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Evolutionary Genetics - Science topic

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I want to use BEAST to do EBSP analyses with two loci. I open two "input.nex" files in BEAUti to generate a "output.xml" file (In the Trees panel select Extended Bayesian skyline plot for the tree prior), and then run BEAST. I do not know if this is right and I do not know what to do next. I can not construct the trend of demographic history in Tracer just like BSP. I got one log file but two trees files (for each locus), and I do not know how to import both tree files into Tracer.
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One of the best websites to find the answers to these questions is the following link:
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I like to download latest version of MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 but the official link ( http://e.informer.com/megasoftware.net/mega.php ) is not working here. Anyone to help me by downloading and sending me the download link of google drive or dropbox please.
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Sharing of registered copy will be the violation of the user agreement. You can download it by using the following link - https://megasoftware.net/
If you still failed to download, then I would suggest to email the MEGA team. Good luck.
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I have prepared a nj phylogenetic tree using ape package in R. But due to large number of sequences and taxa, the tips of the tree looks overlapping. How can I increase the distance between the branches, so that my tree can be viewed properly with all the tips?
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You may find it easier to just view the tree in a graphical tree browser: http://tree.bio.ed.ac.uk/software/figtree/
Output using ape write.tree, then import to figtree
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Anyone know how to interpret the matrix of distance genetic whose analysis were performed in the software MEGA 5.0 (Tamura et al. 2011) using the pairwise method with the p-distance model?
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If you multiple those values per 100 you will get the percentage of difference (0.7% and 25%).
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Many species of living organisms have colonized the Earth, and this may have happened sequentially. Which of these communities was more susceptible to evolution? Is it about natural selection?
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Hi,
I'm a beginner in MEGA software. I have 89 protein sequence for which I need to construct a phylogenetic tree using bootstrap method with 1000 replication with data set parameter with complete deletion.
But I am not able to construct a tree because of 3 sequence whose protein length is very less when compared to other 86 sequence. Even I tried by deleting non conserved regions in all protein sequence but still I am not able to get a tree because the size of the smaller proteins become smaller and smaller.
Kindly help me out in solving this problem.
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Try to make a distance matrix with pairwise distance method with input an alignment file in the .meg format. With lots of dissimilarities, value should be replaced by n/c.
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Hi all,
I would like to estimate the relative rates of evolution of a bacterial gene locus (protein-coding) across time. The length of the locus ranges between 10000bp and 25000bp. I have performed multiple sequence alignment using CLUSTALW in MEGA6 using 90 sequences corresponding to the locus. I would like to create a model to estimate the relative rates of evolution of each locus - how rapidly a sequence can change into any other 89 sequences. I would like to check rates of recombination and base substitutions among the sequences. Please tell me any method or protocol for estimating the evolutionary rates.
Thank you.
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10,000 to 25,000 bases sounds like more than a single bacterial gene. Are you looking at a complete operon or something even larger? To measure rate of change vs time, you need many dated events in the phylogeny (evolutionary history) and for most bacteria we do not have a real solid fossil record for example for telling us when Eshcerichia coli last shared a common ancestor with Salmonella typhi. As you note, recombination is rampant within most genomic regions of that size over timescales far shorter than many other evolutionary processes. And the more similar the bacterial "species" or "strains" are to each other the more often they recombine and the less easy it is to detect the recombination events. Escherichia coli exchange plasmids and phages much more often with other Escherichia coli, than they do with Listeria or other more distantly related bacteria.
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Why transition from moneocious to Dioecious and different forms of  Dioecious were found in some plant families? Is this an evolutionary adaptation or due to some other reasons?
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I advise you to read:
Plant Breeding Systems by A. J. Richards, second edition 1997; Chapman & Hall. 
I think this will help you better understand the evolution of plant breeding systems. 
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Hi everybody,
For my study, I need several life history traits:
- size of organisms
- number of offspring
- longevity
- their reproduction
and so on...
So I'm looking for databases for protist, plants, fungi, metazoa... I know this database: http://genomics.senescence.info/species/. Do you know any other?
Thank you very much.
Benoît
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Hi everybody,
Thank you very much for your answers. I will check all your links and come back to you soon.
Cheers,
Benoît
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Since amino acids are degenerate in nature, the amount of variation will be higher than its respective nucleotide sequence so will it make sense to construct a phylogeny tree using the protein code?
Also, how different should the sequences be from each other to be marked as a different lineage or under a different internode?
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As usual in science, it depends on the aim of your study. If you are trying to unveil the taxonomy of an unknown species, I would suggest you to work with 16S for bacteria/archea and 18S for eukaryotes.
If you are studying protein coding genes, as mentioned by Dr. Kumar, it might be more reliable to work with aminoacidic sequences (or translated nucleotidic sequences), as they have a higher information content ( 5x fold).
About the threshold of similarity in clustering sequences, it mostly based on experience on the sequences you are working with. It depends if you are working with nucleotides or coding sequences, the expected divergence between sequences, the evolutionary rate (K) of that region and the evolutionary distance between organisms that harbour the sequences. On top of that, there is also the aim of the study. It is not the same comparing variations among closely related populations (high similarity is expected) than variants between sequences that belong to different orders.
I would suggest you to read the books and reviews of Dr. Felsenstein, to learn the best approaches to your problem, as well as the most common pitfalls.
Cheers.
JMC
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I need to reconstruct ancestral sequences in evolution of short peptides. Trying all possible models in FastML I obtained results that just didn't make much sense. In Mesquite there are currently no available likelihood models for protein evolution... 
For me this is a first experience in this field. You, who do have some experience with peptide (or more likely protein) evolution reconstructions, which programmme would you recommend to use?
Thanks
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Use MEGA7. The King of them all
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...and how you might deal with it in population genetic studies?
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Two good references on microsatellites in mitochondria:
Lunt DH, Whipple, LE, Hyman. 1998. Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Molecular Ecology, 7, 1441-1455
Mayer F, Kerth G. 2005. Microsatellite evolution in the mitochondrial genome of Bechstein's bat (Myotis bechsteinii). Journal of Molecular Ecology. 61. 408-416
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Hi, I am working on calculating the divergence times for a group of bacteria (all part of the same family) with less than 5% 16S rRNA sequence difference.
The typical rate of change in 16S rRNA in the literature is a relatively uniform rate of 1% per 50 million years. My question is can I use MEGA7 (TimeTree) or BEAST under uniform clock rate assumptions to calculate divergence times and construct a phylogenetic tree based on divergences based only on the sequence differences of the aligned sequences from the groups of bacteria?
Am I missing something? If they rate is uniform and I don't have multiple calibration points etc. do I still need complex assumptions or use Bayesian methods? Thanks.
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Dear Reginald, 
It is almost never a good idea to assume uniform rates.  In addition, rRNA genes tend to have rate covariances among sites due to rRNA secondary structure, which can be accounted for using appropriate Bayesian models.  So resist using the quick and simple solution, because it may not be accurate and will give you a false degree of confidence in your tree topology.  
Regards, 
Dave
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I have a SNP dataset that contains several cryptic species. I can separate the individuals into groups using STRUCTURE and PCA, but I'd like to give them a nice number so we can say that yes, they are actually substantially differentiated.
