Questions related to Evolutionary Biology
In Evolutionar Biology, Epigenetics has become part of the explanations for changes in the phenotype across generations. But can these changes directed to specific phenotypic traits along many generations be converted into DNA mutations?
Kindly discuss your ideas and viewpoints on the origin of life and the RNA world hypothesis.
What are the contradictory views on why researchers are still unsure about the origin of life through RNA or such analogous molecular intermediate pre-cursors preceding its existence?
"The general notion of an “RNA World” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this “RNA-first” view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA." - Robertson and Joyce
[This is as per the explanation by Michael P Robertson and Gerald F Joyce in the article: "The origins of the RNA world." published in the Cold Spring Harb. Perspect. Biol. 4, a003608 (2012).]
The scientific community must resolve this contradicting conjecture through rational discussion and debate backed by strong experimental evidence on what must be the pre-cursor molecule to the Origin of Life if it is not RNA!
The phrase “evolutionary success” sometimes appears in scientific productions. However, the concept seems to be based primarily upon quantitative data. For instance, Rodents are said to be “evolutionarily successful” because about 40% of Mammals are Rodents (about 2000 species out of 5000 Mammal species). In the same view, seed plants are considered “evolutionarily successful” because most modern-day plants produce seeds.
In this perspective, multicellular organisms are sometimes considered as having had little evolutionary success, if not being anecdotal, because they are hugely outnumbered by unicellular prokaryotes. As Gould stated: “We live now in the ‘age of bacteria’”.
Nevertheless, I was wondering whether such a vantage point was not biased. As a matter of fact, why consider that being successful necessarily means being numerous? There are no known animals able to run as fast as cheetahs: does that not make cheetahs evolutionarily successful? In a much more anthropocentric way, no known organism displays such a big brain as ours: does this make us a success of evolution?
Should we prefer qualitative assessments over quantitative ones?
I am searching for good recordings of distress calls emitted by American crocodiles, in particular by hatchlings. The longer the better. If not, also distress call recordings of other crocodilian species are fine.
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.
I am struggling with a constant problem with a csv extension while preparing data for MuSSE model analysis: have tried to do a bunch of stuff to fix a problem but no success - always the same thing ("All names must be length 1"). I would very grateful for your help! :)
library(diversitree) dat="MuSSE_hosts.csv" dat<- read.table("MuSSE_hosts.csv", header=TRUE, dec=".", sep=",", row.names=1) mat <- dat[,2:ncol(dat)] lik.0 <- make.musse.multitrait(tree, mat, depth=0) Error in check.states.musse.multitrait(tree, states, strict = strict, : All names must be length 1
Thank you a lot in advance!
I am planning on starting grad school in about a year and a half but you can never start researching project advisors too soon!
I am interested in investigating the use of fungal parasites of insects such as Cordyceps in integrated pest management. Unfortunately, this seems to be an unpopular field of study, as so far in my searches I have only seen professors who study plant-insect relationships in IPM, but not fungal-insect relationships in IPM. Ideally, I am hoping to stay on the west coast of the US. My undergraduate background is in ecology and evolutionary biology, but I am currently broadening my skills in molecular lab techniques.
Faculty pages on university websites cannot always represent the scope of a professor's research interests. That said, can anyone recommend a recommend a colleague of theirs who might be looking for graduate students in a year and a half, and with a background in mycology, entomology, and IPM?
Even tigers and lions kill just to survive. Lions kill other lions' cubs just because of "the egoistic gen". However, we kill - yearly (!) - hundreds and hundreds million of animals just for our food (and we most likely are successors of fruits-eating animals, as, e.g., also Pan paniscus are) and for mere entertainment (so called "hunting" - the same predators' "virtue" ) and simply disgusting pleasure (furs). We are keeping them in frightening conditions in meantime. (As if they were not living soul persons just as we all are?) And we kill them for nothing in millions just under suspection of slightest endangering for our own health:
In early November, the Danish government announced a plan to slaughter 15 million mink due to emerging fears of the COVID-19 mutation, which could be transmitted from these animals to humans. At a press conference held on November 4, Prime Minister Mette Frederiksen announced that twelve people had contracted the mutant virus and added that mink are "considered a threat to public health".
