Evolutionary Biology - Science topic

Hello Ziaedin; Testability is a requirement for hypothesis testing. The panspermia proposal isn't testable in an obvious way. However the suggestion that H1N1 has an extraterrestrial origin is. If it originated away from Earth, it should have genetic characters that are unique. It evidently doesn't! At least none of the vast literature about that critter suggests an extraterrestrial origin...hypothesis disproven!?

Best regards, Jim Des Lauriers

Yes.

Tristan Beckwith my dear friend, there is evolution relationship between plants and algae. primitive plants are evolved from the these algae. the non vascular plants that are dominate in early earth are evolved from green algae. after, vascular plants are dominate on earth. that is brief history about plants evolution. in simple we can say freshwater green algae are ancestors of plant. After, these plants able to adapted to the various environment system due to their well develop vascular systems. some of them are adapted to the saline water. the some plants species which is able see in ocean belongs to the angiosperms.

Please find about much details, If i am wrong please correct me because knowledge of science is update in day by day. therefore thing I know can be bit change within time. therefore find about deeply about your matter.

Best wish Poornima Nadun

We are not supposed to ignore our cultural biases in humanities research but rather to learn to work around them. First try to understand what does Eurocentrism means to you. Second try to identify its manifestation in your work, last determine its role in your work

hope it helped a bit

Dear Afonso Henrique Leal , light was recently thrown on the origin of epigenetic changes when I investigated immunological phenomena with a method of developing theories which illustrates reality instead of making logical deductions from observations and which requires verification of the results obtained before they are accepted as knowledge by ensuring that consequences of such results are drawn and compared with facts for complete agreement.

What I found is that certain pathological mechanisms took control of the genome when the law that governed the species at their origin was violated and these mechanisms make changes to the genome to bring about structure and function for a purpose which is not for the good of the organism as Darwin assumed when he inferred from inference that the similarities that exist between the species are consequences of origin from a common ancestor.

These changes which are directed to specific phenotypic traits must necessarily not be converted into DNA mutations because the beneficial mechanisms are the ones that control the DNA at the beginning of life and the conditions that permit such perpetuation of the species by such mechanisms must necessarily not permit such pathological mechanisms to make changes to the DNA. Mutations must be a consequence of the changes that such beneficial mechanisms make to the genome when the information they must act upon becomes different from what it was inception.

I will begin presenting the evolutionary theory which has crystallized out of this illustration of reality in a paper dedicated to the subject and I will let you know when it is completed. But you can read the little about this theory which I wrote in my papers on immunity.Thanks for the opportunity to answer your question.

One of the issues that is holding the concept of an RNA world back from being more scientifically useful - irrespective of whether there ever was such a thing - is that we don't use the idea in the scientific way it was intended. Just like any other prebiotic scenario, it is not (nor has it ever been) a scientific hypothesis. In fact, scenarios are usually not intended as such. Scenario authors from all niches (including RNA world) have pointed out that scenarios themselves are untestable. However, they guide thinking and allow to conceive of hypotheses that are testable. If we go through the old literature we find very explicit passages to support this fact.

For the specific authors advanced in the question, G.F. Joyce and L.E. Orgel, we have a passage from 1999 in "prospects for understanding the origins of the RNA world". (The RNA World 2nd ed. 49-77).

"The presumed RNA World should be viewed as a milestone, a plateau in the early history of life on earth. So too, the concept of an RNA World has been a milestone in the scientific study of life's origins. Although this concept does not explain how life originated, it has helped to guide scientific thinking and has served to focus experimental efforts."

You can find this point of view expressed in foundational work for all niches related to the popular scenarios today. But you can also find it for scenarios most people in origins have never heard of. E.g. the idea that celllular life started with terpenoids found in G. Ourisson and Y. Nakatomi's "the terpenoid theory of the origin of cellular life: the evolution of terpenoids to cholesterol. (1994) Chem & Biol. 1 11-23".

"The hypothesis provides an attractive way of ordering the terpenoids: like all evolutionary theories, it cannot be tested directly. The ideas summarized here do, however, suggest a multitude of experiments having some bearing on the fundamental and fascinating question: how did the first cells appear? We hope to carry out some of them."

A related line of thought - but highly influential - is the exposition by Harold J. Morowitz from 1992 in his book "Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis". If we go to the conclusion, we find this explicit clarification on the distinction between a genuine scientific theory and a scenario:

"at this stage of the thought process, it is important to focus on the hypothesis that intermediary metabolism recapitulates prebiotic chemical evolution. This hypothesis is not a strictly vulnerable theory in the Popperian sense, but it does provide us with a valuable heuristic method for using modern knowledge of biochemistry to search for events that have left their trace. If the intermediary metabolism of autotrophs does not recapitulate biogenesis, then the discontinuities will have to be explained."