For my last project we were just using single sequences, so I could calculate plain old sequence divergence. Is there anything like this for SNP data?
Alternatively, I do have the sequences the SNPs were retrieved from. Is there a way to calculate divergence using many sequences?
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Hi Emma,
 If you want to calculate the genetic diversity of a single population, there are several estimates that you can use such as the allelic diversity, proportion of polymorphic loci, observed and expected heterozygosity, and gene diversity of Nei (pretty much the same that you use for sequence data). A very friendly software that estimates all these parameters is GenAlEx (http://biology-assets.anu.edu.au/GenAlEx/Welcome.html).
 Now, if you want to quantify the level of population subdivision, as Manolo suggested, F-statistics are more appropriate. PopGenome package is one of the best alternatives in this regard, although there are also other free available softwares such as Genepop (http://genepop.curtin.edu.au/) that are also pretty easy to use.
Cheers,
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So, it's a common notion that must be only one haplotype of mtDNA in the organism, but may somebody knows examples when it is not true?
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Dear Oleksandr,
Regaring the frequence, it is hard to answer, Shokralla et al. 2014 found 10% of ambiguities in a large dataset of DNA barcodes (possibly numts or heteroplasmy). For numts, there seem to be no phylogenetic congruence with their presence/frequence, indeed, when examing two close congeneric species of beetles, we found one free of numts while the other was mush affected. (https://www.researchgate.net/publication/272359549_Ghost_mtDNA_haplotypes_generated_by_fortuitous_NUMTs_can_deeply_disturb_infra-specific_genetic_diversity_and_phylogeographic_pattern)
I hope this helps
Julien
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Hi all,
I have pooled RAD-seq data (multiple individuals sequenced in a single library prep) and I am interested in haplotype frequencies.
Reads have been mapped to a de novo reference and I have a BAM file for each population.
It seems reasonable to assume that haplotypes frequencies could be called from BAM files in a manner analogous to determining allele frequencies in sequenced pools; e.g. counts of different haplotypes in the sample.
However, I cannot seem to find any good software specifically designed to deal with pooled RAD data. GATK and HaploPool, for example, are extremely limited by ploidy size. Collen Beck's rad_haplotyper (https://github.com/chollenbeck/rad_haplotyper) is nice to use and good for RAD data but assumes individuals as the sequenced unit; at most it would only provide information about which populations are likely fixed for particular haplotypes.
Does anyone have good recommendations?
Cheers,
~ Josh
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@Ivan and @Yann: Thanks for comments. I am using Freebayes to call SNPs because it has an argument that considers the mapped BAM files as deriving from pooled samples. BUT I REALLY WANT HAPLOTYPES!
Also, I have worked with the Popoolation tools before, but my understanding is that they are better suited to projects where you have much larger contigs (e.g. choromosomes as opposed to RAD fragments).
It confuses me that so little has been done to achieve this gap in analysis tools.
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Guys, i want to analyse some CP gene sequences of some plant RNA viruses by HyPhy package (SLAC, FEL, REL) and also dN/dS. but i am stuck, plz help
Sample article (see materials and methods)
doi:10.1007/s00705-015-2729-z
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Thank you Artur Burzynski
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The computation of phylogeny used to rely on sequence comparison (i.e. alignment). For genetically similar strains or species, there is typically only a few variations detectable in the aa/nt sequences of single-copy or selected gene list. On the other hand, the selection of gene list is also difficult. A prepared set of conserved genes can be efficient but may lead to bias. As an alternative, single-copy method can include more information, but a gene cannot be selected if it has no orthologs identified in the other strains/species. In case that recombination or horizontal transfer happened and even was involved in phenotype or adaptability of a pathogen, the transferred element would therefore not be included in the reconstruction of phylogeny. A problem in tracking the spread route can thus happen.
My question is: can it be possible to include genome recombination information into the reconstruction of phylogeny, or is there available method to select a suitable gene set for sequence alignment and phylogeny computation?
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The answers to your questions really depend a lot on what type of organism you are studying.  Horizontal transfer between bacteria is quite a bit different than horizontal transfer between mammals, for example.  Some viruses undergo recombination quite frequently, and others do not.  In some mammals we can be certain that there has been no gene flow between isolated populations for x number of years, and in other mammals we are not so certain of total isolation. 
Even with very clear speciation events, such as modern humans now being a completely separate species from Chimpanzees, we have evidence of incomplete lineage sorting in the distant past when the human lineage split from chimpanzees, and introgresssion in more recent splits such as Neanderthals with modern humans.
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I'm doing a population genetic study on microsnail and I've found very high intraspecific genetic divergence between isolated population at very small scale. I'm curious to compare my results with similar studies on population structure of small organisms with very poor dispersal ability. Do you have any paper in mind?
It could be fresh water organisms in close-by ponds, or two population of invertebrates on the opposite sides of a river.
I know that "small scale" is relative to size and dispersal ability, but I'm curious to see what is the absolute shorter distance at which we can observe conspicuous allopatric divergence between populations in eukaryotes. 
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Hello Giacomo;
     Species of ants in which the new queens disperse by walking are good candidates for differentiating populations in the fashion that you are thinking about. Here is a reference for an example that might be of interest.
      Jowers, MJ, et. al. 2014. Recent speciation and secondary contace in endemic ants. Molecular Ecol. doi: 10.1111/mec.12749.
Regards, Jim des Lauriers
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What are the factors that affect on the significance of the natural selection tests used in DNAsp?
I am searching if there is natural selection in my gene or not? And i used different tests as Tajima's D, Fu's and D, and Fu's and F. In one test Ithe genes seems to be neutral but in other test have significant values.
I am calculating Fst, Nm, No. Of Haplotype, nucleotide diversity, ka/ks ratio, etc.
How can i BiIOLOGICALLY interpret my results?
Any suggested references!
Thank you 
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Thanks alot Dragos, 
Those papers where of great help to me.
Appreciate it 😊
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Im working with environmental Vibrio strains and I have used 16S to preliminary taxonomic identification (besides I know that is not the best marker for vibrios, but it is  the data that we get). I ran a phylogenetic reconstruction but the bootstrap values are very low, close to 0.
The overal mean distance betwen the sequences (25 in total) is >0,02 and I used the Jukes Cantor model and complete deletion.
Is it able to be improved  or it is because the phylogenetic signal of the 16S gene is not good enough to discriminate the clades?
thanks
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If your sequences are good you could try aligning them to a 16S rRNA secondary structure model which relies on conserved and semi conserved regions. Gaps in the alignment then have more meaning instead of just being removed before computation. Alignment programs such as Infernal and Pynast which come packaged with QIIME do this sort of alignment.
The Ribosomal Database project also performs this type of alignment on all sequences that are submitted and the website also has tools for building phylogenetic trees.
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Is there any difference in them molecular level? Even though it is produced from different combinations of genetic code but produces the same amino acid, is it acceptable between eukaryotes and prokaryotes ? 
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If you are asking if there is any difference between glycine coded by GGA and glycine coded by GGC. The answer is 'no'.