15 mln vs. 12 - isn't it a clear evidence of presumption of Homo sapiens sapiens
to be actually the most predatory (and beyond compare measure EXTRAORDINARY) of species of whole the Multiverse, therefore?
Dania. Władze wybiły norki. Teraz ich truchła wychodzą z ziemi (wprost.pl)
Are there any cyclical animal populations in the tropic?
I've been writing an evolutionary biology hypothesis, that claims that cyclical animal populations are actually a population-wide multi-year hormone cycles; not that different from menstrual cycles: https://www.researchgate.net/project/80-year-generational-hypothalamic-hormone-cycle-spanning-across-4-generations
The current assumption is that the annual changes in daylight enables the "counting" of years for biology, but since the amount of daylight is quite stable in the tropic, the "counting" of years wouldn't be possible there. This is why I'm asking: are there any cyclical animal populations in the tropic? The requirements are that the cycle is multi-year and has similar characteristics compared to the other cyclical populations (of lemmings, voles, hares, etc.)
Good day. A simple two-day field activity will be done in an island. Currently, I am thinking to use a single family of gastropods in mangrove, compare color and measurements of of the shells between habitats (such as ground gastropods vs. gastropods on mangrove leaf and trunk and branches). Please advise. Thanks.
I am currently an undergraduate student (major in biological science) who is looking for a Master of Science in Plant Systematics and Evolution Biology aspects. My result in university is quite good but then I have no prior experience in doing research. I have a strong interests in evolutionary biology in plants, and I really hope that I can polish my scientific knowledge and research skills by studying master. Can anyone recommend me some suggestions regarding the following questions?
Any institute that you recommend me to do my Master in Plant Science?
Does lack of experience in research deprive you of Master admission?
Any suggestion that can help me?
I've tried several programs (e.g. TreeView, FigTree, MEGA, Archaeopteryx, Mesquite) but they just display node numbers and branch lengths. I'm using the software SYMMETREE to infer diversification rate shifts on particular nodes within a tree. Results refer to "branch numbers" which, according to the manual, can be displayed using MacClade. However, I´m not using a Mac OS platform.
I have a phylogeny and two categorical traits (one binary, one multi-state) mapped to its tips. My claim is that there is a correlation in their phylogenetic distribution, i.e. that they evolved in concert, or dependently.
How can I test that formally?
I have tested for phylogenetic signal using Fritz' D (Fritz & Purvis 2010,
of which there is plenty. But I am stumped on how to show that there is a correlation in presence/absence of one trait and the state of another. I can visualise that in a traitgram/phylomorphospace plot in phytools, but that doesn't give me a number that says "these are not independent".
In principle, phylogenetic independent contrasts (Felsenstein 1985) could be used to test for correlation, right? But PIC is for continuous characters, not categorical ones.
I have found phylogenetic logistic regression (Ives & Garland 2010, https://academic.oup.com/sysbio/article/59/1/9/1723322), but this is only for binary traits. I have read the "Analysis of Phylogenetics and Evolution in R" (Paradis 2012) and "Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology" (Garamszegi (Ed.) 2014) books and googled myself to perplexion. I hope someone more knowledgeable can help me!
Many thanks in advance.
Recently, Christopher Monit, Richard A. Goldstein & Greg J. Towers published an article entitled 'ChromaClade: combined visualisation of phylogenetic and sequence data' in BMC Evolutionary Biology volume 19, Article number: 186 (October, 2019).
In all respects this looks like a very interesting tool to analyze sequence data and phylogenies. Has anyone tried it? Could you comment on the outputs please?
Thanks for your time.
Who gives the last word about the evolutionary process, genetics or ecology?
In other words, are ecological interactions driven by any genetic phenomenon? Or is it genetics that has been molded by ecology?
