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Consider the following two situations:

  1. A species X has trait $T_1$ that is gradually selected for by some characteristic $E_1$ in some ecological niche but it turns out that the genes for $T_1$ also "turn on" genes for trait $T_2$ so that eventually species X with trait $T_1$ also have $T_2$. Then it turns out that $T_2$ is evolutionarily advantageous i.e it does help in increasing fitness because of some characteristic $E_2$ in that same ecological niche.

  2. A species X has $T_1$ that is selected for by some characteristic $E_1$ in some ecological niche, this ecological niche also has characteristic $E_2$ that separately selects for $T_2$.

Both of these cases have as the end product $T_1$ and $T_2$ being advantageous for survival but in one case $T_2$ was selected for and in the other it's usefulness was accidental. What in the theory of natural selection distinguishes these two cases? To put things more bluntly, you are an evolutionary biologist and you are telling the standard story that corresponds to situation 2, how do you know (from the theory of natural selection) that we can discount situation 1?

I did a research project for my undergraduate research where I simulated mutations of cells in a petri dish and I know that mathematically these two cases can be disentangled because they lead to two different cluster size distributions with different scaling laws. As a physicist I know what to do but does a evolutionary biologist using theory of natural selection know what to do.

Update: The point is that in case 1 $E_1$ and $E_2$ could act at different times so that only $T_1$ is responsible for survival and $E_2$ while acting $T_2$ was completely useless for it's survival i.e other species disappeared not because they didn't have $T_2$ but because they didn't have $T_1$. Then a naive biologist could tell separate evolutionary stories assuming that $T_1$ and $T_2$ were selected for separately because when the biologist is observing the situation both $E_1$ and $E_2$ are present and $T_1$ and $T_2$ are present. In other words, he or she would assume case 2 occured. In this case, random mutations and natural selection as told in science classes is completely useless because of $\textit{dynamics}$ in the environment and $\textit{correlations}$ that prevent mutations from being just random.

Why does this bother me? Well, because I hear evolutionary accounts that span hundreds of millions of years and it would seem simply applying the Darwinian story naively could make wrong predictions all over the place. I haven't seen people worry about this as they give evolutionary accounts for everything. From sexual behaviors to marketing.

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  • $\begingroup$ I am not sure I understand the question. How is your question different from a classical correlation vs causation question in statistics? $\endgroup$ – Remi.b Dec 19 '17 at 11:05
  • $\begingroup$ Note by the way that you seem to confound the concepts of "environment" with the concept of "ecological niche". You might want to have a look at their definitions. $\endgroup$ – Remi.b Dec 19 '17 at 11:06
  • $\begingroup$ @Remi.b that may well be true that in my question I confound the two, but looking at the definition of "ecological niche" I think my question still runs through. $\endgroup$ – Amara Dec 19 '17 at 13:40
  • $\begingroup$ @Remi.b I can rephrase the question in terms of correlation vs causation. The simple story is that traits that correlate with survival or fitness are responsible for survival i.e they are selected for. But in case $1$ $T_2$ is correlated with survival or fitness a posteriori but is in fact not selected for. $\endgroup$ – Amara Dec 19 '17 at 14:20
  • $\begingroup$ So is your question "Are biologists aware of the causation vs correlation problem or are they noobs in statistics?" :) $\endgroup$ – Remi.b Dec 20 '17 at 9:02
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Are biologists aware of the causation vs correlation problem or are they noobs in statistics?

Evolutionary biologists tend to be pretty good statisticians. For historical consideration, Pearson is the father of the concept of correlation and was a biostatistician and Fisher is (one of) the father of evolutionary genetics and is also a famous statistician (invented the Fisher's exact test, t.test and Anova). Many of the modern developments in modern statistics were brought about by geneticists (incl. developments in HMM, ABC, FDR, etc...).

So, yes we are aware of the causation vs correlation problem.

In the theory of natural selection, can the two situations be disentangled especially when one is talking about evolutionary accounts that are on the order of hundreds of millions of years[?]

Just like in any other causation vs correlation problem, no it is not easy to disentangle the two. If the specific hypothesis put under testing is subject to experimental manipulation, then yes, it is often feasible to disentangle the two. Otherwise, in a purely observational study, one can logically reason and argue for one rather than another causality relationship but in essence, you cannot know in a purely observational study whether a correlation is representing a direct causation.

The follow-up question might then be

Is experimental manipulation feasible in evolutionary biology?

The answer is yes. Not for all questions though.

First there are evolution experiments. An evolution experiment is just like what is sounds like. You put a population in a controlled environment and let it evolve. Repeat the process many time to have a decent sample size. There are also many question of interest to evolutionary biology that can be studied through experimental manipulation (and not only observatory studies) that do not require an evolution experiment.