In certain different systems, the codon table varies.  eg AGA is arginine generally, but a stop codon in the mitochondrial genome.
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For divergence time estimation
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Hi,
There is no generally accepted substitution rate. You can calibrate a sutitabele substitution rate for your target marker using geological events or fossil records in BEAST software. Hope this helps.
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These days, I have been thinking about speciation and diversification. If we make the most simple assumption as below, we come to the one species model. The questions could be below -
1. If there is only 1 species with only 1 gene, how does this species evolve? Can we illustrate the species evolutionary history with mathematics?
2. If there are m species, with n genes for each one, how does the species diversity evolve? There are no interactions between species/genes. Can we illustrate the species diversity evolve with mathematics?
Without answers to the 1st, we can not go to the 2nd for more than 2 species/genes. 
I do appreciate if you would kindly offer some references or clues. 
Best,
cd
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Dear CD,
the question you are dealing with is of primary importance and will require an impressive amount of reflexion! However, I think that a previous question is to be solved, concerning what the species is? It seems to me quite evident, that your concept of species is not nominalistic, but realistic, by considering species as real natural entities in the frame of life. In this case, my opinion is, that you have to explicitly choose between a relational concept of species ( see e. g. Ernst Mayr and followers) and a non relational one (see e. g. Paterson, Lambert, Eldredge). Personally I wrote a few papers about this topic, mainly from a biogeographical standpoint. I’ll very glad to send you some .pdf documents, anyway, you may download it from my ResearchGate page. Please keep in touch.
Bests
                                                      Mario
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Currently, I'm trying to make plant phylogeny reconstruction using Bayesian inference and have a need in applying two different evolutionary models for different parts of sequences in one sampling because they have a secondary structure with paired and unpaired regions (ssRNA and dsRNA) which has an influence on nucleotide substitution frequency. I want to take into account such impacts. Is it possible to calculate Bayesian inference for phylogenetic purposes using two different evolutionary models with different parameters for different parts of one sampling of sequences simultaneously?
Thank you in advance.
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Yes, you can divide your dataset into partitions and apply different sequence evolution models to those partitions. A common framework might first involve using PartitionFinder (http://www.robertlanfear.com/partitionfinder/) to delineate partitions and their respective "best" models.
Sounds like you are using Mr. Bayes? You would then define your partitions in the Mr. Bayes command block of your nexus file.
For some help in configuring your nexus file for a partitioned dataset, see: http://mrbayes.sourceforge.net/wiki/index.php/Analyzing_a_Partitioned_Data_Set
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I want to analyse coding nucleotide sequences using NJ phylogeny and I am wondering which model is better for my data set. Tamura Nei or Tajima Nei?
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I would use ML or Bayesian rather than NJ. You can test models in programs e.g. JModeltest.
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I am working on population biology of a pest. I have used gene specific marker and got some haplotypes. I want to know what to do further and how to find their relationship. Please help. 
Thank you.
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You may try to use the software Network 5.0.0.1 . Use the method Median-Joining, then draw the network. To create the file for Network, use the software DnaSP, you can generate haplotype list and save it in the proper format. You may also divide samples in different populations, generate the haplotype list and save in the proper format for using it in the sotware Arlequin v.3.5 . In this last software you can perform a multitude of analyses, such as AMOVA, pairwise Fst, neutrality tests and so on.
Gustavo
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Sequence X: 5UTR-NS_Polyprotein-Promoter-Structural_Polyprotein-3UTR
On the scenario above, would you consider 5 partitions, or you would break apart the Structural and Non-Structural (NS) proteins? Given that they are read from start until stop, would be fair to assume that the polyproteins are single blocks and the proteins within shouldn't evolve separately?
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Thank you both! I used PartitionFinder2, split in 5 partitions (5UTR-NS_Polyprotein-Promoter-Structural_Polyprotein-3UTR) for an alignment with 340 genomes (same virus). Unfortunately, RefSeq sequence for this particular genome just shows the structure as 5 partitions and some of the genomes (about 50) that have the proteins within each polyprotein annotated, have variation regarding to the actual real size and boundaries of each protein. Based on that, I decided to go with 5 partitions instead of more and assume the boundaries based on the RefSeq. Better safe than sorry? Asking here, critics are more than welcome, better here than when paper is under peer-review.
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I stumbled upon a study in which distinct SNPs in the fetal haemoglobin of Llamas supposedly made their erythrocytes to have more affinity towards oxygen, giving an advantage in their high altitude habitat, contrary to their camel cousins who lacked such mutation. Is it possible to retrace this back to humans?
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Dear  Rajit ,
im not genetic expert .. just astrobiologist .Dont' you think  better to go with paleo habitat . Biogeographical variation can be effected to genetic too. See Two branches of a Homo erectus exodus out of Africa could both have the genetic mutation that resulted in Homo sapiens springing up in two different location, it is probably highly unlikely, but possible. Three or more locations to have the same genetic mutation would be near impossible. Recent DNA testing indicates that Homo Sapiens left Africa, but some of them returned many thousands of years later.
On purely speculation, what could be a more likely scenario is that an early predecessor to Homo sapiens left Africa, developed into Homo habilis or another species, then returned to Africa where they then continued to changed until Homo sapiens developed. Hominidae appear to have developed in what would become southern Europe, southern Asia/India, and eastern Africa. There were Hominids in India knapping Acheulean artifacts during the late middle Pleistocene. Could a species develop in the Ganges River Valley or Yellow River Valley and then return to Africa to further develop while that lineage died out?
The question also is how complete is our fossil record? At this point not very complete at all. Do we find more early fossils in eastern Africa because of better preservation than some other locations, like India or China? I am sure someone has looked into that. Still, we possibly have fossil evidence for only a tenth of the Hominid line, maybe more, maybe less. While paleoanthropologists have sequenced the fossils that we have, it is now looking like there were many hominid species running around Africa at the same time. Who knows how many more branches and dead ends of the family tree there are as yet undiscovered. And why Africa? More biodiversity? More competing species? More competition period? & why high altitude ? 
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There are many methods used in phylogeny viz. Maximum Likelihood Tree; Neighbor-Joining Tree;   Minimum evolution Tree; UPGMA TREE & Maximum Parsimony Tree.
I have simply two questions
Whats a criteria for new species and how molecular studies will support?
Which will be best method for species relationship or identification of new species/genus?
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Parsimony is outdated. Go for both Maximum Likelihood (ML) and Bayesian analyses.
For ML analysis can use Garli, RaxML or IQTree. For Bayesian try MrBayes or BEAST.
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I have a genomic dataset for tree populations. I would like to compare the current genetic diversity with the genetic diversity i.e. 20,000 years BP. Would bit be possible to do that using coalescent simulations + model testing approach?
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Dear Dr. Rosalia.,
Here are a couple of papers which could be of some help.
Alcala, N. & Vuilleumier, S. Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations. Proc. R. Soc. B 281, 20141369 (2014).
Good luck!
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Can someone help me in understanding the relation between Tajima's D test and ZnS test for linkage disequilibrium? And how does recombination influence the statistics? Basically, the Tajima's D test reveals the deviation of neutral model at intron 1, however, ZnS test shows that the exon 1 and 2 show significant LD. These observations seem to be not consistent to each other. How can I explain this? Thank you!