[I’m a Brazilian biologist and writer. I write about science – I have just released a new book, O que é darwinismo (What is Darwinism, in Portuguese) – and would like to know the opinion of colleagues from other countries (from any field of scientific knowledge).]
See also What do you think about fitness, adaptation and natural selection? (https://www.researchgate.net/post/What_do_you_think_about_fitness_adaptation_and_natural_selection)
Hello. I am looking for a cheaper alternative to propionic acid which I can use for breeding Drosophila. I am currently teaching Evolutionary Biology and I would like my students to conduct experiment using Drosophila melanogaster. I would like them to breed these flies, expose them to different conditions and see if there are changes in their morphology. I think this would be a great experience for my Biology students to do this experiment.
I have tried using vinegar as alternative during my previous classes last semester but it was not very effective and we have acquired poor results.
Can someone provide suggestions on which methods / softwares can perform fast and reliable estimates of diversification rates (speciation - extinction) using very large phylogenetic trees (> 10 000 tips)?
"There has been a long and bitter controversy as to whether groups as cohesive wholes can serve as targets of selection. The answer is “it depends.” There are different kinds of assemblages of individuals (“groups”), some of which do and others which do not qualify as targets of selection." Ernst Mayr
According to the theory of natural selection, selected clone of bacteria are capable of tolerating specific stress factors. But when does this selection happen? Does it happen before the exposure to particular factor? Or is it a consequence of exposure to a particular factor? Is the specific clone of bacteria inherently resistant to that specific stress factor or does it acquire resistance following exposure to that particular factor?
I want to work on scientific investigation (Ecology+Genetics) and community based conservation of two threatened species i.e. the Himalayan Gray Langur and the Himalayan Musk deer in western Himalayan areas of Pakistan. Can any body would like to guide me that which can be the funding resources for these researches?
I do not have network publisher a paid component of this software.
I am extracting host DNA from fecal samples. However, feces contains lot of microbes and their DNA too gets extracted during DNA extraction procedure.
I want to get rid/minimise the microbial DNA. It is causing a lot of issues in my PCRs (lots of misamplification). Is there an inexpensive method to do so?
Please respond to this quote above. This was written to me in response to a discussion on biological species concepts and evolutionary
I am wondering if there was anyone interested in have a look at a draft of a follow up paper to my (and James Maclaurin's) 2016 paper 'The Value of Phylogenetic Diversity'. I am working on it just now. It would be good to get someone working on this project to have a look as it should be relevant. Here is the abstract.
Preserving the Tree of Life
Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. I draw from the species concept debate to argue for a particular set of desiderata for “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata biodiversity should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the tree of life.
I would like to perform positive selection analysis among mammals. I am mostly interested in positive selection in humans and I have started off with around 100 mammals species and looking for a way to find the ideal number of species I can use to detect the selection.
I want to have a balance in the evolutionary distances between the species I will include: not too distant or not too divergent. Previous discussions give a minimum number of species to include in a positive selection analysis; however, not much information is given about the maximum number.
What is the appropriate number of species that should be used in positive selection analysis and what would be the maximum? Also, what interval of evolutionary distance should be used to be able to detect the positive selection and avoid false positives at the same time?
I remember quite some time ago I came across an interesting quote which I believe was attributed to the evolutionary biologist Theodosius Dobzhansky. If I recall right, it was in one of G.G. Simpson's books in which he was recounting some of the discussion around the time the modern synthesis of evolution was being formulated. The quote was something along the lines of "that's a wonderful story. But it's wrong." I have been trying to find what the exact quote was for reference but I do not think I have the original book where I saw it anymore. Any information on the context of this quote or if I have it wrongly attributed would be appreciated.
Citations that appear in the BODY of published papers contribute to metrics (e.g. h-index) that account for the impact of the work of a particular researcher. I acknowledge that the suitability of these indexes is debatable. In the meantime, I wonder why the citations that appear in Supporting Information (particularly those that refers to relevant methods and databases that were used in the papers) are not included in the calculation of such indexes.
