easy tutorials for phylogenetic regressions and correlations on R program. Consider that I'm a roockie using R program. However, I think that despite everything is possible to get the skill. Very thank for some help.
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Hi So many thanks
Greetings
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I have just begun my PhD at University of Wisconsin -- Madison, and I am interested in studying the phylogenetic relationships among members of Dysphania and the Dysphanieae tribe, as well as the terpene composition of their essential oils. Would you be interested in collaborating to understand relationships within this group?
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Yes. i am interested too.
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Greetings,
Can anyone help me with a bootstrap resampling problem in TNT?
I am currently running an analysis with TNT in a data matrix composed by morphological characters (105 discrete and 25 continuous characters) and 87 taxa. From previous tests on TNT, I reached the conclusion that my dataset is rather complex, thus searches with default parameters for both traditional and newtech search cannot find the best result. I have been using a script with the following commands for my searches:
keep 0 ;
ttags - ;
hold 99999;
rseed 1 ;
sect:slack 1000 ;
xmult= hit 3 level 7 rat 10 drift 10; bb;
HOWEVER, I have been finding problems to run bootstrap support for this dataset: I cannot finish running the analysis. The resampling always stops doing new replicates before reaching the 500 replicates I have set. The bootstrap running analysis window will stop updating altogether for hours, until I manually stop the analysis.
These are the commands I have been using for the bootstrap search:
keep 0 ;
ttags - ;
hold 99999;
rseed 1 ;
sect:slack 1000 ;
ttags = ;
resample boot replications 500 [xmult= hit 2 level 5 rat 10 drift 10; bb] frequency gc ;
I have tried changing the parameters for the bootstrap analysis and using the default parameters from TNT, BUT they either still cannot finish 500 replicates, or when they finish the bootstrap values are exceedingly low (most likely because the resampling is not managing to find topologies close to the optimal I have found with the search).
Would anyone have any tips on how to change the parameters and commands to finish the 500 (or even 1000) replicates I am trying to achieve, while managing to do a good enough resampling of my data?
If desired, I can e-mail the matrix I am using and both scripts.
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You might try PAUP 4 as it is designed for parsimony analysis too and does the bootstrap as well as a few other parsimony measures. Perhaps if you ran it on a public server you could let it run longer. I like the Cipres Portal (https://www.phylo.org/restusers/login.action).
On the other hand, I suspect that you will still get very small bootstrap values and perhaps even smaller if you use the more complex model. This is because the bootstrap samples your data with replacement (so it is the same size as the original sample). Naturally some informative data will not be sampled at all for a given replicate and others may be sampled more than once. The idea is that a data set with strong phylogenetic signal will be included in many replicates while a small amount of signal which may have influenced the original tree will not be sampled in as many replicates. The bootstrap proportion is the number of times a particular pattern in your data is sampled divided by the total number number of replicates. So seldom sampled rare phylogenetic patterns will appear in only a small proportion of the replicates. With 500 replicates a value of 10 means that only 50 trees (10%) will have that branching pattern (clade). If the data is rich in phylogenetically informative data that has consistent patterns rather than conflicting patterns then you will get high bootstrap values.
Unfortunately the bootstrap does not recognized whether you model is good or not except in the sense that a complex model requires more parameters and so will require many more unique patterns to resolve the tree. As an aside, this is exactly why genomic-sized phylogenies almost always have very high bootstrap values. But as they are very large data sets, computers cannot yet compute trees with any but the most simple models with a few parameters. These models often do not adequately model the complexity of sequence evolutionary history and so the simple models are biased and provide very high support for the wrong tree. The same holds for any kind of statistical analysis. A poor model will give biased results. So your simple model may not be at all a good idea. On the other hand your data may be too limited to fully resolve the tree.
However, all is not lost, because we are often not interested in having high support for every single branch or clade. Perhaps you only want to know a-priori whether a certain clade is monophyletic. And suppose your data has enough data to resolve that particular clade. Then the support on the other clades is much less important than finding good support for your clade of interest.
Also you can in some programs (TNT I think, and PAUP I know) perform a Templeton (a paired test on the data for several trees - Kishino-Hsagawa for nucleotide data) test on your data by comparing the tree with monophyletic clade with trees that are not monophyletic. If the tree score is the same for both tree topologies then you can at least say that you monophyly cannot be rejected. Or if one tree is significantly better than another then you can say with confidence that you reject the other tree.
Should you need more advice please contact me again. This is a very common problem for phylogenetics in general.
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Hi everyone. I am looking for a paper about how to specify prior in phylogenetic analysis, for teaching an advanced course.
Usually I use this one, which is very nice, but I am looking for something more recent
Alfaro, M. E., & Holder, M. T. (2006). The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Evol. Syst., 37, 19-42.
Also I know this one, but is bit too much for my students
Wang, Y., & Yang, Z. (2014). Priors in Bayesian phylogenetics. Bayesian Phylogenetics: Methods, Algorithms, and Applications, eds Chen MH, Kuo L, Lewis PO (CRC Press, Boca Raton, FL), 5-24.
Thanks in advance!
Cheers!
Ricardo
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Might be too basic but see:
A biologist’s guide to Bayesian phylogenetic analysis
Also a case study:
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I'm a third year uni student, and have an assignment to do on phylogenetics. We can choose any question to ask as long as it can be answered with a phylogenetic tree. We will then search for data online using genbank etc, analyse the data, create a tree, and discuss. I think what's getting to me is such a broad spectrum. I was thinking hip dysplasia in dogs but am completely open to other suggestions. But I need to start by asking a specific question, and I'd really appreciate some help with that. Thank you
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Following Thierry B Hoareau 's suggestion, a pretty commonly used statistic for testing for phylogenetic signal in trait data is the K statistic from Blomberg et al. 2003 (attached), which basically asks if the given tree better explains your trait data (=incidence rates of hip dysplasia) than if we randomly permuted the trait data on the tree. If there if phylogenetic signal (=related individuals have more similar traits), then the fit of the tree to your data should be much better than to the random permutations. It wouldn't be too hard to do this test- you will need to create a table 'coding' the tips with your trait data:
e.g.