More than 2 decades back, many authors made a clear distinction regarding this nuance. Scenarios are here to help: they guide thinking and design experiments. They only guide thinking in a scientifically meaningful direction as long as we can easily abondon scenarios and enthusiastically continue replacing them with new, more informed scenarios. A situation where a scenario gets entrenched and where researchers treat it as a scientific hypothesis is - by construction - hard to escape.

In fact, this is exactly the situation that many researchers have described around the 80s, when criticism mounted against the prebiotic broth scenario. The passage from Wächtershäuser's 1988 "Theory of a Surface Metabolism" is telling:

"The prebiotic broth theory has received devastating criticism for being logically paradoxical (11, 135), incompatible with thermodynamics (11, 144, 160), chemically and geochemically implausible (134, 136, 144), discontinuous with biology and biochemistry (160), and experimentally refuted (135, 160). The reason for the tenacity with which it is retained as accepted dogma has been forcefully and clearly stated by Scherer (126): "If this rejection is substantiated, there will remain no scientifically valid model of the selforganization of the first living cells on earth."

Clearly, the broth scenario had overstayed its welcome. One reason for this is that its 'claims' (which for a scenario can only be speculations) were too much in contradiction with claims from fields of science that do not suffer the same restrictions when it comes to testing and refuting their theories. One example of a very controversial idea that can be found in Haldane's formulation of a broth scenario, is the purported necessity of a long, highly functional protein randomly emerging from a soup, as an extremely rare event: we expect this to be prohibitively unlikely and hence a far from parsimonious explanation.

Quite a few of the critiques voiced against the prebiotic broth scenario are equally valid critiques of some scenarios we have today, including RNA world.

The RNA world is an old and multifaceted concept. There are contrasting formulations that make different claims (to be interpreted as speculations) about history. As with the prebiotic broth scenario (and any scenario), it has raised genuine scientific objections. These have remained largely unadressed, in spite of its long dominance.

It is instructive to bear in mind that scenarios don't come from nowhere. They're fairly detailed speculations about purported historical events. To make them, each author makes assumptions. Some of these concern speculations that later became testable, e.g. about chemistry and physics. You will find different scenario authors make different assumptions and different arguments (and flaws therein). There's an inevitable bias here with respect to the fields an author is trained in. Some of the foundational assumptions in popular scenarios like RNA world are at least 50 years old, but some unchallenged assumptions date back to a literature that is more than a century old. A time before IUPAC, modern quantum mechanics, genetics, and so forth.

That has been enough time to forget that scenarios like RNA world are by construction not testable hypotheses and that they were not intended as such. Scenarios are here to guide thinking, to inspire experiments. The best thing a scenario can do for us, is generate insights that spur us to change the way we think and thereby necessitate replacing our old scenarios with new ones, and repeat the cycle. The science coming out of the community today is a lot more conducive to doing that than previously.

The same cannot be said for the rather myopic RNA-centric framing of a question in the cited passage, which attempts to elevate RNA world to more than a scenario. Rather than forcing ourselves to think about the rather narrow and outdated proposal by Joyce and Robertson, ("consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule"), it is more productive to critically revisit all the things that have been assumed and argued when the concept of an RNA world was conceived and how which of these premises are considered valid or plausible today, and which ones back then. Is there a formulation of RNA world for abiogenesis that is logically sufficient? And if so is it logically necessary that abiogenesis proceeded this way?

It is also instructive to check how much of the logic was sound. e.g. the rhetorical tricks employed in RNA world introduce all sorts of hidden assumptionsm.

As an example of the latter: some still justify an RNA world by the party trick 'chicken-and-egg' question 'protein or RNA, which came first?', only to conclude with 'RNA, it encodes proteins' and hastily conclude with an even stronger 'RNA-first' for abiogenesis. 'chicken-and-egg' fallacies are nothing new in origins. In fact, they were already identified as such long ago. E.g. in chapter 8 of "Seven Clues to the Origin of Life (1985)" by Cairns-Smith, there's an illustrated passage detailing that these types of paradoxes in origins frame the question in a manner that prevent us from considering scaffolds.

"

The fact is that even the so-called simple organisms such as E. coli are very complex enterprises with all sorts of things going on together. There is plenty of scope for accidental discoveries of effective new combinations of subsystems. It seems inevitable that every so often an older way of doing things will be displaced by a newer way that depends on a new set of subsystems. It is then that seemingly paradoxical collaborations may come about.

