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Phylogenetics - Science topic
Explore the latest questions and answers in Phylogenetics, and find Phylogenetics experts.
Questions related to Phylogenetics
How can large-scale phylogenomic datasets be improved to reduce uncertainty in tree resolution?
I study plants and I've never come across a paper where the outgroup is a selfer. Is it okay if that is the case?
I used Beast to analyse COI sequence (741 bp) in a bat species, and the analysis clearly indicated that instead of one species, we had two different ones. I'd like to estimate the divergance date between these two genetic clades. I decided to use Beast. However, I have no fossil Datong information, so in BEAUti I fixed mean substitution rate to '1'. I received the tree with ages of nodes estimated in units: substitution per site (as stated in the manual). Is it possible to 'translate' this information into years, for example using the substitution rate for a particular gene?
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
I'm currently working on resolving a phylogenetic tree, and I'm wondering if it's possible to combine both mitochondrial and nuclear genes to achieve a more accurate result.
I've been battling with codes and it's no use. There must be a way to select a group of taxa as the outgroup, but I couldn't find how.
I suppose that the alternative path is to make the whole analysis and constraint that group as a family.
Any thoughts on how to resolve this?
I am using MEGA to build a phylogenetic tree using two genes. They were already aligned separatelly using MUSCLE, but now I don't know how to continue...
What is the explanation of this change which has affected the well-known Cupressus lusitanica (I assume some phylogenetic studies)
Is this a definitive change and should we use this new scientific name, or continue using Cupressus as a synonym?
I am working on a dataset with 65 individuals that belong to 6 species. I am trying to use a linear model that corrects for phylogenetic relatedness amongst individuals, however I am concerned that this is reducing the power of my models given that my effective sample size is small, due to having only 6 species. IS 6 species too few to incorporate phylogeny?
Hello,
I am facing the following situation:
I have two species phylogenies of groups very distantly related to each other. For each tip (species) I have the value for a continuous trait. I would like to check whether or not there is a significant difference between the two groups, while accounting for within-group relatedness.
AFAIK, this type of analysis is usually done with a phylogenetic ANOVA test, e.g. as implemented in the R package phytools. However, the function expects a single phylogeny, not two.
Can anyone suggest a software that can do what I need, or help me think of a procedure for performing the analysis?
Thanks!
Dear colleagues,
I need a laboratory for the phylogenetic study of fishes, I have a new species that has never been identified before, so please could anyone of you guide me ?
By the way, it's a new fish in northern Algeria.
I hope I could find help from you!
Thank you in advance
Please provide answer as we have got burkholderia cepacia n purified water which is identified as herbaspirillum huttiense during further analysis.
I am trying to compare 2 population using GenAlex (haploid), but I would like to add the region factor, the problem is that both populations are distributed in the same regions and I can't find a way to insert this type of data...
Hi,
I am trying to do phylogenetic independent contrasts for my honours project however, when using the code
pic.bl<-pic(female.body.length,cent.tree)
pic.gw<-pic(avg.egg.diameter..mm.,cent.tree)
fit.pic<-lm(pic.gw~pic.bl+0)
fit.pic
I keep getting the error - 'phy' is not rooted and fully dichotomous
Would some be able to explain why this is/ have any way to resolve it?
Thank you in advance
Emily
I do not find clear to which specie the aforementioned organism belongs. On some sites, I read that it references to a group of unclassified species instead ofjust one. I would appreciate if anyone may enlighten me with a taxonomy/phylogenetic approach.
Thanks in advance!
I would like to know what are the differences between phylogenetic conflicts in the trees and also the meaning of lack of resolution (solved and unsolved trees) and the presence of conflicts. Can you tell me how we can evaluate the resolution and conflict of a phylogenetic analysis?
Thank you for your responses.
Best,
Houtan
I am working with an enzyme with high substrate specificity and only a few bacteria have it. I recently discovered that my protein has extremely high structural similarity with a protein present in all bacteria. The substrates are somewhat similar but definitely not the same. The sequence identity is ~30%, and the active site residues are lining up pretty well. I just don't know what kind of phylogenetic analyses I can perform to explore this relationship further. Is there any way to determine if this other protein is in fact an ancestral version of my protein of interest?
Dear all,
I have been testing a dataset of sequences for the best substitution models to use in phylogenetic reconstruction. Each dataset used was tested for models independently three times (using jModelTest 2.1.10), yet each of the three runs gave different results when it comes to BIC value (I refer to it because next step is employing BI) - therefore proposing a different model for each run.
Can anyone offer some insight into what model to select in such cicrumstances and/or why that matters?
Thank You for Your replies
Hello, I am researching the phylogenetic tree of snakes. (bayesian Inference tree and molecular clock..)
My sequences are 1300 bp, but sequences of outgroups are about 600 bp.
Can I change the difference of about 700bp to a missing data and analyze it?
especially phylogenetic tree(ML, BI tree) and Relaxed molecular clock(using BEAST2).
I have a published phylogenetic tree but no access to the rough data used to generate the tree. I want to compare among clades in terms of morphological characters. How do I include the phylogenetic correction? Should I just measure the distance between clades and use this as my phylogenetic correction? The phytools package in R assumes I have the rough tree data, and I don´t. Some suggestions will be most welcomed.
Does it vary with the abundance of homologues and phylogenetic relationship of source organism with the organism (either within the same genus or across different kingdom) from which we want to discover/mine the homologue?
Any details (Books , courses, slides, articles) can help me. what are the difference between botanical and phylogenetic classification? Thank for your response
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!
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
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.
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.
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
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?
Experiencing slight difference in the results of tress obtained from BEAST and Maximum Likelihood...
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:
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!
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.
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.
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
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
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.
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.
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?
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!
Better means it gives faster results and higher likelihood!
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?
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?
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?
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
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
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
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?
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.
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.
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.
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
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
Need a detailed tutorial on XLSTAT ( Input type format, output file, drawing conclusions etc) Unable to find online.
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?
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
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
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).
Normally dN/dS ratios are calculated and interpreted as below one negative selection, above 1 is positive selection and 1 means neutral selection. How to interpret dS/dN ratios? Programs like SNAP provides dS/dN graphs and ratios.
For example:
Averages of all pairwise comparisons: ds = 0.1678, dn = 0.4090, ds/dn = 0.4072, ps/pn = 0.4707
Please see image as well.
Can somebody explains it in simple words as I am not much familiar with this?
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?
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!
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?
Which is one is better in between 16S rRNA and microsatellite phylogentic study?
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.
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.
I have four whole genomes sequencing of E. coli isolates , and I wanna to classify in phylogenetics groups.
Whats is the best ways?
Thanks.
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
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.
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?
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?
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)?
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.
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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