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Dear Tânia:
You have a couple of issues here. First, TajD. As you probably know, a significant negative value of TajD means either a recent selective sweep (or linkage to it) or a recent population expansion following a bottleneck. In order to distinguish between the two possibilities, you need to compare "many" genes (as population expansion should be detected on all sequences, whereas a selective sweep would be exclusive to some selected gene).
On the other hand,the  DnaSp manual (the help included in the program) indicates that for Coalescent Simulations the intermediate level of recombination is the case for most nuclear genes (except if you hve a hotspot) and that you should use the value of per gene recombination parameter R. Therefore, do not separate exons and introns. Use the whole gene sequence for your estimates.
Finally, please note that you can use ZZ=Za-ZnS to detect intragenic recombination.
Hope this helps
Pablo.
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I have genomic data (500 loci) is necessary to obtain the evolution model of all this 500 loci and what program i use to do that? modeltest? partionfinder?
thanks!
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thanks Tyler
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I wanted to know whether the universal primers like ITS, matK etc can help in resolving the members of a monotypic( single species) genus.
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Hi Sora,
After the clarification you provided let me ensure you that there is no clear case can answer your question in a general form. You have to test it first, the easiest way is to search for the ITS and/or matK sequences of the species under study at any nt database, then do a simple analysis to determine whether the species posses an intra-specific variations enough for your study. The other way is to select few of the most different samples (e.g. different locations, morphotraits, collection period... etc.) and  sequence the ITS and/or matK before proceeding with all your samples.
I may also recommend combining a cpDNA region (e.g. ycf, rbcL...etc.) along with the nuclear ones as the genetic variation and phylogeny are something a bit different from DNA barcoding.
Best of Luck! 
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For year I have been looking some information to help me to understand the signification of this kind of morphology in the liver of a species of Cuban hutia (only is present in Capromys pilorides). See picture attached. In all mammals of the world, only C. pilorides and the Hispaniola hutia (Plagiodontia aedium) have this type of reticulated liver. In both cases the liver have this reticule during all life and is present in embryos states too. The other species of the family have the liver with smooth superficies like other all world mammals.
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Hi Jonathan, yes the modification was recognized during the sp. description in 1822 by Say (in C. pilorides), later Owen wrote about this rare modification. It is not a pathology .I dont know any studies about histology. The modification is like to those changes in structures that  looking for more superficy. However I dont know or remember if the cell in liver border are different function than cell from depper part. I need to check. the case is that this kind of liver could have a more superficy that the normal liver. I connect with the mistery every some time.
A hitological study could be important but functional and metabolism of blood and comparative studies with the othes spp. could be very important too.
I have been very interested in this problems for year, thinking that it could be important for liver anatomy studies, blood metabolism, etc.
There are not anything in literature and I have been looking for any other papers about liver and it are no helping me so much.
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Hello everyone,
I am a very new user of MrBayes 3.2. Please help with my doubt.
I have constructed a phylogenetic tree of 43 sequences using MEGA and MrBayes. I have attached both the files here. I am getting a correct tree pattern in MEGA_Neighour joining.nwk tree file as expected. But in MrBayes.con.tre tree, Rabbit_CXCL1 and Rabbit_CXCL2 are seperated from the entire tree, even though the nucleotide sequences of those two are not so different than rest of the sequences. I want a MrBayes tree with those two sequences incorporated. So, apart from .con.tre, can I use some other tree from MrBayes output file?
There are many trees in .t file. Can I choose any one among them? Or is there a particular criteria to select one?
Thank you in advance.
Regards,
Minal
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As long as you do not want to do any fancy things like doing your own post analysis of the markov chain of hypotheses, only the consensus tree is of interest for you.
I do not understand what the problem is with the two sequences being separated from the rest of the tree. Each group of two sequences are separated from the rest of the tree. Your NJ tree is a cladogram without branch lengths. Therefore the amount of separation cannot be compared among the two trees.
Best Christoph
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Is it possible or acceptable to tell that a gene may be older than its homologues only from the observation that it contains relatively more GC % ? How much difference in GC content qualifies to tell a gene is a younger/older acquisition ? 
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Yes. I am trying to select the oldest member among members of an enzyme family to make rooted phylogenetic tree. 
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Does evolution selects on absolute "random" mutations? If not, is life capable of directing mutation to where it wants?
To clarify, I want to focus particularly on the possibility of a so-called "mutagenesis machinery" that allows life to assign the stress with an attribute that elevates the mutational rate, say, on a specific chromosome or a specific set of genes, be it what stress the cell is facing. This process then allows cell to rapidly search this "mutation space" rather than trying out in every direction. The question is solely asking whether such directed mutagenesis could be possible given our understanding of molecular biology.
On a macroscopic level, we already know that selective fixation of random mutations potentiates the species to re-adapt itself to a specific environment. My question is whether this adaptation itself can be adapted to some extent, over the whole course of molecular evolution.The result of UV-stressing experiment would hold whether this hypothesized machinery exist or not. UV stress is an extreme example in that the integrity of the genetic information is damaged. It will therefore be a good topic to expand. However I myself is not familiar with the current consensus in evolutionary biology so may need some time to catch up.
To extend, this hypothesized machinery would therefore need some form of "memory" that allows it to learn the kind of stress it's facing. It's a bit like machine learning, where feedback are deposited to instruct further behavior.
The question is solely inspired by the idea of "improving an algorithm by iterations" in other fields.
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Relevant paper in PNAS
"With hundreds of Escherichia coli cell lines evolving in a near-neutral scenario under exposure to the fluoroquinolone norfloxacin, this study reveals a significant linear relationship between the mutation rate and antibiotic concentration, while also demonstrating that antibiotic treatment compromises the efficiency of DNA oxidative-damage repair and postreplicative mismatch repair. Thus, antibiotics not only impose a selective challenge to target and off-target bacteria but also accelerate the rate of adaptation by magnifying the rate at which advantageous mutations arise."
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Could somebody advise some good software or online tools which could detect genomic rearrangements? The prediction of possible break points or suggestions on the underlying mechanisms would also be great. I have fasta files for several chloroplast genomes, where I have a huge inversion and some other complex rearrangement and I would like to determine the punctual end points for the inversion.
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For me PipMaker (http://pipmaker.bx.psu.edu/pipmaker/) or BRIG (http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402) seems to be working better. I can also use ACT to get a closer view of BRIG results. I'm finding it hard to view the blocks in MAUVE and then spot the differences. 
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Chimps are present but in between links or other species between them and humans got extinct?
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I think that the main problem here, regarding fossils in chimp's evolutionary lineage, is the problem with fossilization in Africa. Generally, the conditions for fossilization are not so good there. The fossils of hominids are present because they seem to be very abundant all over Africa. Chimps and their ancestors probably were presented with small populations and in areas with even worse conditions for fossilization. That's my opinion...
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I´m searching an R package or command line program to calculate heterozygosity-excess (similar to BOTTLENECK, Piry et al. 1999) and m-ratio (Garza and Williamson, 2001) tests for population bottlenecks based on microsatellites. 