To see how, consider this very simplified model - an arch of stones: This might seem to be a paradoxical structure if you had been told that it arose from a succession of small modifications, that it had been built one stone at a time.

scaffolds that starts like this:

This might seem to be a paradoxical structure if you had been told that it arose from a succession of small modifications, that it had been built one stone at a time. How can you build any kind of arch gradually? The answer is with a supporting scaffolding. In this case you might have used a scaffolding of stones. First you would build a wall, one stone at a time:

Then you would remove stones to leave the 'paradoxical' structure.

"

It should be noted that in 2022, even in RNA-world, very few scholars remain that find RNA-first a convincing idea. As a scenario, however, it is not useless: it is instructive to consider what the underlying ideas are that at some point in time made such a highly specific idea compelling to so many of us.

A fixed motif in scenario papers is to start explicitly and implicitly assuming a few things about what chemistry can and cannot do and some properties of abiogenesis. These sort of assumptions used to be spelled out routinely, also outside scenario papers. Let me give two examples.

The original 1953 paper for the "Frank Model" "on spontaneous asymmetric synthesis", has the passages

".. the defining property of a living entity the ability to reproduce its own kind ...

confining attention to chemical molecules, the complexity of any having this essential property of life is likely to be great enough to make it highly improbable that it has a centre of symmetry."

(*I should point out that Frank makes an important error here: the capacity for molecular reproduction is not a molecular property but a property of a reaction network. If we add an additional thermodynamic criterion this property is autocatalysis and we can then check this claim from the IUPAC definition: https://goldbook.iupac.org/terms/view/C00876. It turns out there are trivial ways to make small networks that have this property https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d67469df42226f44295/original/emergent-autocat-animation.gif.)

The point to retain here is that Frank considers it to be generally accepted that one can assume this property to be prohibitively rare in chemistry. This belief was wideheld, and we can e.g. read in "the units of selection" (1970) by Lewontin a summary on scientific views on abiogenesis

"The present view ... Since there was no autocatalysis, there was no reproduction or heredity and so no possibility of natural selection."

The coacervates in Oparins scenario were notably invoked to adress this issue.

When it comes to assumptions in scenarios, this systematically involved conjecturing that chemistry 'in the wild' intrinsically and deterministically becomes a 'mess', undergoing no meaningful complexification, and for which no reproduction and evolution can reasonably be expected. From there, it appears that no process of abiogenesis should conceivably occur naturally, and thereafter some specific sequence of exceptional events is proposed as plausible, because it appears to be the sole contender.

Let us make more explicit why this is not an innocent procedure:

We still find our understanding of 'basic chemistry' to be plagued with limitations and long-lived misinterpretations (e.g. 2 days ago we learned that methyl substitution destabilizes radicals instead of the textbook knowledge that it stabilizes them ).

Moving beyond the basics, we by and large lack a lot of formal theory, experiment, or even a simple reference frame for the things that happen then. Joyce and Robertson honor the tradition of purporting from the outset that 'chemistry in the wild' becomes an intractable mess. The issue is that we don't know at all if that's the case. We cannot assume this from the outset, we need to extensively study it. We require extensive experiments and theory and a reference frame for all the phenomenology associatied with complex systems (e.g. multiple components, compartments, multiple forms of nonequilibrium driving, length scales, time scales).

In making the routine assumption of 'messy, intractable chemistry that can neither complexify nor multiply', we have decided in advance that, once we finally understand 'chemistry in the wild' with its 'so-called intractible mixtures', it cannot have any bearing on abiogenesis. Let alone explain it.

That is a disproportionately bold conjecture about fundamental science, and a very consequential one: all historical scenarios - RNA world being one out of many - have been justified by formulating conjectures of this sort (many authors also insist on other properties, e.g. chemistry being deterministic). Clearly, it should be the first priority of everyone in the field to test this conjecture, by extensively and rigorously studying complex chemical systems as an end in itself. If the conjecture is correct, it provides an important validation for historical scenario approaches. If the conjecture turn out wrong, we are in a much better position to conceive of more scientifically informed scenarios, but potentially the approach will change entirely.

In presenting it as such, I am making it appear as if it could be an open question whether the chemical conjectures underpinning our scenarios in origins may be true or not. In fact, we have learned quite a few things in the meantime. And some clumsy mistakes were made elsewhere.

- Determinism:

When it comes to chemistry being deterministic (a key tennet of e.g. Sutherlands scenario and Wächtershäusers surface metabolism): upon critical evaluation of what is known of basic chemistry this idea becomes unacceptable, especially when considering the chemical processes on the surface of a planet, as opposed to a quick reaction in pyrex.

1) insofar as it is reproducible, modern chemistry owes much of it to big strides of standardization in glassware, methodology, synthesis protocols (e.g. usage of stirring bars).

2) lab chemistry exhibits many forms of contingency. This is particularly the case when it comes to phase behavior, e.g. habit modification, polymorphism. Aspirin purportedly has 8 reported polymorphs, phenobarbitone 13.