I'm aware of quite a few sites out there (e.g. morphobrowser, morphosource, nespos, evans) but I'm always looking for more.
In particular, I'm looking for ones that have CT scans high quality enough to do research with...i.e. the Digital Morphology Museum, KUPRI has a TON of amazing primate CT scans for free download. However, they're not particularly high quality, making it difficult to use for anything other than gross geometric measurements and/or teaching.
The currently accepted value of the proportion of female births in large European-race populations is 0.485 (Bayesian Data Analysis, 3rd edition, Gelman et al.).
Do we know why the probability of being born male or female deviates from 0.5?
Thank you for your insights
I could list thousands of real world examples in which a cultural belief (e.g. Religion or political ideology ) in any particular area is attributing towards some form of social ill. However, I will only list one real world example for this case study, due in part, because cultural belief can cause some of the worst social pathological behavior to manifest and I,for one, wouldn't want to stir a psychological hornets nest. And that's why I've been very hesitant to get involved on a political level in the context of this case study. The reason I'm referring this case study to you ( the scientific community) is due to the fact that the more logical minds think about any particular problem the more probable a solution can be found to mitigate that problem.
A community is seriously contaminating the air they breath with toxic smoke (there isn't a "healthy" smoke). Whilst they do have the choice to not emit toxic smoke in there local environment.e.g. By using more cleaner technologies to heat there homes. They "choose" not to. The reasons why this form of social self harm exists (other than when there is no choice.e.g. Burn Coal or freeze) is only because of ignorance in most cases.
This ignorance is based on a central cultural presumption. A belief that blinds them from the facts, thus they act without due care and attention.
The community (a significant percentage of the people in the community that contribute towards a negative health difference to the overall air quality) are choosing to behave in a way that, evidence has shown, seriously harms health ( e.g. Coal/wood smoke is far more toxic than cigarette smoke).
They don't (are not cognitively indoctrinated too) accept the facts due to a habitual cognitive bias ( driven in part by a religious upbringing in which they are indoctrinated in such away that they avoid certain facts that contradicts their central premise (belief/opinion) and or ideological/financial incentive).
local industry actively promotes ( and part takes) in the ritual of burning stuff in the local environment and is financially motivated to promote the burning of wood and coal.
The culture is comparably wealthy in so that most (if not all) do not even consider the alternative cleaner options. New homes are built and coal fire places and or wood burners are installed.
Fact 5. The local governing bodies are part of the coal/wood burning culture thus are not interested in mitigating the problem (e.g. Smoke control regulations).
Fact 6. Some of the narratives promoted by local business ( financially associated within the tree to burning wood economy) suggest that burning wood for heating is a sustainable method to mitigate climate change.i.e. Tree's fix Carbon from the air and burning wood releases the carbon back into the Air ( and in local peoples lungs). Whilst this narrative is correct, they then go on to add the "carbon neutral" narrative, which is completely incorrect. For example, it takes a lot of industry (predominantly a diesel driven industry) to grow tree plantations and get those tree's processed and into houses as logs. Furthermore, the conifer tree plantations take up most of the forested areas of the local landscape and being of a monoculture design, are not self sustaining in the long term.e.g. Loss of fertile soils and loss of the carbon ( carbon capture cycle. Thus on a large scale disruptive to the ecosystem ).
So given the particulates (sorry, pun intended), the particulars of this case, does anyone have any suggestions what methods could be used in order to reduce smoke emissions thus improve the general health of the area. Other than replacing the entire culture with more intelligent thoughtful people, I'm at a loss in how to help these poor "souls" out.
(THE ANSWER: I asked the question and now, on June 30, 2019, it is answered to my satisfaction by the knowledgeable people who contribute here and especially by Aleš Kralj, Jun 28, 2019 , who asserted that evolution is fundamentally unpredictable. The Theory of Evolution as it is used here refers to “macroevolution.” A theory is expected to both explain and predict; the theory of evolution only explains. The theory of evolution is not a theory and it is suggested calling it a working hypothesis: the working hypothesis of evolution.
