Inbreeding and fitness in mysid shrimps

There is an interesting new paper on a subject that often drives much discussion in this blog at least: how bad is inbreeding. The answer of course depends on several issues such as the intensity of inbreeding (not a mere true/false dichotomy) and the environmental pressure.

This paper deals with these matters in an experimental set with Americamysis bahia, a species of mysid shrimps.

Jeffrey E. Markert et al.,Population genetic diversity and fitness in multiple environments. BMC Evolutionary Biology, 2010. Open access.

The authors created a number of extremely inbred populations by

1. Taking a single pregnant female (presumably impregnated by a single male, as is typical in this species) from the main population (AMX) and removing it when the brood was released

2. Taking then one impregnated female from one of the resulting populations and another from a different one and placing them in the same tank until the brood was released.

3. Taking then one single impregnated female from the population resulting from step 2.

Overall it means that the hyper-inbred brood at the start of the experiment, described as 1X, had went through a narrow 2-4-2 bottleneck, being the equivalent to having 2.4 founders.

Populations of the type 2X, 6X and 8X were generated by mixing the respective number of 1X inbred populations, so they represent lesser degrees of inbreeding each.

By the end of the experiment, after 40 weeks, these were some of the results (more tables, graphs and explanations in the paper):



Figure 1 - Population fitness, estimated with Median Population Size (A), Last Census size (B), and Reproductive Index (C) [not shown here].
Paired box plots define the median and middle two quantiles in stressful (left) and permissive environments (right). Lower case letters unite groups that are not statistically distinguishable using post-hoc tests (Tukey’s HSD) at α = 0.05.

We can see that extremely inbred populations performed badly, specially in stressful environments (low salinity) but that not so extremely inbred ones performed reasonably well, specially in permissive (normal) environments.

While the results should not be strictly extrapolable to other species, we can reasonably conclude that a very low number of effective population founders (5 or so) seriously hampers survivability, specially in challenging environments, where essentially means a death sentence. However a not so tiny number of founders (25-30) can do quite well, in particular if the environment is favorable.

Big brains not always better

At least in birds.

That's what Catalan researchers (in association with British and Canadian ones) have found among passeriformes: that migratory species have systematically smaller brains than resident ones. This seems to be caused because big brains with high exploratory behavior (pretty similar to our concept of intelligence) could be even dangerous for species that change space so often.

In the words of lead researcher, Daniel Sol:

For birds that travel a lot, exploring their surroundings produces more costs than benefits since the information which is useful in one place is not necessarily so in another. It also exposes them to more dangers. For these reasons we believe that for these species, their innate behaviour can be more useful than learned behaviour.

I find this association of brain size with what I'd call curiosity, intelligence, for what else is the ability to study your surroundings to exploit them optimally and maybe even creatively manipulate them, as do some birds such as crows.

More information at:

• D. Sol et al, Evolutionary Divergence in Brain Size between Migratory and Resident Birds. PLoS ONE 2010. Open access.
• Science Daily.

Polyamory prevents extinction

... in fruit flies at least.

Tom A.R. Price et al, Polyandry Prevents Extinction. Current Biology, 2010.

There's also an article at Science Daily.

There seems to be a sex-ratio distortion (SR) X chromosome among some males that kills all the Y chromosome sperm before it can fertilize the egg, hence tending to produce an all-female offspring. By mating with various males, females prevent that this SR chromosome can become dominant up to the point of becoming a female-only population bound to extinction.

From the paper:

SR is a naturally occurring X chromosome meiotic driver that kills the Y chromosome-bearing sperm of male carriers [9,17]. SR therefore results in all-female broods and is inherited by all of the offspring of females that mate with male carriers [18,19]. This transmission advantage allows SR to spread through populations. However, the loss of half of the sperm produced by SR carriers makes them poor sperm competitors, with SR males...

Fruit fly populations in which females were forced by researchers (who acted as some sort of religious police, like in Saudi Arabia) to mate only with one male each, ended up after just 15 generations too crowded with this SR chromosome and five out of twelve (almost 50%) went extinct. Instead the control populations where free mating was allowed, remained healthy and kept the SR chromosome under control.