3) glassware is cleaned between reactions, thereby making successive reactions in the same glassware independent. In nature, this property of independence is absent. In fact, effort to make an evolutionary classification of minerals are rooted in the opposite: that certain minerals start to form conditional on the presence of certain others. (https://pubs.geoscienceworld.org/msa/ammin/article/104/6/810/570840/An-evolutionary-system-of-mineralogy-Proposal-for)

- Autocatalysis:

A first issue to get out of the way is the misconception that autocatalysis is prohibitively rare. A prominent PI in origins (RNA world, not a chemist) told me that chemists throughout history have found exactly one example. Claims about the contents of a literature one cannot realistically have read in a lifetime is a common error we can find in the origins literature. Below are some reviews.

I should stress that these reviews discuss examples from a few niches in chemistry. These reviews do at least allow to have 100s of counterexamples to dubious claims about no autocatalysis in chemistry, but it's only a small fraction. Virtually all branches of chemistry have regular reports of autocatalysis, but very few focus on autocatalysis in its own right. And hence most branches do not review their reported examples.

By critically examining the IUPAC definitions, one can show that autocatalysis is dramatially more widespread than long thought. In part, this is because the definition applies to a wealth of situations where the term is not routinely employed. By examinging the requirements of autocatalysis as an emergent network property, one can demonstrate that this property emerges particularly readily in a heterogeneous / multicompartment context. With the disclaimer that I'm an author I refer to the following:

- Messy chemistry:

Refreshing counterexamples are afforded by the literature on systems chemistry and dynamic combinatorial libraries.

In the context of origins, a recent work that is greatly aiding in fixing our misconceptions is : https://www.nature.com/articles/s41557-022-00956-7

Where a reaction of purported immense complexity is found to exhibit highly reproducible and ordered behavior as function of environmental inputs. How chemistry exactly works on this level is still poorly understood. I think I do, but it'll have to await peer review. But we cannot in good scientific conscience take for granted anymore that chemistry becomes messy and intractable. When we do the experiments, we see something very different.

in conclusion, I want to come back to the final point of the question

No. The sientific community should strive to do what it can justify scientifically. Those that find it fruitful to relegate the RNA world - which is not a hypothesis - are justified in doing so. Notably because it is is founded on scientifically refuted premises and logical errors.

Those that find ways to make it fruitful to keep it are justified in doing so: it's a scenario, one can draw inspiration from it. Perhaps a thoroughly altered version can be developed that fixes previous issues.

Above all else, RNA is an amazing molecule that has been used for fundamental research that concerns everyone in origins, and will continue to do so irrespective of how serious the RNA world scenario is still taken.

What the origins of life community needs, first and foremost, however, is concern itself with more important matters.

Complex chemistry needs to be studied thoroughly on an experimental and theoretical level.

New scenarios are needed. And these scenarios should no longer require chemistry to have properties it doesn't have, and vice versa. These scenarios should also explicitly be appraciated for what they are, an for what they're not. They're here to help, to guide thinking, inspire experiments, produce testable predictions, update our beliefs. They are not scientific hypotheses in and of themselves.

Success is a subjective term. The use of subjective terms is a problem in science - See discussion "Terms ambiguity in research - Pros and Cons" (https://www.researchgate.net/post/Terms_ambiguity_in_research-Pros_and_Cons).

When you apply the term "success" to something with a long history, like "biological evolution," new problems arise with that subjectivity. A lot would depend on which timeframe you choose. Here is an example. Suppose you have selected the number of descendants' branches counted by the number of species as a criterion of evolutionary success. Then you have to choose the timeframe to which you want to apply this criterion. The winners would be different for different timeframes. If the timescale is when life exists on Earth, the apparent winner is the first common ancestor of all living things. What would happen if you chose one billion years as the timeframe. Then the winner would be different if you apply this timeframe to the beginning of life on Earth or recent times.

Differences in distress: Variance and production of American Crocodile ( Crocodylus acutus ) distress calls in Belize

Visit to that article

Jingjing Li

One of the best websites to find the answers to these questions is the following link:

Thank you a lot for your help!

I work with entomopathogens fungus in biological control with avocado, berries and citrus pest. But I'm in Mexico, Universidad de Guadalajara.

In the USA, the Californian Universities has a lot of tradition about thouse topics (Berkley, Riverside, Davis, etc)

Those genes are called orphan genes (https://en.wikipedia.org/wiki/Orphan_gene) and they are widespread. The thing is: it doesn't pose a problem for the theory of evolution. The theory is so strong, that it rather poses a problem for the genes, so to say: we must find an explanation how those genes can arise (the wikipedia article mentions some hypotheses).