Would be great if anybody has an idea about that as I have lots of datasets to work on.
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Hi Martin,
The R package diveRsity may be useful for this, specifically the basicStat function which will do Hardy-Weinberg Equilibrium tests to look at homozygosity/heterozygosity excesses. Alternatively, the Hwxtest R package might also do the job. More information on these is available in the links below.
Cheers,
ML
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Hi all,
I would like to test a null that mtDNA and Y-DNA sequences I have are evolving under neutral conditions. I don't have much experience with coalescent models, but I'd like to use the sequence files that I have as an input, and then apply a coalescent simulation from there.
Any suggestions?
Thanks in advance!
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Tim
there are a few. I  suggest you have a look at R. Hudson's 'ms' or  B. Peng's 'SimuPop' or even perhaps Arlequin.
good luck
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An Australian women genetic researcher has said that "Y" chromosomes will come to an end in a few years since the number of genes in Y chromosome fell from 1000 + numbers to 100 recently . Any ideas / Suggestions on this?
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That lady is Jenny Marshall Graves and she is absolutely right but as the first response suggests, this is happening slowly over time.  Only mole vole's need to worry currently.
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I have seen in many papers for eg. written like that "The Pairwise distances of the ITS region between species of the ‘glaseri’ group". Below diagonal: percentage similarity; above diagonal: total character differences. I know only how to prepare Below diagonal: percentage similarity; but unaware about how to prepare  above diagonal: total character differences. Can anyone please provide me the details of how to prepare this in pairwise alignment via mega. I have attached a file also to make my question more clear so that you could get my question what I actually want. 
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In Mega 6 and 7 the process is the same. You should calculate the "percentage" similarity (p or k2p or other model) and No. of differences in two step and merge the two matrix.
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Dear all, I am looking for a web tool to calculate the evolutionary selection pressure of a gene. Any suggstions please? 
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Thanks Stalin
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I want to know what is this mean?
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Some context would be helpful. 
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Hi all,
I am trying to use SPAGEDI v 1.5 to compare RST and FST statistics by pRst. However, the manual is not helpful on how I can compute these calculations. Would anyone know what steps to follow?
Thanks and best regards
Michael J. Jowers
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Hernando,
I am so sorry, I never got to thank you regarding my question on Spagedi!! I just realized! Many thanks and very much apperciated!
Muchas gracias!
Michael
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There can be many reasons for evolutionary conservation/change of a particular gene. The reasons may vary from different perspectives - sequence, structure and function. Has any research or review article given a comparative account on these factors?
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I think we need to distinguish between mutation and substitution, substitutions being mutations that are passed on to subsequent generations.  Mutations happen essentially randomly (factors such as CpG notwithstanding), whereas selection and drift play a role in determining whether a given mutation is passed on to subsequent generations.  It appears that Abhishek is referring to substitutions and not mutations, since he mentions gene function and protein structure, whereas all the answers only mention the term mutation(s).  Manolo says "regions under strong purifying selection might have lower mutation rates."  I think he meant to refer to "substitutions" rather than mutations, because selection can only act on a change after it has already occurred (mutation has happened).
The following publications may not address all the points Abhishek raises, but I believe they may serve to answer some.  These are two papers that Subramanian and  Kumar published in 2006 (you might want to check other papers by Kumar as well):
1. Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates. Mol. Biol. Evol., 23(12):2283–2287
2. Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics, 7:306 
Hope this helps.
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Hi All
Can any one suggest me the position of mutation spot in a probe to distinguish wild type strains from mutants using reverse line blot assay. I have manually selected a short region where wild and mutant strains vary and designed probes with mutation sites located at the center. Does the mutation sites affect hybridization efficiency.
Suggestions and papers are welcome!
Thanks & Regards
Pranay
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Dear Marcos
Thanks for the advice. FRET system is new to me but looks like the method that's is appropriate to me as I have less probes and more samples. I will read about it and get back to you for further queries. Kindly share if you have any good papers about FRET system.
Regards
Pranay 
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In phylogenetic tree I have used four species genes including my own gene family and all were divided into 4 groups equally.  One of the reviewer ask me to show out-group in phylogenetic tree analysis. I am confused, either out-group member should be related to my own gene family or another genes used for tree analysis. How to solve this problem? Please anyone guide me or provide me a reference so I can understand in detail. 
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It depends on your paper topic. If you just want to describe that there is a new gene family then not necessarily, but if you want to talk about the evolution of your new gene family then definitely yes.
If you have an outgroup, you can root the tree with that outgroup, and only then you can interpret your tree as a phylogeny (without an outgroup it is just a dendrogram, not a phylogeny). To discuss evolution using a tree, you need a direction to decide which nodes are truly ancestral and which are not. This is only possible to accomplish with an outgroup.
I didn't quite understand the data basis of your (one?) tree. Did I understand correctly that you have data for four species and all copies of your gene family for those four species? What do you mean with "another genes"? Do you have data for other genes for your four species in the same alignment/tree?
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I'm currently looked for any phylogenies on Pan and/or Gorilla Y-chromosome. I've managed to locate a few phylogenies for Pan on using mtDNA (such as Stone et al., 2010; Bjork et al., 2011), but thus far nothing on Y-chromosomal phylogenies. Has any work been done on this in the past?
Thanks in advance
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Hi Tim,
These are a little dated, but may be useful to your work.
Best, Steve
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I am working with a model provided by the Lancaster Environment Centre and am looking for real-world instances. The model (I apologise for not providing the mathematical basis on here, however I have not been told the formulae used to ascertain the model) looks at the relative proportions of resistant and susceptible organisms in a fictitious population that would develop across 500 generations depending on: 
1) the severity of disease (%);
2) the frequency of the disease within the population (%);
3) the cost of resistance (%).
Does anyone know of any plant species that do have a changing cost of resistance across generations? 
Any help provided is greatly appreciated
Matthew
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Hello everyone! Recently, I read an article published in the year 2000, the author only used slow-evolving positions (sush as positions with a sigle substitution  ) to build phylogenetic trees, I want to know whether this method has defect or not and whether it is suitable. Thanks for any reply!
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Slow evolving characters are less likely to exhibit homoplasy, so they are indeed excellent phylogenetic markers.  The tradeoff is that those characters may not mark short internodes, so it is possible the data will not have enough variation to resolve all of the nodes.  Also, note that the older the node the slower you want your characters to evolve because evolution tends to obscure the contrasts between sister clades with time.
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Specifically, this question is linked to part 2 of my thesis. The abstract is posted under my contributions for clarification.
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No. I am not familiar with the testing procedure.
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We know that the contamination can act as a selective force favoring  two types of genotypes: susceptible genotype or tolerant genotype. can someone tell me if Perna perna and Mytilus galloproviancialis are the good models for this type of study?  
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Actually, I don't understand that question. All bugs containing DNA are "good models" to study genetic diversity!
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I was reading research papers about genome comparison in chimps and humans where I found this term many times. It is given in units of percentage.
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A substitution rate is not the same as sequence identity.