You seem to be particularly interested in the reconstruction of past evolutionary history of a lineage (evolution biology is much more than a 'historic' reconstruction of life on earth), I would like to highlight that in purely observation studies and in experimental studies not involving evolution experiments, there are plenty of methods to reconstruct past events. Consider for example the loss of genetic diversity at linked variants (selective sweep) caused by positive selection. If two traits are correlated through time (which is very hard to figure out in absence of good fossil records) or correlated over several species (consider having a look at phylogenetic contrasts methods and more modern version of inference of selection over phylogenies), then if selection occurred in a single of the two traits, you should expect to see a differential loss of heterozygosity among the genetic markers explaining ariance for one trait and for the other.

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  • $\begingroup$ I am sure biologists are aware of the generic problem of causation vs correlation problem any one in the sciences is. You have merely diluted the force of my question to simply being about whether biologists have opened up books on statistics, I know they have. But that is not my question. In the theory of natural selection, can the two situations be disentangled especially when one is talking about evolutionary accounts that are on the order of hundreds of millions of years. How would one do that generically in the theory of natural selection. $\endgroup$ – Amara Jan 1 '18 at 17:17
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Unless the selective pressure applied by $E_1$ and $E_2$ are applied at different times, it seems like the two scenarios you described are equivalent. In other words, if in both ecological niches, $E_1$ and $E_2$ were present from the start, and both $T_1$ and $T_2$ were present from the start, then absent other factors, the process and result are the same.

However, if you are saying that in the first scenario, $E_2$ was applied only after $E_1$ was selected for, then it is likely that $T_2$ was a genetic hitchhiker, i.e. it didn't provide any advantage before, but the niche has changed and now it provides an advantage. If this is what you're talking about, then you want to look into the concept of genetic drift. Basically, genetic drift is the random mutation of alleles. Genetic drift can lead to speciation if groups of the same species are separated by some sort of barrier to reproduction.

One way to determine if a gene is being actively selected for is to calculate the $K_a/K_s$ ratio which compares the rates of non-synonymous and synonymous substitutions, respectively.

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  • $\begingroup$ In case 1, $T_2$ only appeared because a mutation caused $T_1$ so that $T_2$ is a hitchhicker and was not selected for and so $E_2$ was applied after $E_1$. A naive post hoc evolutionary story would simply observe that $T_2$ is advantageous and so was selected for but this would be wrong. I know these can be disentangled mathematically but these sorts of stories are told about evolutionary processes that happened over billion of years where we might not have access to data that could disentangle these two situations. This is my worry. Has this been thought about? $\endgroup$ – Amara Dec 18 '17 at 21:59
  • $\begingroup$ "A naive post hoc evolutionary story would simply observe that T2 is advantageous and so was selected for but this would be wrong." This wouldn't necessarily be wrong. T2 was in fact selected for, just at a later time than T1. So it sounds almost like you're after the relative time of emergence/selection of 2 traits? In that case, you could maybe build separate phylogenies for each gene/set of genes, and then compare branch times, but other than that, I'm not sure. $\endgroup$ – ndusek Dec 18 '17 at 22:13
  • $\begingroup$ Yes relative time of emergence is everything! Because in the first case it is possible for species $X$ to survive only because of $T_1$ while other species disappear. $T_2$ would emerge later on but it would serve no purpose in the competition because $E_2$ emerged in the environment and acted on $X$ much later on. A naive biologist would simply conclude that $T_2$ was selected for because of $E_2$ but that would be wrong. It would seem random mutations and natural selection is too simplistic. There can be correlations in mutations and dynamics in the environment $\endgroup$ – Amara Dec 18 '17 at 22:45
  • $\begingroup$ Ok, I understand now! It seems to me that there are some methods that exist to determine the relative age of certain segments of a genome based on how many/what type of mutations have been accumulated, but I am not familiar with these methods. Additionally, you may be able to tease out relative emergence by looking for other organisms that have $T_1$ but not $T_2$ (or vis versa), indicating that certain subsets of the population were exposed to $E_2$ while others were not. But this is getting beyond my expertise. At least I finally figured out the proper mathematics formatting! $\endgroup$ – ndusek Dec 18 '17 at 22:57
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Firstly, I think that you should take a look at the genetic mechanisms behind convergent evolution.

In addition to the above statements, I would say that for your null hypothesis, you would need a situation where if there is a T1 then there is an E1 such that T1 positively regulates T2. Therefore, we can infer that T1 also has T2. I also believe that you can frame this statement using universal instantiation, if you are familiar with either logic or discrete mathematics.

For the second situation in your original question, we could say that there exists a T1 such that characteristic E1 and E2 could result in T2.