Of couse, there is cyclical animal population variantoin in hole planet due periodic elleven years variation in solar irradiation

Another experiment was to remove calling treefrogs from their calling site and displace them by 0.5m, 1.0m, 2m, 5m, etc. and observe the length of time needed for the frog to return. It is best to mark the frog to be sure the same individual is the one re-occupying the "vacated" calling site. It is surprising how little time is required for a return from 5m in some species, for example. This can be followed up by introducing clear plastic barriers on the homeward path and quantifying the barrier size that actually blocks the frog's successful return (small barriers are easily negotiated in some species).

Shivaji University, Mumbai is the right option to Pursue Master Degree. It is one of the best University having good Plant Taxonomists in Department of Botany. Professors from Shivaji University Contributed a lot in discovering new plant taxa. Instead of M.Phil, I suggest to enroll Ph.D in B.S.I, under the supervision of any Scientist instead of Universities. For molecular systematics, Delhi University is the right one for M.Sc and Ph.D.

Dear Pedro,

The following may be helpful for you.

Good luck,

https://www.doaks.org/research/byzantine/scholarly-activities/byzantine-studies-fall-workshop/naturepaper09.pdf

Yes, ape in R is a good option

For the sake of providing a direct answer to the SPECIFIC question you asked, the following R code will do exactly what you require, and output the tree to a PDFfile in your current working directory

library(ape)

tree = read.nexus(file="path\to\file")

tree_export = "tree.pdf"

pdf(file=tree_export, width=6, height=6)

plot(tree, cex =0.5, use.edge.length=FALSE)

axisPhylo()

edgelabels(cex = 0.25, width = 0.1)

dev.off()

depending on your tree structure just play around with the "cex"and "width" parameters to make the branch numbers readable, the above peramters are reasonable starting points.

The above code assumes your tree is in Nexus format. For the commonly used Newick format do this:

library(ape)

tree = read.tree(file="path\to\file")

tree_export = "tree.pdf"

pdf(file=tree_export, width=6, height=6)

plot(tree, cex =0.5, use.edge.length=FALSE)

axisPhylo()

edgelabels(cex = 0.25, width = 0.1)

dev.off()

i.e. swap "read.nexus" for "read.tree" function

Rutger is quite right. You have an 18-parameter model with dependence, and an 8-parameter model without dependence. You can compute the lnL_18 (for the dependence model) and lnL_8 (for the independence model), and use a likelihood ratio test with likelihood ratio chi-square = 2(lnL_18 - lnL_8) with 10 degrees of freedom (for the null hypothesis that the dependence model and the independence model fit the data equally well).

Brian Thomas Foley, would you mind sharing some of the tools you've employed to visualize amino acid mutations on a phylogenetic tree? I am having trouble running ChromaClade

Nobel Prize winner Niko Tinbergen observed in his now classic 1963 paper, "On the aims and methods of ethology" (Zeitschrift fur Tierpsychologie 20: 410-433) that in order to adequately analyze observed patterns of behavioural ecology in a species, it is necessary to distinguish between *ultimate* and *proximate* causative factors. Ultimate factors include: i) the *function* (or "adaptive value") of a behaviour, and ii) the "phylogeny" (or evolutionary history) of a behaviour; proximate factors include: i) *ontogeny* (or behavioural changes related tp growth and development), and ii)*proximate conditions* (i.e., that which has happened in the recent past and that which is going on under current ecological conditions). So, what is needed in trying to gain insight on biological evolution is an holistic perspective that incorporates *both* genetics and ecology. A perfect example of the value of this integrated approach is the need for up-to-date data in both the genetic and ecological realms in order to deal with conservation biology issues.

The propionic acid is in the fly food as a general microbial inhibitor, I have been able to get away without it as long as some other preservative is present (e.g. methylparaben/Tegosept, but this might not be cheaper).

If you really want to save on cost, you might be better off going with some oldschool way, like culturing flies on a banana/yeast mix (see attachment). I would keep an eye out for mold and bacteria though.

BAMM, LASER, and APE

Mr. Pegman; Selection of any kind might lead to what is called an adaptation - that is, in hindsight, we can see that some phenotype is under positive selection and the reproductive status of the population improves. That's all.

Creation and design have no place whatsoever is any scientific discussion. The propositions are either untestable or have been disproven so many times that is tiresome to dwell on them. Best regards, Jim Des Lauriers

Thanks for all the tips! This was extremely helpful

Take a look at the The Mohamed bin Zayed Species Conservation Fund: https://www.speciesconservation.org/

Dear Carolina Soliani

You should download stable version, link works.