Sequence identity is measured in %. But a substitution rate is measesured in substitutions per site and time (e.g. years).
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After some difficulties, working around security features, I have managed to download and install the source code. Now I am having difficulty getting it to read my data. I get the error "Cannot open data file "<filename>"
If it is being used by another application, close it first, then press RETURN
Otherwise enter a new name for the data file
Press ctrl+c if you wish to stop the program now:
Has anyone else had this problem? Did you manage to solve it?
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Please be aware that "sudo" means that the software has root = complete access to your computer and private data. It is a command for administrators and should be used only in such situations. 
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There are a lot of species tree methods out there today (BEST, STAR, MP-EST, ASTRAL, BUCKy, STEM-hy, *BEAST, etc.) and everyone seems to use a different method. I thought it would be interesting to hear what opinions people have on the different methods, especially with respect to NGS data where computational speeds may be very important and locus size are often small.
This is not really a direct question per se, but instead more of a discussion that I think would be very interesting and I hope others would enjoy.
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I have developed SISRS to estimate phylogenies from NGS data.
SISRS outputs an alignment of orthologous variable sites without using a reference genome. Given the amount of data produced I recommend SVD-quartets or a RAxML analysis of concatenated data with a model that compensates for exclusion on invariable sites. The loci incorporating these sites produce near-perfect estimates of divergence dates.
It's actually a bit strange to me that you ask about NGS and species trees. Do you mean many aligned loci? phylogenomics? Why the NGS part of this question?
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I have an observation and a correlation that is strong enough to present in a preliminary and semi-quantitative form before the full study ends.  If one calculates the distance in nucleotides between stop codons within each of the six reading frames of the entire genome of bacteria, you will find this "non-stop" DNA (nsDNA) can be partitioned into two categories.  Short nsDNA is highly correlated with pathogens while long nsDNA seems to be correlated with bacteria that live in a community (such as soil or gut).  The difference is easily observed in histograms, especially if only the longest 10 nsDNAs are plotted.  One then sees that the communal nsDNA is about five to ten times longer than the pathogen nsDNA.  (Nonribosomal peptide synthase (NPS) is an outlier at 15,000+ amino acid residues.)
In addition, we find that about 50% of all nsDNA has an opposing frame that is also nsDNA. Usually, this would be taken to be a Complementary Protein (CP) pair. However, taking the reverse complement of a protein-encoding sequence seems an unlikely way to make a second functional protein.  Only the second position of the codon remains at the second position: hydrophobic NTN becomes hydrophilic NAN, and NCN which is tightly constrained in selection of both hydropathy and molar volume (HMV) becomes NGN which encodes a set of amino acid residues which are extreme outliers in HMV.  The wobble of position 3 (supporting redundancy) becomes the stringency of position 1 - important in determining amino acid identity.  This is a highly contradictive method for creating a new protein.  This suggests more of a regulatory nature for most of CP nsDNA.  In fact, we would like to suggest that this RNA-RNA regulation could in-part be intercellular and support the coordinated metabolism of the community.
Other than the length measurements, our analyses are limited to correlation, not causation. Therefore, to go forward with this hypothesis, one would have to find a molecular mechanism for these mRNAs to interact between pairs or among groups of different species in this putative multicellular "organism".
If one added computational analyses for a starting methionine, transcriptional and translational signals, the CP nsDNA would be slightly shortened and could be aptly named a DORF because it is part of a double ORF.
I would be very pleased if my preeminent graduate student of 25 years ago (Adam Arkin) redid these calculations.
Note that the length differences between communal and pathogenic nsDNA must go through a normalization in consideration of the much smaller genome size of the latter.
Random 50% GC 4M bp {404, 368, 347, 332, 332, 326, 317, 317, 317, 314}
Random 70% GC 4M bp {314, 272, 266, 254, 254, 251, 248, 248, 245, 242}
Random 30% GC 4M bp {272, 230, 221, 212, 206, 203, 200, 197, 194, 194}
Rerun 30% {239, 227, 221, 215, 212, 212, 209, 206, 197, 191}
Human Chromosome 21q 29M bp {3041, 2633, 1718, 1682, 1589, 1478, 1445, 1361, 1211, 1154}
Elephant shark 18M bp {1865, 1535, 1223, 1211, 1175, 1121, 989, 980, 932, 932}
Azotobacter_vinelandii {13022, 4466, 4292, 4211, 4145, 4022, 4007, 3962, 3929, 3917}
Pseudomonas aeruginosa PA96 {7931, 6584, 6365, 4775, 4760, 4454, 4325, 4271, 4235, 4211}
Rhodobacter capsulatus SB1003 {6209, 6146, 5513, 4343, 4259, 4205, 3914, 3824, 3752, 3650}
Stenotrophonas maltophilia {5843, 5675, 5021, 4919, 4499, 4274, 4259, 4214, 3902, 3878}
Synehococcus sp. WH 5701 {4094, 2855, 2750, 2552, 2528, 2519, 2489, 2423, 2396, 2357}
Halobacterium salinarum R1 {3482, 3131, 2936, 2783, 2756, 2729, 2720, 2681, 2576, 2576}
E. Coli K-12 MG1655 {2975, 2897, 2534, 2411, 2258, 2147, 2096, 1817, 1793, 1778}
Pichia sorbitophila CBS7064 chr N {1184, 1094, 983, 935, 875, 872, 872, 857, 848, 839}
Bacillus cereus NC7401 {1148, 1058, 980, 920, 920, 914, 797, 746, 731, 713}
Streptococcus pneumoniae PCS8235 {1007, 947, 779, 746, 737, 737, 731, 704, 701, 701}
Vibrio cholerae {983, 914, 869, 860, 854, 827, 800, 785, 758, 743}
Spathaspora_passalidarum {935, 872, 710, 629, 614, 590, 587, 581, 581, 578}
Staphlococcus aureus MRSA252 {782, 767, 521, 509, 479, 467, 455, 425, 398, 392}
Helicobacter_pylori _ 2018 {704, 551, 530, 497, 473, 458, 458, 455, 455, 452}
Sulfolobus acidocaldarius DSM 639 {617, 419, 371, 341, 341, 335, 326, 323, 323, 320}
Clostoridium botulinum {518, 497, 452, 413, 413, 410, 389, 383, 380, 377}
Borrelia burgdorferi B31 {494, 449, 446, 431, 407, 389, 389, 383, 371, 368}
Prochlorococcus marinus MED4 {410, 386, 338, 335, 320, 320, 314, 308, 305, 296} (verified twice )
Mycoplasma genitalium G-37 {410, 344, 332, 302, 293, 293, 266, 257, 254, 242}
{Sequence Position (end), CP Length} Top 10
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Artur,
Thank you again for kindly answering this question.  As far as defining things, nothing would be better than the computer code.  There you can see what exactly I did.
I had no intention of working on this problem.  My goal was to show that Mathematica could be used in genomics such that any scientist (no programming background) could read it, understand it, and make simple modifications immediately.