Breed hip_prob
Dalmation 0.12
Labrador 0.18
...
...
And you can use an R package called 'picante' to perform the test with only a few lines (from http://picante.r-forge.r-project.org/picante-intro.pdf):
#first install packages:
install.packages(c("ape", "picante"))
#then do the analysis:
library(ape) #loads packages
library(picante)
tree <- read.tree("/path/to/newick") #read tree
traits<- read.table("/path/to/table") #read traits
traits <- traits[tree$tip.label, ] #align with the tip data
multiPhylosignal(traits, tree) #test for phylo signal
which you can do using Rstudio (https://rstudio.com/).
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Which is the best program for constructing a Phylogenetic Dendrograms from RAPD gel image or RAPD gel score data?
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SPSS program is one of the easiest tools to draw a dendrogram from RAPD data.
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For phylogenetic studies, it is good to choose orthologous genes instead of paralogous genes. My question is, How to recognize whether a gene is orthologous or paralogous? Can you please give reference?
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I mostly agree with the answers above, but the sentence "That is, alleles passing a given similarity are considered orthologs, those not passing are considered paralogs." makes no sense to me. Recently duplicated genes (although there could also be other reasons for high similarity) genes often have very high levels of similarity (we are talking 99.9%), and they are still paralogs.
Furthermore, I am not sure that I fully understand the question.
The silly answer is that you recognize orthologous genes by belonging to two different species, and paralogous by belonging to a single species.
So the way I understand the question is:
If you have a gene X from two species (1X and 2X), how can you be sure that this gene has not undergone duplication in both species, resulting in the existence of paralogues Xa and Xb.
So now you are wondering whether you may be using 1Xa and 2Xb in your dataset. Is that the question?
The answer to that question is, first we have to assess whether it matters at all.
Gene duplication can lead to: 1. loss of function, 2. evolution of novel functions, or even 3. co-existence of two gene copies with almost identical functions.
The distinction between genes with 'same' and 'different' functions can be very arbitrary.
If you have the case 3, or simply a very recent duplication event, mirrored in high level of similarity, it may not matter at all.
So you may conduct pairwise similarity analyses on your dataset, and then identify the outliers with respect to the expected phylogenetic relationships. As mentioned in the reply above, this means that you cannot set a single threshold for similarity, as phlyogenetically distant taxa are expected to have low(er) similarity. Therefore, you should infer a similarity curve with respect to presumed phylogenetic distance, and then look for outliers from that curve. Somewhat complicated.
Outliers may indicate function loss, novel functions (in these two cases, these genes cannot be considered orthologues any more), but also a (mostly) orthologous gene undergoing an exceptionally high mutation rate, which can be driven both by adaptive and nonadaptive pressures.
In either case, these outliers are not particularly suitable for inferring phylogenies, and probably should be removed from the dataset, as they produce compositional heterogeneity and can cause long-branch artefacts.
I would probably try running analyses using a model designed for comp. het. (e.g PhyloBayes CAT-GTR model) on datasets both including and excluding the 'problematic' genes.
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anybody please help me, how we can differentiate Wolbachia infections into different groups (somewhere  Wolbachia infections divided into 8 or 11 or 13 groups), i found Wolbachia in my test specimen but now i don't know which group this infection will fall? 
and how we construct phylogenetic relationship between my test specimen and other organisms from different orders 
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excuse me, what are the specific specific primers to detect Wolbachia species not only subgroups?
Thanks
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Hello,
I use Geneious and installed the RaxML plug-in to run maximum likelihood phylogenetic analyses.
When running a neighbor-joining tree build, I get what I would expect to be the substitution rates. (For example, <0.001 for clade A.) However, when using the same genetic data to build a tree using RaxML, the substitution rates are unexpectedly high. (For example, >0.04 for clade A.) One note, I am running rapid bootstrapping when building the ML tree. Not sure if that is the issue.
Any suggestions?
Thanks,
Peter
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Got it! Figured it out. Really appreciate the response.
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Does exist a modern phylogentic / molecular study, or being in preparation, on the Pieridae and Papilionidae including African ones (with a large spectrum including at least all the "species groups").
I seen some general papers but Africa is always poorly included and never with large set of species or including different "species groups" of each genus.
thanks, Thierry
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Nice for African Eurema, I started with them recently. Sure they need study.
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I have sequenced a vp1 partial gene of FMD virus and I have detected serotype O with sequence similarity of 95% to the closest on on blast search. I am struggling on how to determine the topotype of my sequence as well as lineage by phylogic tree, after I constructed the tree by nighbour joining it showed that my sequence is to far by distance from the closest one. 
the phylogenic tree is attached. 
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collect the reference sequences then follow the published paper for determining the linage.
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I am comparing phylogenetic data sets in elasmobranchs from GenBank, and am under the assumption that in most species COI will be faster, or have a higher mutation rate, even though both loci are constrained by functional requirements of metabolism, since both are housekeeping genes. But certain authors have suggested that when a COI data set doesn't show differentiation, we should try adding NADH2, but I am not convinced this is a productive direction to take the project.
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The genbank database has tons of elastimobranch complete mtDNA. So should be straightforward to see what the maternally inherited mtDNA has to say about the evolution of this large and important group.
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samples will be serum
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Yes
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In phylogenetic studies why concatenate dataset from nuclear orgin with dataset from chloroplast orgin? Both datasets are different.
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