Kiavash

Yes this question can really only be addressed in a helpful manner with more information about your needs and unfortunately your budget. But basically eDNA techniques are emerging that allow simultaneous amplification/sequencing of all of the OTUs that successfully amplify, so by definition this approach uses universal primers for markers usually such as 16S rRNA and ITS, internally transcribed spacer region, or COI cytochrome c oxidase I, then the resulting sequences are blasted against NCBI database to determine biodiversity in the sample. But if you are using a more traditional PCR approach where you want to specifically amplify only certain target lineages, one possibility is use species of specific primers. Depending on the species of interest, this can be tricky if such PCR primers are not available, but you can design your own primers that specifically amplify only the species of interest, provided there are DNA sequences available for these taxa.

Hello Asif; If you intend to reply, think carefully about what your goal is. I used to engage in exchanges like the one you anticipate. I mistakenly thought that if I could explain some aspect of evolutionary theory or some particular data set, then I could help the person understand the general idea. That doesn't seem to be true. The issue is an ideological one, not a lack of information. Some years ago I wrote an essay intended to help science teachers with exactly this problem. Its title is "The Creation/Evolution Dispute: a Teacher's Handbook". Look it up on ResearchGate. Best regards, Jim Des Lauriers

I realise I never followed this up with the published paper. Here it is for anyone who is interested.

Lean, C. H. (2017). Biodiversity Realism: Preserving the tree of life. Biology & Philosophy, 32(6), 1083-1103.

Cheers,

Chris

Hello Ozge,

For selection analyses you want to be in a range where your rate of synonymous substitutions (dS) is not saturated. If this rate is too high then any methods based on dN/dS will not be appropriate.

In mammals, Rodents or Simian primates are great sets of species to detect signatures of selection (over 20 assembled genome in each). In general I would say that between 50-70My of evolution is a good amount for selection analyses in mammals.

As far as number of species, there is a great study by Sarah Sawyer's group that looked into this. I would recommend to aim for 20. If you are using likelihood methods you will run into computational hurdles with more species. But I would advise against using the entirety of mammals to run any type of selection.

I hope it helps.

Cheers,

Antoine.

Patrice Showers Corneli

If it helps, I believe it was a G.G. Simpson volume reminiscing about the history of the discipline and what he had seen during the crucial periods of formation of the modern synthesis. Or a biography of Simpson talking about the history of the modern synthesis.

See also

A clear treatment on the topic of sex ratios can be found in this book;

Charnov, E.L. 1982. The Theory of Sex Allocation. Princeton University Press.

Gary;

Start casting about for your credible voice now. That voice can use all of the background information, literature research, and legwork that you can provide as a "good lieutenant". By providing that kind of quiet support the public face of your effort is less likely to burn out and will also gain confidence in the validity of the effort.

I, and others, started working on the preservation of a tract of land in this community and were pitted against entrenched real estate development interests. The strategy that I've suggested to you is the one we used. Progress was glacially slow with plenty of setbacks and some crucial "victories". The faces have mostly changed but the goal remained. Now, 40 years later that tract of land, and an area that doubled the total area, is about to be placed in permanent conservancy. This old war-horse is mostly out to pasture but still feels the warm joy of seeing a good thing through to a happy conclusion. As you pointed out, it took far longer than it should have. But in hindsight that's OK.

Best, Jim Des Lauriers

@ Md Zafar Alam Bhuiyan

@Hamid Gadouri

@ Everyone and Anyone

Here I would hope for a discussion based only on “natural” philosophy. Not a discussion that in anyway involves theology, or any other school of knowledge.

Basically is there a “Theory of Evolution” or only empiricism?

The best way to answer the question about what kinds of files can be opened in R software is to find the relevant Task View on CRAN. Below I've copied what the Phylogenetics Task View says about reading trees into R. As for ancestral state estimation, the literature is quite large and several of the recent, most flexible methods for quantitative traits, are not implemented in R. A nice recent summary/tutorial that emphasizes methods that are available in R is by Liam Revell, the author of the phytools package: http://www.phytools.org/eqg2015/asr.html

As for getting trees into R, from the Task View:

Getting trees into R : Trees in R are usually stored in the S3 phylo class (implemented in ape), though the S4 phylo4 class (implemented in phylobase) is also available. ape can read trees from external files in newick format (sometimes popularly known as phylip format) or NEXUS format. It can also read trees input by hand as a newick string (i.e., "(human,(chimp,bonobo));"). phylobase and its lighter weight sibling rncl can use the Nexus Class Library to read NEXUS, Newick, and other tree formats. treebase can search for and load trees from the online tree repository TreeBASE, rdryad can pull data from the online data repository Dryad. RNeXML can read, write, and process metadata for the NeXML format. PHYLOCH can load trees from BEAST, MrBayes, and other phylogenetics programs (PHYLOCH is only available from the author's website). phyext2 can read and write various tree formats, including simmap formats. rotl can pull in a synthetic tree and individual study trees from the Open Tree of Life project. The treeio package can read trees in Newick, Nexus, New Hampshire eXtended format (NHX), jplace and Phylip formats and data output from BEAST, EPA, HyPhy, MrBayes, PAML, PHYLDOG, pplacer, r8s, RAxML and RevBayes. phylogram can convert Newick files into dendrogram objects.

