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37

TL;DR: There is a dearth of actual experimental evidence. However: there is at least one study that confirmed the process ([STUDY #7] - Myxococcus xanthus; by Fiegna and Velicer, 2003). Another study experimentally confirmed higher extinction risk as well ([STUDY #8] - Paul F. Doherty's study of dimorphic bird species an [STUDY #9] - Denson K. McLain). ...


17

There is a recent paper that introduced the first molecular-level whole-cell simulation. Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 DOI: 10.1016/j.cell.2012.05.044 The ...


12

Cat claws are growing all the time, like horse hooves, or human nails. However, cats and horses usually use their claws/hooves, so they get shortened through mechanical action. An indoor cat may need their claws trimmed if it doesn't use them enough (that's why cats will want to scratch everywhere), or if has supernumerary toes that don't normally touch the ...


10

Population dynamics occupies a whole subset of mathematical biology. Perhaps the most pragmatic uses for modelling population dynamics come from the fields of epidemiology for modelling disease infection and transmission through a population (one such article), or ecology modelling things like forestation, fishing dynamics, predator-prey relationships (an ...


8

Leonardo's already given you an excellent answer, but I thought I'd add my perspective. I'm a mathematical epidemiologist, so I'd at least like to believe these types of models are useful. For me, there are a number of things population dynamics models are especially useful for: Highlighting data requirements. Yes, models need data, as you've mentioned. ...


8

When I think about your question of natural examples of XOR, it pushes me to think about what type of natural environments (i.e., evolutionary pressures) would lead to the selection of an XOR equivalent. When we implemented a synthetic XOR by "double flipping" one transcription terminator as a type of gene expression "check valve" it was the case that I ...


7

Two previous answers listed many applications of population dynamics models. I want to add that they are also important for conservation of endangered species. For example classical stage-class model (Crouse et al 1987, free copy) indicate that the most effective way to protect sea turtles is reducing mortality of large juveniles. Moreover, you don't have ...


6

The smallest unit that can be selected is, of course, the single nucleotide. The most striking examples of this are Single Nucleotide Polymorphisms (SNPs), many of which confer selective (dis)advantages. To take a simple example, imagine a SNP that introduces a frameshift mutation, rendering a gene incapable of producing its protein. If that protein is ...


6

That's an interesting conjecture about the total amount of genetic variation that is possible. I would modify a few things. First, since the size of genomes varies greatly among organisms (from 0.5 Mb to 15 Mb just for prokaryotes), there should be a fifth character in your set, representing the absence of a nucleotide. There are also issues of whether ...


6

Yes, we can say the number of species is limited as you conjecture. However, quick estimation shows that the limitation has no apparent usefulness: A reasonable estimate of the largest known genome is 150 GB (150,000,000,000 or 1.5e11 nucleobases). The limit would be 4 raised to that power. That limit is so high that it is too large for most calculators ...


6

This question is really asking for examples, and the list of ways that knowledge of physics can be used in biology could be very long. However, here are a couple of examples: Systems ecology, especially with regard to energy and nutrient flow. This type of ecology can be strongly influenced by physics. For one example see the book Theoretical Ecosystem ...


5

The frequency fluctuations will be determined by a standard model of selection as found in any basic population genetics text. In this scenario they take a very basic form: during each long period $i$ the frequency of $A_1$ increases from $f_i$ to $f_i\cdot (1+s_1)^{n_1}$ and during each short period $j$ the frequency of $A_1$ decreases from $f_j$ to ...


5

There are a number of more recent papers dealing with phylogenetic methods in reconstructing language history as well, including work by Colin Renfrew and Quentin Atkinson. Here are two recent high-profile papers. Unfortunately, both are still behind paywalls, but even reading the list of papers they cite / that cite them would be a great way to answer your ...


5

The Karr et al. paper attempts to capture most of the details in their model by combining features from the genome, transcriptome, proteome, and metabolome. This work heavily builds off of the coarse-grained models that you ask of especially on the work from Bernhard Palsson from which Markus Covert did his training. The answer to your question rests ...


5

Very little is known about the structure of fitness landscapes. H.A. Orr (2005; also Whitlock et al., 1995; Kryazhimskiy et al., 2009) explains that most experimental results do not actually attempt to measure the fitness landscape, but instead report just the average fitness versus time and average number of acquired adaptations versus time. This can't be ...