This seems to have implications beyond Drosophila pseudoobscura, the species used in this research, because both the "selfish" SR chromosome and the existence of promiscuity seem to be widespread through the animal kingdom.

It is quite curious how selfish genes, or in this case full chromosomes, do seem to exist but nevertheless they are not advantageous to their carriers. It is also curious how a mere drive in favor of diversity, such as promiscuity, helps to keep such genetic nuisances under control.

Inefficient selection behind complexity

In the pure Darwinian scenario of draconian selection that can exist for instance among microorganisms, which are numerous enough for drift and randomness not to be a factor, and among whom competence is maximized like in the ideal free market of liberal economists, all accidental extra copies of genes (paralogs) are eventually erased because they are inefficient.

But among a much smaller population, like humans, Darwinian evolution works inefficiently and these troublesome extra copies of genes do in fact persist. In principle paralogs are problematic and can cause degenerative diseases like Alzheimer because they produce less efficient proteins. But what Ariel Fernández and Jianping Chen of the University of Texas have found is that these paralogs also drive complexity, that it is the accumulation of these errors by drift what in fact generates complexity, that complexity can only arise when selective evolution becomes weak and drift (chaos) rules instead.

After all every order is just a subset of pure Chaos, right?

Source: Science Daily.
Original paper: Human capacitance to dosage imbalance: Coping with inefficient selection. Genome Research 2009 (paywall).
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Adaptative evolution does not alter neutral mutation rates

A new research paper appears to demonstrate that adaptative evolution happens along the lines of neutral stochastic evolution and is not accelerated.

Kryazhimskiy S, Tkacik G, Plotkin JB, The dynamics of adaptation on correlated fitness landscapes. PNAS 2009 (right now the PDF is freely available)

From the Press release:

A major conclusion of the work is that for some organisms, possibly including humans, continued evolution will not translate into ever-increasing fitness. Moreover, a population may accrue mutations at a constant rate –- a pattern long considered the hallmark of “neutral” or non-Darwinian evolution -– even when the mutations experience Darwinian selection.

(...)

According to the study, a population’s fitness and substitution trajectories —t he mutations acquired to achieve higher fitness — depend not on the full distribution of fitness effects of available mutations but rather on the expected fixation probability and the expected fitness increment of mutations. (...)

Researchers demonstrated that linear substitution trajectories that signify a constant rate of accruing mutations, long considered the hallmark of neutral evolution, can arise even when mutations are strongly beneficial.

If confirmed, this research should lay to rest the hypothesis that dismiss the informative value of genetic phylogenies based on presumpt adaptative selection: adaptative or not, mutations accumulate on similar rates, depending mostly on other factors, like population size (greater or weaker drift, possibly leading to fixation).
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God, the Universe and everything else

I was just watching one of those chapters of Richard Dawkins' series on evolution and religion. Naturally I share nearly every point of Dawkins' discourse, after all I was quite a typical atheist for some 15 or 20 years of my life, since I reached puberty till I neared my thirties.

In my opinion, Dawkins' discourse is one step behind and probably need some psychedelic experiences to get refined. Or at least some good re-reading of Spinoza's Ethics' first chapters.

Thanks largely to Spinoza, I have for a decade now overcome in my discourse and thought the monotheistic or theistic (I call that "alientheism" in fact) monopoly of God. God is not some peculiar Judaistic (or whatever) cultural and ideological interpretation of God but, philosophically speaking the ultimate cause of existence.

This ultimate cause has not yet been satisfactorily explained via science but much less via religion. Naturally, I do not pretend to understand It to the ultimate detail either but it's obvious from scientific knowledge (not just evolutionary biology but nearly everything else (tectonics, astronomy, archaeology...) that the traditional religious myths are totally wrong.

So the alientheist religions basically lie about God and therefore they are a form of idolatry: idolatry of words. Their golden calf is a book or series of books that just utter nonsense. Ok some of those myths may still keep some truth in regard to Hebrew history or, arguably, some good ethical advise. But otherwise they are just nonsense and those who defend them are blatant liars. And those who have faith are mere idolaters who worship words, not God.