Hi Arman,

As other people suggested, all the explanation should be in the legend of the figure. Often, the number on the scale should be the percentage of genetic variation. For example, if this was the case of your figure, the scale would suggest a 0.2 (20%) genetic variation for the length of the scale. However, in this case you would not be able to have a total distance >1. For phylogenetic studies, this length would be usually much shorter, with a scale bar at about 2-5%. However, this is not always the case, and that's why scale bars should always be explained under the figures.

In your example, "number of differences between the sequences" is to say the least incomplete (and it is not your fault for not understanding). They may be referring to something they explained better in the text? Maybe "differences" is referring to specific sites in the protein?

Also, just to be sure it is clear, I showed in the figure how to calculate the distance between the proteins. You have to consider the full length of both the branches up to the point these are connected (in RED in the attached figure). In your case, the branches A-1 and B-4 are connected only at the base of the tree. Therefore the distance between them is APPROXIMATELY 12 times the scale bar, or 2.4 "differences". In case you need a more precise measurement, however, you would need to create a distance matrix using the sequences that have been used to generate the tree.

Hope this will be helpful!

If you multiple those values per 100 you will get the percentage of difference (0.7% and 25%).

Hi Lu,

the chances just depend if the plasmid transfection/nucleofection of the RNP were successful. If the gRNA is properly designed (PAM sequence, uniqueness, etc.) it will always cut. Repair after NHEJ is totally random, and usually about 1 -10 bp are deleted but insertions are not rare either. Therefore, the length in difference cannot be an indicator for gRNA efficiency as, as long there has been been some indel and you verify it by sequencing that the target protein is disrupted, all gRNA are equally efficient.

I let you this interesting Addgene blogsite: http://blog.addgene.org/crispr-101-non-homologous-end-joining

The idea that DNA sequences swamp out morphological characters simply by virtue of their greater number of characters is not necessarily true. DNA is almost always very homoplastic, and if there is a good morphological signal in the data, it usually prevails. In my experience, morphology and molecules for my group (butterflies) are usually in agreement with one another. See

Simonsen, T. J., N. Wahlberg, A. V. Z. Brower, and R. de Jong. 2006. Morphology, molecules and fritillaries: approaching a stable phylogeny for Argynnini (Lepidoptera: Nymphalidae). Insect Syst. Evol. 37:405-418.

Wahlberg, N., M. F. Braby, A. V. Z. Brower, R. de Jong, M.-M. Lee, S. Nylin, N. E. Pierce, F. A. H. Sperling, R. Vila, A. D. Warren, and E. Zakharov. 2005. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc. R. Soc. Lond. B 272:1577-1586.

Brower, A. V. Z., N. Wahlberg, J. R. Ogawa, M. Boppre, and R. I. Vane-Wright. 2010. Phylogenetic relationships among genera of danaine butterflies (Lepidoptera: Nymphalidae) as implied by morphology and DNA sequences. Systematics and Biodiversity 8:75-89.

I highly recommend anything written by Lynn Margulis, as this idea was her original concept a long time before it was generally accepted by the scientific community!

Hi, Christian,

I think that a good example may be the fact of enucleated red blood cells in the lungless salamanders (Plethodontidae). This trait is independent of similar situation in mammals.

Regards,

Alexey

I agree perfectly with Brian sometimes if you do not have specific problem being an out group also used to make a direction to the tree is better to use a mid point rooting that is a sort of average of a probable root due at a probable ancestor

Thanks for replying and I'm really sorry about the late reply!

Hi. Jmodeltest is best for your work, Ofcourse Mega6 or 7 version has Modeltest and based on your sequences, you can select the best model.

Your assumption is reasonable. Another possibility is simply that one of the genes has been lost. Some fish species have had 2 rounds of genome duplications and afterwards lost some of the duplicated genes. Doing a synteny analysis, as Abhishek Kumar also recommended, would enable you to distinguish between gene loss and gene conversion.

I just want to add: the CAT-like models for maximum likelihood are C10 to C60, which are supported in IQ-TREE. So you can use this when PhyloBayes is too slow. We also just published an approximation, which speeds up the analysis under such model without loss of accuracy:

Check the attached articles.