5

You either want a introductory book in evolutionary biology or a book that offers mathematical models of evolutionary processes. In my first class of evolutionary biology I had this textbook: Futuyama, Evolution I think it gives a good start to the field and offers a good overview of the difference subfields. If you think you already know enough about the ...


5

First of all, here is a program which simulates the evolution of the G-matrix over multiple generations, it's a few years old (they seem to have stopped developing it) and I've only played with it briefly. This could solve how to model the evolution of the G-matrix. Fisher's fundamental theorem is a great place to start off with the theory of this: The ...


4

What you are describing usually falls under the category of computational biology or just mathematical biology. Unfortunately, the biggest part of this field is bioinformatics, or the application of statistical and/or dynamical programming techniques to sequence data. You exclude this in your question, and I would agree with you that it is a "boring" topic ...


4

The chaotic behaviour you are referring to (at least the one described in your link in the comments) is a property of the discrete version of the logistic equation, where you get chaotic dynamics at growth rates above ~3.55 (see the logistic map). The behaviour of this equation has been described in a classic paper by Robert May (1976). As you increase ...


4

This is derived from studying how heterozygosity changes over time. The standard equation for change in heterozygosity ($H$) with constant population size ($N$) is: $H_t = \left(1 - \frac{1}{2N}\right)^tH_0$ When $N$ varies between generations you use the product of this formula: $H_t = \left(1 - \frac{1}{2N_0}\right)\left(1 - ...


3

This question has been around for a while, so I'll try to start with a partial answer. The basic assumptions of the standard Wright-Fisher-Model are: Constant population size $N$. Discrete, non-overlapping generations. Neutrality (e.g. all individuals are equally likely to reproduce) I prefer looking at the model for haploid/chromosomes. If you bundle ...


3

He defines lineage selection as selection for traits which increase the fitness of a group of plasmids, rather than an individual plasmid with in a cell or a particular cell containing plasmids. He says that the unit of selection are "plasmid-host clades" : in other words the unit of selection is the group of closely related plasmids in separate cells. It is ...


3

Relating to your last comment on random fluctuations in survival, a recent theoretical paper by Lee et al. 2011 studies the effect of mating systems on demographic stochasticity in small population. No empirical data there though. Their main conclusion is that polygyny (in relation with sex ratio) can lead to high demographic variance, therefore lowering ...


3

I'm going to define a species according to the biological species concept, probably the most widely "accepted" species concept where a species is a group of individuals that reproduce, or have the potential to do so. Using a simplified example I will show you that gene*environment interactions affecting phenotype can allow separate species to occur despite ...


3

This is a little tricky. First of all lets be clear about 'bringing together favorable alleles' (or any alleles) represented by site mutations on 2 chromosomes: --------A------------------ X ------------------B-------- If the two dashed lines are two copies of the same chromosome, then a recombination event at X may produce: ...


3

I am presenting a speculative approach since nobody has mentioned about any existent models yet. Assuming that selection is based on performance in certain tasks; performance is a function of traits which in-turn is a function of genotype. Performance is a non-linear function of genotype and selection imposes a cutoff/bandpass filter on the performance ...


3

Fishers Geometric Model (FGM) is a theoretical prediction about the adaptation process in traits. There are a number of things to establish before attempting comprehend FGM. Firstly, shifts in an adaptive landscape, in natural scenarios, are generally quite small. Because populations have been evolving for such a long time and the small shifts in adaptive ...


2

Many years ago I worked in the field of bacterial chemotaxis, and your question brought this paper to mind: JL Spudich & DE Koshland Jr. (1976) Non-genetic individuality: chance in the single cell. Nature 262:467-471. The authors report an analysis of the chemotactic behaviour of individual bacterial cells from a single homogeneous culture. They ...


2

Nothing is at a genome-wide local equilibrium. Graham Bell wrote fairly extensively on this (IIRC). Some loci will be at what are likely global optimums (e.g. Cytochrome oxidase) will be at local but not global optimums (e.g. low-fitness malaria resistance vs. high fitness malaria resistance: for the extremely cool story check out this page) will not ...



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