The only valid "scripture" of God is in the facts of life and existence. Of course lies like those uttered in the Bible, the Talmud or the Quran are also facts of life (no more than, say, The Satanic Verses or Les Fleurs du Mal), what tells me that God also enjoys some deceit. Nothing that Spinoza would argue against, obviously, because for him God has infintite attributes, including deceit and manipulation. A perfect and absolute God cannot lack anything, as the Manicheistic preachers want us to believe.

So what's the truth about God? Just look around you in the facts of life, like the biological dance and the cosmological one as well. That is what we know about God.

For some God would be not really present but alien to all this reality, yet its conscious creator. But to these I can't but argue that the artist is always in the artwork, that the two cannot be detached. Who is Van Gogh? Some "crazy" redhair with a troubled life or his marvelous paitings that shatter every soul? Or both? At least we know something about Van Goghs real life. But what about Homer? Like with God, we can only judge him for his works.

So, lacking any evidence of the existence of an alien creator God, I argue that it is pointless and fundamentally not different from an ominpresent holistic God: the Pan Theos. Pantheism is, of course, not essentially different from atheism, just that we pantheists don't let the idolaters of words and doctrines to monopolize such a fundamental concept. Also we are less concerned about death than both atheists and alientheists because we are quite consicous that our individuality is mostly a short temporal illusion and what really matters, if anything, is the whole: the cosmic dance, God, of which we are just manifestations.

Actually I need this understanding in order to relax from the incredible dramatic self-destruction we are engaged in. After all, if we cannot stop it, if humankind and life-as-we-know-it is going to vanish in the next decades or so, I can be confident that the Universe as such will keep going. We can only cause so much destruction after all. It would be a terrible pity that we'd misuse such fantastic cognitive and creative capabilities as we have as species and the lusty thriving beauty of Earth and I hope we can still reverse the process. But if these hopes happen to be wrong, I know that the essence behind all that will still be there. It could be worse, I guess.

Enough for today. Enjoy.
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Complexity is simple: proteins auto-assemble just naturally

Researchers from the United States have discovered that bacterial proteins self-assemble stochastically (that is: randomly) and not directed by any centralized force of any sort. This random system is probably also found in eukaryotic cells like ours.

In spite of this randomness, patterns emerge and the system just works fine, as Alan Turing had predicted for a different context some 60 years ago.

According to co-researcher Jan Liphardt:

Random lateral protein diffusion and protein-protein interactions are probably sufficient to generate the observed complex, ordered patterns. This simple stochastic self-assembly mechanism, which can create and maintain periodic structures in biological membranes without direct cytoskeletal involvement or active transport, may prove to be widespread in both prokaryotic and eukaryotic cells.

Source: Science Daily

Research paper (open access): Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, et al. (2009) Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy. PLoS Biol 7(6): e1000137. doi:10.1371/journal.pbio.1000137

Author Summary:

Cells arrange their components—proteins, lipids, and nucleic acids—in organized and reproducible ways to optimize the activities of these components and, therefore, to improve cell efficiency and survival. Eukaryotic cells have a complex arrangement of subcellular structures such as membrane-bound organelles and cytoskeletal transport systems. However, subcellular organization is also important in prokaryotic cells, including rod-shaped bacteria such as E. coli, most of which lack such well-developed systems of organelles and motor proteins for transporting cellular cargoes. In fact, it has remained somewhat mysterious how bacteria are able to organize and spatially segregate their interiors. The E. coli chemotaxis network, a system important for the bacterial response to environmental cues, is one of the best-understood biological signal transduction pathways and serves as a useful model for studying bacterial spatial organization because its components display a nonrandom, periodic distribution in mature cells. Chemotaxis receptors aggregate and cluster into large sensory complexes that localize to the poles of bacteria. To understand how these clusters form and what controls their size and density, we use ultrahigh-resolution light microscopy, called photoactivated localization microscopy (PALM), to visualize individual chemoreceptors in single E. coli cells. From these high-resolution images, we determined that receptors are not actively distributed or attached to specific locations in cells. Instead, we show that random receptor diffusion and receptor–receptor interactions are sufficient to generate the observed complex, ordered pattern. This simple mechanism, termed stochastic self-assembly, may prove to be widespread in both prokaryotic and eukaryotic cells.
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Weed defeats Monsanto

Monsanto, the monopolistic monster that is behind most transgenic crops and related herbicides, notably Roundup, is facing an unexpected enemy: evolution.