With the question answered to my satisfaction, I am now leaving the discussion. You may wish to continue.)
Science is based on observations. Empirical relationships between observations are called laws. For example, a graph of the position of an object vs. time is an expression of a law.
Theory is based on things you cannot measure; for example, one cannot measure momentum or energy, but only calculate them. If the imaginary things can be used to predict laws or observations you have a theory. If your theory cannot predict something that is observed …. or predicts something that is not observed . . . forget-about-it..... the theory not the observation! If your theory can not predict anything, the theory cannot be tested . . .why did you bother in the first place? Theories come and go. Scientists hide theories that do not work. ... What does oxygen mean? . . . is oxygen really needed to make an acid? That theory has come and gone. Where did phlogiston go?
Do you believe in the Theory of Evolution? What can you predict right now from the Theory of Evolution? What new species will be discovered?
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?
Woese and Fox (1977) stated that "phylogenetic relationships cannot be reliably established in terms of noncomparable properties" and that "a comparative approach that can measure degree of difference in comparable structures is required." What I don't understand is if this only applies to living (=extant) organisms or if one can determine (infer?) phylogenetic relationships even between fossils...
As a part of interest, I wanted to know the details of Hypothesis that One prokaryote engulfed the other bacteria and during the course of evolution other bacteria remained as symbiont latter we call it as Mitochondria.
Would you please elaborate this concept.....
I mean cases that are not results of parallelism or convergent evolution.
We presented an example of Devonian ammonoids, but I have never heard of other good examples published since.
Monnet, C., Klug, C. & De Baets, K. (2011): Parallel evolution controlled by adaptation and covariation in ammonoid cephalopods. BMC Evolutionary Biology, 11 (115): 1-21.
I have 12 species from same genus. For supermatrix approach we generally use the multiple sequence alignment single copy orthologs sequences then concatenate them and remove the badly aligned columns and generate ML trees. In my case I got around 2000 single copy orthologs that I used.
To add outgroup species, do I first need to cluster the outgroup sequences with my 12 species sequences? If the reply is yes, then I wonder it may decrease the number of single copy orthologs as they are the possibly the part of core genome and I suppose probably they all not will be present in outgroup or may be removed by MCL clustering because of less similarity than others.
I have once been asked about the methods for studying ancient DNA, and I am rather naive for knowing too little about studies on Ancient DNA. I am hoping to receive more information about sequencing Ancient DNA (Again other than mtDNA and Chloroplast DNA) for studying ancient samples. In particular Human samples.
(Assume we're gonna study them through pedigree diagram, are there any more specific methods for studying the Ancient DNA samples: Such as Haplotypes)
I am trying to understand the molecular evolution of a gene family that composes of only two members (let's say X1 and X2). I have looked into the genomic neighborhoods of X1 and X2 in various species using Genomic Alignments in Ensembl and constructed a genomic neighborhood illustration of other genes flanking X1 and X2. However, my Blast searches didn't detect X2 in some fish species. When I looked into the genomic neighborhood of X2 in these fish species, I saw another X1 like sequence instead. I am thinking that maybe X2 was converted into X1 after the duplication event, but how can I prove that? My assumption may be stupid because I am not very experienced with genetics and concepts of evolutionary biology, but any help would be appreciated.
With HIV-1 phylogenies we quite often have data sets where we know important details about the true evolutionary history. For one example, with a local transmission chain such as husband to wife to infant chain we can often know for certain who was infected first and the dates of transmission events etc. In other cases the rough epidemiology is known so that we can tell that an epidemic spread out from a point source introduction.
Very often, or perhaps always given certain relative levels of diversity involved, the phylogenetic trees produced from a data set show a misrooting of one or more subclades which essentially turns that subclade "inside out" by putting the more diverse sequences rooted to the outgroup. The explanation seems to be the "long branches attract problem". In the father->mother->infant case for example, the sequences from the infant often appear on a branch in between the father and mother, when we know for certain that this is "out of order".