So, I just randomly picked the idea of measuring the distances between stop codons in all six reading frames (separately).  I was intrigued by one thing:  Why would a protein the size of peptide synthase have an opposing DNA (opposite frame) with no stop codons?  That implies selection for protein synthesis, yet this hypothetical protein is reverse collated - using reverse complement codons.  If there is something about the genetic code that facilitates such a transformation, I sure would want to know.
With a title like this: "A novel method for accurate operon predictions in all sequenced prokaryotes", I would think Arkin could verify this effect, overnight!
Doug
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I need this information for a paper about the involvement of this gene families in the aluminum tolerance.
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Hope that the following papers will be of some help.
1.Aluminum-activated citrate and malate transporters from the
MATE and ALMT families function independently to confer
Arabidopsis aluminum tolerance
Jiping Liu, Jurandir V. Magalhaes, Jon Shaff1 and Leon V. Kochian
2. Transcriptional regulation of aluminium tolerance genes
Emmanuel Delhaize, Jian Feng Ma and Peter R. Ryan
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COI gene is used for genetic populations and historical demography studies. I would like to estimate the time of demographic expansions using Tau, but I need the mutation rate of the COI marker.
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It depends on your timescale of interest. If you are trying to estimate dates from within the last ~1-3 million years (sounds like that is what you are doing), the rate is going to be (apparently) higher (and with larger error) than if your question has to do with older events. This is because of a phenomenon called time-dependency of molecular rates (Ho et al. 2005). It is still a bit controversial, but when I used demographic models of expansion to model the known expansion onto the Sunda Shelf in 3 marine invertebrates, I found elevated rates in CO1 - higher than the typical 1%/million years that is calibrated from fossils or older vicariant events (Crandall et al. 2012). My results are for marine inverts, but are probably relevant to marine fishes, since my feeling is that time-dependency is driven by coalescent effective population size.
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I have demonstrated a project, assessing the genetic diversity of breeds of an animal using SSR markers. I've got the allelic data from GeneMapperv.3.7 but i have no idea how to plot the dendrogram to show the genetic distance and what is the software through which I can calculate the Cophenetic Coefficient for my data? Can anyone guide me through this? 
I have also attached an excel file containing the allelic data.
Thank you
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  • If you have the SSR data in binary matrix (so your object is not diploid), then I supose you to use the Treecon software (as I wrote in my last comment).
  • If you have the SSR data for diploids, then you don't need to convert it to binary matrix, just normalize the geneMapper data and use the Powermarker software
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How can I calculate p value for rate analysis of particular lineage? I have used Mega 6 for estimation of dN/dS ratio ?
Kindly guide me.
 I have used 5 primates (human. Chimp, gorilla etc) orthologous sequence for rate analysis (dN/dS ) using Li Wu Lu method. Now I want to calculate P value for estimated dN/dS of each terminal branch (like for human branch).
I used the following method is it correct?
I wanted to calculate p value for dN/dS ratio of human lineage. I used z test formula mentioned in mega manual i.e. Z = (dN - dS) / SQRT(Var(dS) + Var(dN)).
In (dN - dS), I placed human dN and dS value.  For calculation of variance, I used dN and dS  value of all the terminal and ancestral lineage branches, e,g Var(human dN, chimpanzee dN, gorilla dN, orangutan dN, human-chimp ancestor dN, human-chimp-gorilla ancestor dN ).
After getting z value I calculated p value using online software.
Thanks
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ok Thanks
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sometimes, we can see ecological pressure effect in gradual evolution and sometimes, a kind of interaction gene-from-gene. Which of them is more important in gradual evolution?
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What do we understand as gradual evolution? Evolution occurs in all life forms from viruses to prokaryotes to diverse eukaryotes, such as invertebrates and vertebrates and plants. Prokaryotes evolve largely by means of horizontal gene transfer and natural selection, e.g. resistance to antibiotics. Vertebrates have many facilitators of evolution, such as whole genome duplications, point mutations, retroviral endogenisations, and  numerous others, together with natural selection. I take it that gradual evolution would mean adaptations rather than speciation or large innovations, such as the evolution of the placenta, for example . Intra-genomic potential* together with ecological pressure, both biotic and abiotic, and natural selection would be the main drivers of adaptation or gradual evolution in many eukaryotes. However, much evolution occurs in a punctuated equilibrium manner in eukaryotes. 
I hope this helps you,
Regards,
Keith
* Intra-genomic potential, as defined in the TE-Thrust hypothesis, is a continuum from realisable adaptive potential to realisable evolutionary potential.
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The number of Tranposable Elements included in the analysis is only a fraction of all the TEs present in the genomes or the copies have been all rearranged in the considered categories? It would be possible to include an higher number of Elements in such an analysis or there are particularly reasons to restrict it to this portion of TEs?
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Their approach only works when a TE inserts into another TE.  Thus, the vast majority of Alu elements do not have insertions in them and would not work.  Basically, it will work best when the original element is either fairly long (not SINEs) and also fairly old, providing lots of opportunities for other elements to insert and disrupt them.
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I generated a phylogenetic reconstruction of protein homologous belongs to different taxa using NJ method with 5000 bootstrap support . However, two sequences which showed relatively high sequence similarity (Obtained by MatGat software) clustered separately in the tree diagram, while there are closely clustering with relatively less similar sequences, respectively.  Is there any reasonable explanation behind this type of observations?
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You might want to use the nucleotide sequences. Nucleotide sequences are less homoplasious and more informative than amino acid ones. If the sequences are much divergente, you may codon-align them (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896173/). Good luck!
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should the gene tree match with the species tree? I am inferring a phylogenetic tree for a nuclear receptor and I would like to know if the gene tree must match necessarily with that of species, in order to reconstruct the most common ancestors for some internal nodes.
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There are several biological processes that can make gene trees different from species trees. Lineage sorting, hybridization/gene flow, gene duplication, horizontal gene transfer...
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I get some sequences of a intron to reconstruct phylogeny, but sequence alignment of this gene is difficult because it's sequence is consist of repeat regions and sequence length variation is considerable. Does anybody know how to deal with this problem?
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It's a general problem not only for introns but also for microsatellites and so on. But also no general answer how to improve the alignment is exist. But you can do some steps to improve it:
1. Be sure, that all your sequences are in the same direction
2. Check the results by using different algorythms (Clustal, MUSCLE and so on) and features (i.e. penalties and so on)
3. If it would be not helpful, you can try the algorythm for SSR alignment (information from http://link.springer.com/article/10.1186%2F1756-0500-4-239#page-1):
1- User must identify the following items:
a. Data set file
b. Repeated units
c. SSR length (first and last nucleotide)
2- Identify the sequences that do not match the first
repeated unit from the beginning of the selected SSR
region
3- Do this for each repeated unit
a. Put the tandem repeat in a temporary array
b. Check if the next nucleotides match the next
repeated unit
c. If not, put the unmatched nucleotides in
another temporary array
d. Fill the gaps to the longest sequence of the
repeats in the same array
e. Merge the temporary arrays
4- Put your results instead of the SSR region.