After some time of preeminence of genetically modified crops in the USA, crops immune to Roundup, unlike any other plant (in principle), some weeds are taking advantage of the unnatural situation and adapting faster than the mega-corporation can research and react: Amaranthus palmeri, also known as pigweed, has developed immunity to Roundup and is rapidly expanding by the US crop fields, having already caused abandonment of more than 5,000 hectareas, as farmers just don't have any easy solution against it.

The massive use of Roundup in transgenic crop fields has simply exterminated all other plants and weeds, but those who have been able to adapt, in this case this species of amaranth, thrive without competition (as crops are never efficient competitors). The only option would be to supress the weeds manually but that's not any realistic option in the industrialized conditions of US agriculture.

It is suspected that amaranth may have obtained the resistence gene from the very genetically modified crops it is now killing, maybe by crossing or maybe by viral transmission. The massive use of Roundup has only created the perfect conditions in which this weed can now thrive without rivals.

Nature 1 - Capitalism 0 (or did anyone ever believed we could defeat Nature?)

Sources: Rebelión, Wikipedia.
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Experimental evolution in the test tube

Scientists from the Scripps Research Institute, Sarah B. Voytek and Gerald F. Joyce, have experimentally confirmed evolution at RNA level.

Both Joyce and Voytek developed self-replicating RNA molecules that reproduce autonomously and also, sometimes, mutate in the process. These RNA molecules feed on other molecules that they need for their replication process, the type of which may vary. Provided that there is enough food, the RNA replicates at fast rhythm and also mutates, creating new "species" of molecules.

The researchers also pitted two RNA strains in a pot with five different food resources, none of them of prime quality. The two strains eventually evolved as specialists in feeding from two of these available resources, becoming adapted to their particular lab environment. Not just that but their patterns of specialization also were different: one strain became very good at food processing but the other, even gobbling up much less food, managed to generate a much faster reproductive rate, becoming examples of different adaptative strategies through spontaneous evolution.

Source: Science Daily.

Original paper: Sarah B. Voytek and Gerald F. Joyce. Niche partitioning in the coevolution of 2 distinct RNA enzymes. Proceedings of the National Academy of Sciences, Online April 28, 2009.
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Survival of the weakest?

There is an intriguing article at Science Daily: researchers from Ludwig-Maximilians-Universitaet (Munich) have found, both in simulaions and real experiments, that the "weakest" species seems to be the survivor within cyclical competition, contradicting somewhat the usual interpretations of Darwinian evolution and emphasizing the random (or hidden) factors at play. Read more...
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Rapidly evolving speciation gene found.

From Science Daily.

New research on fruit fly's different species' genome has found some immunity related genes that have evolved quickly causing that hybridation among these two species often fails (the offspring die).

It seems that they evolve as response from viral threats as well as defense against the animals' own "malicious" genes (those that are not really of any use other than replicating themselves but that can condition the carrier species' evolution). In the long run this has caused that the two species, isolated from each other by some 3 million years, have not anymore compatible genomes.

After all, like with technology, this seems to be mostly a matter of compatibility and we all know that what works in Windows, seldom does in a Mac (and viceversa).
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Evolution only partly reversible

Interesting article at SD (and presumably interesting original paper too, available for Nature subscribers only, by H. Teotonio et al.)

The researchers reverted a population of lab-bred fruit flies to their natural state, state from which their ancestors were removed in 1975, and observed if and how "reverse evolution" happened through 50 generations. The results are that some traits and genes did reverse fast, while others did slowly and yet others did not de-evolve at all. Overall the flies got only like 50% of their genome back to their ancestral state only, while the phenotype instead in some cases fully reverted to the feral state.