What I want is a tool that allows me to "fix" a known misrooting of a clade, and then calculate the likelihood value (or other such measurement) of the "correct" tree vs the misrooted tree. I can provide sample data sets and tree results to anyone who is interested in this.
I'm using mlcoalsim in order to compare the observed distribution of four summary statistics (neutrality tests) with those obtained from nine different demographical models. Nevertheless, the probability that simulated values be smaller than or equal to the observed values is the same for all nine models (including the standar coalescent model). I suspect that my models are not well inputed (for instance, I'm not sure how to transform times from years to 4N generations. I assumed that t =r/4N; where t is the time in 4N generations and r is the number of generations) or they are not really different. I would be grateful If someone could help me and give me some advices to make a succesfull simulation with mlcoalsim (feel free to write me in Spanish or English).
Thank you in advance.
I read several papers where researchers use several strains of same species for analysis of recombination or selection pressure however there are few papers in which researchers use the multiple species belong to one 'Genus' not the multiple strains belong of one 'Species'. What difference is expected in the result and how it can be interpreted.
I want to know how my pathogenic organism 'Xyz abcde' is evolved (recombination and selection pressure). 5 different strains of 'Xyz abcde' is sequenced while 9 organism in Genus 'Xyz' is sequenced.
Which dataset I should use to proceed and why? How it will make differences in the analysis?
Why internal stop codons appear during process of submission of COX-I or cyto b partial gene sequences to NCBI? And how can we get rid of them? This happened even if the nucleotide sequences are same as of other closely related species already submitted to the gene bank. How can we submit sequences if such error conditions persist?
I need to get some primers, but due to logistic we can not put the in the suitcase and we have to transport them in the hand luggage. We assume we have to use a coolpack, but the flight will take 4 or 5 hours, does anyone know if there would be any effect on the primers?
Thank you very much !
Kind regards, Mara
While calculating the evolutionary divergence as computing pairwise distance, (using p-distance methods and Maximum Composite Likelihood model), the values ranged between 0.002-0.138 (p-distance) and 0.001-0.109 (ML) for between individuals of the same species, and for different species. I have got these value as distance matrix table using MEGA 7 software by inserting the nucleotide sequence of COI gene of 661 bp length. Can somebody tell me what are the actual threshold values of the evolutionary divergence calculated by the above said methods to delimit the distinct species? I mean at which values of these distances we would say that these two species/individuals are of distinct species?
I am trying to understand what drives bioerosion by grazing organisms. I understand that algae are a major food source, but there are often problems in the literature distinguishing between basic herbivory grazing and BIOEROSIONAL grazing. My question is specifically related to what controls bioerosional grazing in reefs with depth, especially related to food sources. Please let me know if you can help.
I have aggression scores which are categorical. I'm interested to see how aggression levels of individuals change over trials (time). I made a random slope random intercept model for boldness scores which are continuous and visualized using the sjPlot package in R. I'm wondering if the same can be applied for categorical response variables. I have been searching along these lines for quite some time, and since my knowledge in statistics is very basic, I don't know if I found anything useful. Any help would be much appreciated. Thanks! Bharat
I have a morphological trait measured in three different populations and I want to know how this character evolved. All the three populations are recent and I do not have information of this character in related or ancestral species. I do have information of the heritability, population size and variability of the trait within the population.
My questions are:
- How can I test if this trait evolved by natural selection?
- Can I do this with a single trait? and with only three almost current populations?
- Is it necessary to evaluate other possible evolutionary (other than natural selection) mechanisms if I want to make a valid conclusion?
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?
For my study, I need several life history traits:
- size of organisms
- number of offspring
- 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.
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?
I need to obtain a substitution rates per site per lineage per Myr in order to calibrate a molecular dating of a phylogeny between individuals from different rivers in South america. I found just one paper at the moment to use that method,that paper is "South American rays came in with the sea", but at the moment it had been difficult to obtain it from any database. Maybe you can suggest me others readings, Thanks!