Remember always that you are modeling phylogenetic relationships, not evolution. Evolution is not necessarily dichotomous as in hierarchic cluster analysis (of which cladistics is a variant) or Markov chains. Cladistics is also blind to ancestor-descendant relationships. The optimal model in cladistics is the most probable or most credible generation of a dichotomous tree that is not found in nature.

I agree with Brian Thomas Foley above that the choice of strains from same/different species/genera eventually will reject the divergence level.

The power of your analyses for selection and recombination will be affected by divergence as it defines how much information you have in your data. If your sequences are too diverse, or if your sequences are too close then you ar unlikely to find a signal (low power). There are many publications by now that have shown this, including some from my own: Anisimova et all 2001, 2002, 2003 and Anisimova and Yang 2007.

So divergence is one factor. Another factor to consider is what type of sampling you have and how well it corresponds to your actual question. Do you have mixed population and species data? Are you interested in lineage-specific effects? Are you interested in detecting episodic selection. Are you contrasting your sets of strains by some criteria (e.g., pathogeneicity or environment, etc.)? Basically, you can analyse any sample set, but the success of your analysis will depend on what specifically questions you are asking and whether your sample is the best one to provide information to answer these questions. So there you have to be careful what tests to set up and how to interpret them. I don't know if this helps, but I don't know specifically your scenario.

If you have partial sequences for protein coding genes, it is likely that they do not start at the first codon position. If that is the case, and you count the triplets from the very first nucleotide, it will lead to a frameshift in the codons, and stop codons are likely to occur. One way of obtaining the right frame is to compare your partial sequence to a fully sequenced gene in a closely related species and see if you can determine the position of the first nucleotide in your partial sequence. Once that is determined, you can then obtain the right coding frame in your sequence and you should then be able to avoid getting any premature (internal) stop codons.

I have generally received primer stock (powder form) in room temperature and I leave them at RT until I dissolve them in water to prepare a stock solution.  If you are transporting primer solution, it is still not a problem to transport them in Ice. The cool pack works for few hours anyway. They are being very stable, they should be fine even in room temperature. 

This artificial "treshold" depends on the marker and the taxonomical group you are working on: you should probably be more specific to have the beginning of an answer.

However, never forget this treshold actually... does not exist. :)

You can empirically measure mean genetic differentiations between species you have defined a priori, but in no wise you can use it to systematically "delimit the species". In particular, since you mentioned a mitochondrial gene (COI), note:

Unfortunately, taxonomy is not (only) about measuring genetic distances. At most, sequences divergence can pinpoint "unconfirmed candidate species" (see Padial et al. (2010): https://doi.org/10.1186/1742-9994-7-16). You then need other types of evidence (nuclear DNA, phenotypical/ecological characters...) to validate whether or not "these two species/individuals are of distinct species".

Best regards.

David,

Have a look at these paper:

I have  short section on bioerosion in the Ecology of Indonesian Seas that you may find of interest; see page 635.

Hope this helps.

Tomas

Thanks much Andrew. Much appreciate your help. I'm looking for ways to do what you suggested. Any suggestions on links/articles that you may know of will be helpful.

Hi,

In addition to the other suggestions, You could try to estimate population genetic differentiation for morphological traits (Qst) between your populations and compare with corresponding Fst estimate (using any molecular marker available). If Qst is significantly larger than Fst you could consider that the difference is caused because natural selection is acting on your morphological trait. There are several studies using Qst/Fst and you can get a typical experiemntal design from them.

Alternatively you may study variation on morphological trait and estimate its relation with fitness (any component) following Arnold and Wade 1984 methodology. If fitness is working on your trait you should find  higher fitness estimate for certain range of the trait distribition...

Best

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. 

Hi everybody,

Thank you very much for your answers. I will check all your links and come back to you soon.

Cheers,

Benoît

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

Thanks so much!

Use MEGA7. The King of them all

Thanks for your answers! I was trying to convince an amateur collector that a particular tooth was not that of a dinosaur, but a mammal incisor.

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

Thanking you, sir. It will help me a lot . 

Transformation does not LEAD to skewed data; rather, transformation changes skewed data to normal :)

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.

Found it: "AnnotationBustR: An R package to extract subsequences from GenBank annotations" Here: https://peerj.com/preprints/2920.pdf  

Yes, as said previously you need to test the ENTIRE data set. However, once you have done that you can do specific analysis of unique haplotypes to provide information of the variation among the variants. 

Dear Alienor,

I would advice you to have a look at the studies of Hans Christian Bjerring here:

Especially interesting may be two of his articles (both are available for downloading directly from Research Gate):

and

Also, you may be interasted in the earlier studies by Gunnar Save-Soderbergh and Malcolm Jollie. Especially this one:

My best,

Alex