The first conclusion is obvious: history cannot be fully reversed, not even in the field of genetics. Historical accidents may change the future indepently of enviromental conditions.

The second conclusion is the somewhat shocking fact that different genetics can encode the same phenotype.

This is most interesting also in regard to humans, I'd say, because people with different genetic backgrounds may happen to converge to a similar phenotype, which is not necesarily just the average of the genes involved. This phenomenon, if my memory doesn't fail, has been noticed in some areas of significative admixture, like Mexico and Sudan, where the resulting phenotype of admixed populations was not merely the simple "hybrid" type but a rather new local phenotype of its own (a new "race" so to say). In different contexts it is very possible that people of varied genetic backgrounds, say Askhenazis and Germans, may converge to similar phenotype without massive admixture (I don't mean here to say that Askhenazis and Germans/Poles are not mixed with each other, they obviously are, but that the resulting phenotype modification of so many milennia of co-residence may be much greater than the mere genetic input, whatever the exact enviromental reasons (climatic, social, whatever).
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Earliest "life form" created in lab, by "in vitro evolution".

This is really bad news for anti-evolutionists (creationists and the like): finally something similar to the earliest form of life has been created artifically: a self-replicating RNA molecule that needs nothing else to perpetuate itself, except molecular bricks (i.e. food).

But even "worse": as scientists failed miserably once and again when using "intelligent design" to do it, the succesful method actually was "in vitro" evolution: let Nature do it in a controlled enviroment.

Of course, the superstitious fanatics will not be persuaded so easily but for all those with an open mindset truth is out there.

It is also important for a true scientific debate: wether the earliest life forms were RNA or DNA based. It is an important piece of evidence in favor of the RNA world model.
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"Life bricks" found in interstellar cloud

From Science Daily.

Researchers from the Astrophysical Institute of the Canary Islands, led by Susana Iglesias, have detected naphtalene, a polycyclic aromatic hydrocarbon, in an interstellar cloud some 700 lightyears away from us. This finding suggests that these materials were probably also present at the formation of the Solar System and Earth, facilitating the formation of life.

P. boisei choose to ignore evolution.

A study by the University of Arkansas has found that our robust extinct relative Paranthropus boisei (also known as the nutcracker man) ate mostly fruit even it was very well adapted to much harder foods like roots and nuts. This introduces an interesting evolutionary paradox: they evolved to ate hard stuff but then they found they could also exploit resources they were not specialized for and choose them preferentially.

It seems that after all, our cousin was more intrinsecally adaptative than simply made-by-evolution. Just like us.

Source: Science Daily: New findings challenge conventional ideas on evolution of human diet and natural selection.

Evolution in large animals can also be very fast

Researchers from the Uiversity of Massachusets have found that certain lizards, when placed in a new enviroment, have evolved very quickly in adaptation to their new mostly vegetal food sources. In as little as 36 years, the little Podaris sicula lizard, has evolved all sorts of adaptations, unheard of in its original enviroment, to better behave as vegetarian (source: Science Daily)

The lizards are native of the Adriatic island of Pod Kopiste, where they feast basically on insects, but because of these ecological nonseneses of postmodernity, some eneded up in the nearby but different island of Pod Mrcaru, where they found aboundance of vegetarin food. In these 36 years, they have changed their bite and also their digestive tract, becoming quite specialized into vegetarianism, in a way unknown to this species. Vegetarianism also changed their habits, losing interest in defending their territories.

Test tube evolution

Science Daily: New Synthetic Enzimes Undergo "Evolution in a Test Tube".

The system was devised to improve computer designed enzymes and the result was astonishing: only 7 "generations" were needed to improve the efficiency of the artificially adaptative trait 200-fold!!!

The researches designed an enzyme that could remove a proton from carbon atoms and, in order to make it at least as good as natural occurring ones, evolution had to be activated artifically. Therefore random mutations were induced into the artificial enzyme and only those that produced the best result were allowed to "survive" and "reproduce". Only 7 rounds of this process multiplied the effectivity by 200.

I infer from this, that under high selective pressure, the relevant adaptations can become dominant and refined in very few generations.