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?
In other words, does any other reptile group have similar teeth? or maybe some sort of mammal incisors that look similar?
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?
I am working on a gene which thought to be increases stress tolerant in plant if up-regulated but evolutionary algorithms shows that gene is evolved by neutral evolution. Now i am confused, how neutral evolution leads to stress adaptation or it is by chance.
I want to compare evolution rate between two set of data (morphological and reproductive traits) because the values of the reproductive traits is very small in compare with morphological traits (both of the same unit and scale [mm]), so I want to perform a log-log regression of species mean trait measurements on species mean thorax volume which I used it as the index of the body size, but I don't know how can I perform it. Thus, I am looking for help or potential collaborator.
thanks for any suggestion.
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?
I'm supplementing an already published genetic database with genes extracted from full mitochondrial genomes from genbank. I have all accession numbers for the complete genomes and I have previous gene sequences too.
I'm using R to do all the downloading and data management but i'm willing to use other open access tools to do the job. So far, my plan is to just download the full genome, replicate it in separate fasta files for each mitochondrial gene, align all the sequences for that specific gene and then trim sequences manually. I could also go genome by genome extracting the genes manually on genbank, but I figure there is a smarter and quicker way to do it.
I have never done anything like this, so I'm playing by ear here. Any tips are welcome.
like the title , i am dealing with some mtDNA sequences, and totally i have 76 partial mtDNA sequences, and have recognized 13 haplotypes from these samples, when i do these tests, which dataset should i use?
I'm looking for informations about the ontogeny and ossification of the parietal, on fossil and living vertebrates.
Speciation is the splitting of a single species into two species and qualifies as a bifurcation phenomenon. Has bifurcation theory ever been applied to speciation? If so, how? Any published references?
Actually I am working with genome based metabolic network reconstruction. But I didn't get any success yet in using a software which can be handy to work with and if someone have used it before in their work please do mention while responding.
I am revising a manuscript for PLoS ONE; it's a modeling study concerning effects of mass extinction on phylogenetic tree balance. It's very similar to Heard & Mooers (2002), but background extinction and diversity-dependence have been added to the model so that the modeled tree recovers to an equilibrium size and then undergoes turnover while evolution continues.
In the discussion, I wanted to be very clear about the limitations of the results, and the conditions under which they would apply, so I raised the following points that the effects of mass extinction on tree balance would not be enduring IF:
i) how traits and rates evolve remain unchanged after the mass extinction
ii) the tree cannot continue to expand indefinitely after either reaching its pre-extinction size, or converging on a new equilibrium size
iii) trait values, and the rates that depend on them, are subject to hard limits that result in eventual erosion of trait/rate variance
iv) there is no mechanism for isolating slowly-diversifying clades from very rapidly-diversifying ones.
And the reviewer's comment was:
"Which raises the obvious question of whether these conditions prevail for real clades! This seems like a real gap in the MS."
Stick foot in mouth time. :(
It seems to me like what they want is a point-by-point justification of each of these, with citations. I think I have (or can easily come up with) references to support points II) and III), but I'm having trouble with point I) and especially point IV. Basically, what the last point is saying is that slowly-diversifying clades can continue to persist if they're isolated in some way (spatial/ecological, temporal etc.) from more rapidly-diversifying related clades. In the model as I have it, no such isolating mechanism exists and so clades with the slowest diversification rates inevitably disappear as the simulation progresses. (NOTE: for point I), the original study provided no biological justification as to why they maintained constant parameters after their mass extinction event.)
Can anybody help me out here? Can you suggest any study that demonstrates for a real clade that more slowly-diversifying members within that clade are somehow isolated from more rapidly-diversifying ones?
Thanks in advance,
Some peoples believe that we can not discriminate subspecies inside a population because of no distinctive genetic differentiations.
There are some different concepts about Insects subspecies, Can we rely on separating subspecies inside a population by genetics? some poepole belive that there are no difference to accept various subspecies inside a population or species?