Information like above also published here: http://www.biomedcentral.com/1756-0500/4/239
For  protein sequences with repeats some special software already created (like RADAR or ExPASy). I don't know much of such software for nucleotide sequences analysis, but maybe it would be helpful: http://last.cbrc.jp/
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Lets say I have a phylogenetic tree and two traits A and B mapped to the tips of the tree, and I want to test the hypothesis that evolution of trait B is contingent on trait A having certain states. For example, if A and B have two possible states, 0 and 1, then, how would be the best way to test that the transition B:0->1 is contingent (or more likely to occur) on A being on state 1?
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Stochastic character mapping, as implemented in programs like SIMMAP (http://www.simmap.com), allows you to test for the correlation (specifically the co-occurence along a phylogeny) of two discrete characters. Technically this is not indicating contingence in an absolute sense (i.e., no causality is inferred), but if the correlation is strong enough, it would likely be consistent with such a hypothesis.
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I am gonna do ssurRNA sequence alignment of Dicyemid. I want to know the relationship of different dicyemid found in different country. Which phylogenetic model should i use? or if you have some better and easier method to describe the ancestor relationship, i would appreciate that.
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A small subunit ribosomal RNA (ssu-rRNA) alignment may not provide solid information on the phylogeny of Dicyemids.  The Dicyemids are a diverse group of mesozoans which could have shared a common ancestor more than 500 million years ago, so the ribosomal RNAs might be quite diverse.  However, the subset of Dicyemids that you study might be less diverse, so you should definitely look at your data and decide.  It will almost certainly be helpful to use an alignment method that takes into account the stem-loop secondary and 3D structure of ribosomal RNA such as the ssu-Aligner at Janelia.  Choosing a good outgroup, and interpretting your resulting tree, will be as or more important that which model of evolution you use.  Start with GTR plus gamma, and/or run ModelTest.  FindModel is a web service based on ModelTest.
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Assume that we are studying population genetic structure of a species and demographic events using nuclear markers and mtDNA sequences. Nuclear gene sequences give information about further past events compared to mtDNA genes as nuclear DNA has a higher effective population size, and slower mutation rates. What about comparison of mtDNA and microsatellites? There are contradictory information in literature. Some researchers say mtDNA recover more ancient events as mutation rate is slower than microsatellites. Some other researchers say,  as being nuclear, microsatellites recover more ancient information due to the larger effective population size despite their high mutation rate.Which one is correct?
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Dear Yeserin,
Nuclear DNA, as you have seen has about four times (assuming balanced sex ratio) the effective population size than mitochondrial DNA in diploid organisms. This extends the expected age of the most recent common ancestor -MRCA- of their genealogies in the same amount, and with it the time frame in which it is possible detectable events that affect genetic variation. So, the general rule is that nuclear markers have the four-fold advantage over mitochondrial markers. The problem with microsatellites is their extremely fast mutation rate which can be three-five orders of magnitude above nuclear and even mitochondrial genes. Such mutation rates provokes a problem of saturation-homoplasy that effectively erases the correlation between the number of mutations and the difference in motif repetitions between two alleles. In other words, the excess of mutations produce that information about past events, which is stored in the statistical patterns of mutations, get effectively lost. In mitochondrial DNA that rarely occurs since there are multiple genes to choose from, and despite some genes could face saturation, other more conserved genes remain useful. As you can guess, there are situations in which a combination of not so large mutation rates in microsats combined with moderate-small populations sizes maintain microsatellites useful and advantageous over mtDNA, while in many others (large mutation rates, large populations) that doesn't occur.
Have a nice day.
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It has been hypothesised, that our observations of the comparison between lower plants and higher plants, for example, might suggest that evolution of diploidy may have been the necessary pre-requisite for the evolution of multicellularity. Is there any solid molecular understanding of as to why that may be. Please cite some of the useful sources, if possible. Thank you.
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One back question:
Who hypothesised this?
And just two notes:
1. Sex is a complicated phenomenon variously defined in different organisms. So I cannot clearly understand what do you exactly mean writing 'evolution of sex'?
2. There are many bisexual unicellular organisms existing for a long time without significant evolutional transformations... and if you compare algae and so on with higher plants, you should keep in mind that the first group is polyphyletic and its evolution occur in many different directions and not always due to multicellularity. Such a way I don't see any ways to prove this at least in general view.
What organisms do you study?
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The human flea, Pulex irritans, is a cosmopolitan flea species that has, in spite of the common name, a wide host spectrum. It is one of six species in the genus Pulex; the other five are all confined to the Nearctic and Neotropical regions. The species is thought to have originated in South America, where its original host may have been the guinea pig or peccary.
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Maybe you will find more recent references, but please refer to Buckland and Sadler, 1989. Journal of Biogeography 16: 115-120. Its abstract states: 
The human flea, Pulex irritans L., has been recovered from archaeological sediments in Viking York (England), Dublin (Ireland) and abandoned farm sites in Norse Greenland. In contrast with the other human ectoparasites, however, the origins of the flea appear to be Central to South American, where several congeners are known. The probable routes by which the species reached Western Europe are discussed and resolved in favour of a Beringian and Asiatic one, at any time during the Postglacial. Although this flea is presently relatively promiscuous, initial evolution is likely to have involved a single host, which should be South American in origin and eventually closely associated with man; the guinea-pig or peccary are suggested. The model, with core area in South America and subsequent spread northwards, has yet to be tested by the examination of suitable deposits in the Americas.
You may also have a look at:
and
Functional and evolutionary ecology of fleas by Boris Krasnov, available at Amazon Books.
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I have sequenced a gene, mutations in which confer resistance to an antibiotic treatment, from the bacteria that are able to grow in the presence of antibiotic. The bacterial clones all share the same genetic background (i.e. closely related) and there are around 60 sequences in total, all of which have non-synonymous substitution(s). I would like to test whether there is evidence of positive/negative selection in this alignment. I used Datamonkey server to perform SLAC, FEL, REL and PARRIS analyses (using an automatic model selection tool) and MEGA Tajima’s Test of Neutrality. SLAC and FEL found no selected sites, while REL found that 230/385 sites were positively selected and PARRIS shows that there is an overall evidence of positive selection. Tajima’s Neutrality Test has a D value of -2.4, indicating a recent selective sweep. Considering that SLAC is a very conservative method, while REL tends to produce high rates of false-positives, I have a hard time interpreting the results. Taking into account the experimental setup, my expectation is that in a population that was under a strong selective pressure (antibiotic treatment) and went through a genetic bottleneck (as Tajima D demonstrates), one could probably expect to have evidence of diversifying selection. Can anyone advise on what method would be the most appropriate to use in this situation or help with interpretation?
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Dear Olga,
PAML is the standar software employed to test positive selection on specific residues. Inside PAML structure you will find the complement CODEML that you need to reach your goal.
It is really easy to use either Linux or windows stations. Next, you will find a full tutorial that will help you a lot with your research. Here is a link in which you will find the best tutorial about CODEML and PAML.
Best,
Andrés
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Indices of phenotypic plasticity commonly used is the relative distance plasticity index  (RDPI) (VALLADARES et al 2006).
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You can see the paper, may be it help you.
Quantitative estimation of phenotypic plasticity: bridging the gap between the evolutionary concept and its ecological applications
Journal of Ecology
Volume 94, Issue 6, pages 1103–1116, November 2006