I prefer to use the language of logic such that we can build a mathematical model (and perhaps an estimate of all of the different combinations) by integrating the Ka/Ks ratio and the use of some sort of Bayesian analysis or graph theory representation to note the spread of genetic drift and an attempt to delineate the different effects that these mutations could have on phenotypes

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  • $\begingroup$ As is obvious, I am not a biologist. Can what is being described in the comments and your answer be applied to evolutionary stories that occur on geological time scales ? That is to say, are these two cases regularly disentangled before people claim what trait was selected for. I am hoping people don't just observe phenotypes and study ecological niches and then weave stories combining the two. $\endgroup$ – Amara Dec 19 '17 at 14:15
  • $\begingroup$ Possibly, I think. What I described is mainly mathematical, and I figured that since you are a physicist, you may know what I am talking about. I only say this because mathematical models in this area are still being developed and the usefulness of these models for biology are still being tested experimentally. I just outlined a more streamlined process to use the mathematical models and current experimental data to test possible disentanglement. $\endgroup$ – user36399 Dec 19 '17 at 16:38
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First selection does not occur at the species level. Scientist don't talk about a species going extinct due to the lack of a gene.

Second you seem to be confusing what evolution can "tell" with what scientists can tell. The spread of a gene is a statistical correlation occurrence, evolution cannot tell what gene causes a phenotype, genomes are selected for whole hog so to speak, (there are some rare exceptions). It is only through recombination that gene can be segregated, in your example it could be determined that T2 is only active when combined with T1 such situations are well known. indeed this is one of the hypothesis as to why various forms of sex/transfer evolved in the first place, to allow the decoupling and loss of disadvantageous genes.

Third entangled linkage and selective pressures are quite common many traits have multiple effects including counter effects and effects contingent on other genes. What you are describing is a regulatory or linked genes vs independent genes. This is the norm for genetics and is extensively studied and is the reason genetics is not as easy as laymen think it is.Very few genes have only a single selective effect and control genes are quite common.

There is even investigation in the fact that un/successful genes are physically linked by and can effect the survival of other genes in the population just by being physically close to anther gene on the genome and thus likely to be passed on together even with recombination. Entire branches of genetics exist to study linkage.

In your own example there is no accidental usefulness, one is simply a linked or regulatory trait while in the other both are independent. So to answer your question yes evolutionary biologist are quite aware of the issue.

What is told in a classroom, especially a basic classroom is a simplified more abstract version of what is known, in your own field nobody is going to start teaching physics with quantum dynamics, or the relativistic effects on a normal trains mass, you start with simpler and somewhat outdated/incomplete equations until the students can grasp the basic concepts. You are not going to talk about Neutron diffraction with students before they understand what friction and mass are. In a description of the evolution of the avian respiratory system or the function of the human facial recognition system, linkage of individual genes is irrelevant, what is being discussed the dis/advantage or function of the phenotype NOT the genotype that brings them about.

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  • $\begingroup$ I am not confusing what biologists can tell with what evolution can tell. In fact this is precisely why I asked the question, the point is when a biologists decides between the two cases does he or she use the theory of natural selection i.e random mutations and survival of the fittest or do they claim to use theory of natural selection but what is really doing the explanation is something else. From the answers it seems what is really doing the explanation is not theory of natural selection per se . $\endgroup$ – Amara May 8 '18 at 21:35
  • $\begingroup$ As to your physics analogy, no physics teacher would claim frictionless incline planes and massless pulleys describe the real world; they are presented as highly idealized simple models. On the other hand, the theory of natural selection is not described in school as a simplified abstract model and it seems to me there are professions that do not treat it as an simplified abstract model i.e evolutionary psychology, hence my confusion. Anyways I think I am getting the idea $\endgroup$ – Amara May 8 '18 at 21:43
  • $\begingroup$ no but they use them in class problems all the time, I'm just trying to explain why your teacher or a paper may not have described in the detail you want. Or to put it another way if I am describing a pulley system used to lift trains the gravitational pull the pulley exerts on the train is not worth worrying about. Everything you are taught in school is simplified. $\endgroup$ – John May 8 '18 at 23:38
  • $\begingroup$ As for what biologists do without an example I can't comment on what you think is happening, It is far too generalized and unclear. If you want to make another question and give an example and ask what is being talked about that's a great use for this site. any number of things could be going on everything from a bad source to confusing phenotype with genotype to mistranslation, ect. $\endgroup$ – John May 8 '18 at 23:43
  • $\begingroup$ For examples Gad Saad a youtube personality and evolutionary biologist claims to study consumerism from an evolutionary perspective or people who speculate about the evolutionary origin of language. It seems to me that in these two examples the back bone of explanation is the simplified abstract model. $\endgroup$ – Amara May 13 '18 at 14:35

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