Archive for the 'Evolution' Category

Dec 08 2022

Ancient Environmental DNA

Published by under Evolution

Our ability to detect, amplify, and sequence tiny amount of DNA has lead to a scientific revolution. We can now take a small sample of water from a lake, and by analyzing the environmental DNA in that water determine all of the things that live in the lake. This is an amazingly powerful tool. My favorite application of this technique was to demonstrate the absence of DNA in Loch Ness from any giant reptile or aquatic dinosaur. So-called eDNA is perhaps the most powerful evidence of a negative, the absence of a creature in an environment – you can’t hide your eDNA.

The ultimate limiting factor on eDNA is how long such DNA will survive. DNA has a half-life, it spontaneously degrades and sheds information, until it is no longer useful for sequencing. Previously scientists extracted DNA from ice cores in Greenland, and were able to sequence DNA up to 800,000 years old. The oldest DNA ever recovered was probably 1.1-1.2 million years old. Based on this  scientists estimated that the ultimate lifespan of usable DNA was about 1 million years. This put the final nail in the coffin of any dreams of a Jurassic park. Non-avian dinosaurs died out 65 million years ago, so none of their DNA should still be left on Earth (the closest we can get is related DNA in birds). But no T. rex DNA in amber.

According to a new assay in the most norther region of Greenland, however, we have to push back the estimate of how long DNA can survive to at least 2 million years. That is a significant increase (but still a long way from T. rex). The site is Kap København Formation located in Peary Land in north Greenland. This is now a barren frozen desert. There are also very few macrofossils here, mostly from a boreal forest and insects, with the only vertebrate being a hare’s tooth. Conditions there are apparently not conducive to fossilization. We do know that 2 million years ago Greenland was much warmer, about 10 degrees C warmer than present. So there is no reason it should not have been teeming with life.

The new analysis of eDNA finds that, in fact, it was. They found DNA from hares, but also other rodents, reindeer, geese, and mastodons. They also found DNA from poplars, birch trees, and thuja trees (a type of coniferous tree), as well as a rich assortment of bushes, herbs, and other flora. Basically this was a mixed forest with a rich ecosystem. In addition they found marine species including horseshoe crab and green algae, confirming the warmer climate.

This ancient eDNA gives us a much more complete picture of the ecosystem than was provided by macrofossils alone. But perhaps more importantly – it demonstrates that eDNA can survive for up to two million years, doubling the previous estimate. The researchers speculate that minerals in the soil bound to the DNA and stabilized it, slowing its degradation. DNA is negatively charged. This property is used to separate out chunks of DNA in a sample by size. You apply a magnetic field which attracts the DNA pieces, which move through a gel at a range proportional to their size. In this case the negatively charged DNA bound to positively charged minerals in the soil. I guess this is the DNA version of fossilization.

The question is – in such environments where DNA is stabilized by binding to minerals, how much is the degradation process slowed down, and therefore how long can DNA survive? DNA breaks down due to “microbial enzymatic activity, mechanical shearing and spontaneous chemical reactions such as hydrolysis and oxidation.” DNA breaks down faster with warmer temperature, so the fact that this DNA remained frozen for so long is crucial. But freezing alone was not enough, which is why scientists think that binding to minerals also played a role.

They measured the “thermal age” of the DNA – if the DNA were at a constant temperature of 10 degrees C how long would it have taken to degrade to its current state – at 2.7 thousand years, 741 times less than its actual age of 2 million years. Therefore it degraded 741 times slower then exposed DNA at 10 degrees C. The average temperature at the site is -17 degrees C. They further found that the DNA was bound mostly to clay minerals, and specifically smectite (and to a lesser degree, quartz).

Perhaps this is the limit of DNA survival – although we thought the previous record of 1.1-1.2 million years was the limit. It is possible there may be environmental conditions elsewhere in the world that could slow DNA degradation even further. Slow DNA degradation by a factor of 30 or so beyond the Kap København Formation and we are getting into the time of dinosaurs. This is probably unlikely. Constant freezing temperatures are required, in addition to geological stability and optimal soil conditions. But I don’t think we can say now that it is impossible, just highly unlikely. I did not see any estimate in the study about the ultimate upper limit of DNA lifespan, but I suspect we will see such analyses based on this latest information.

The best evidence, however, will come from simply looking in new locations for eDNA, especially those that likely have the optimal conditions for maximal DNA longevity. But for now, being able to reconstruct ecosystems from 2 million years ago is still pretty cool.

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Dec 02 2022

Evolution Is Not a Straight Line

Published by under Evolution

Yesterday I wrote about the fact that technological development is not a straight line, with superior technology replacing older technology. That sometimes happens, but so do many other patterns of change. Often competing technologies have a suite of relative strengths and weaknesses, and its hard to predict which one will prevail. Also, competing technologies may exist side-by-side for long periods of time. Sometimes, after experimenting with new technologies, people may revert to older and simpler methods because they are in the mood for a different set of tradeoffs.

Similarly, biological evolution is not a simple straight line with “more advanced” species replacing more primitive ones. Adaption to the local environment is a relative thing, and many biological features have a complex set of tradeoffs. With technological evolution (any cultural evolution) ideas can come from anywhere and spread in any pattern (although some are more likely than others). Biological evolution is more constrained. It can only work with the material it has at hand, and information is passed down mostly vertically, from parents to child. But there is also horizontal gene transfer in evolution, there is hybridization, and even back mutations. The overall pattern is a complex branching bush, spreading out in many directions. Any long term directionality in evolution is likely just an epiphenomenon.

Paleontologists try to reverse engineer the multitudes of complex branching bushes of evolutionary relationships using an incomplete fossil record and, more recently, genetic analysis. But this can be extremely difficult because it may not always be obvious how to draw the lines to connect the dots. The simplest or most obvious pattern may not be true. A recent discovery involving bird evolution highlights this fact. It is now pretty well established that birds evolved from theropod dinosaurs. The evidence is overwhelming and convincing. Creationists, who predicted that birds would forever remain an isolated group, have egg on their face.

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Nov 17 2022

New Method of Speciation

Published by under Evolution

Evolution requires that speciation events occur – events in which one species becomes two. All that is required for a speciation event to occur is that two populations of the same species stop interbreeding. There are two basic types of speciation: allopatric, where the populations are physically separated by geography, and sympatric, where they live in overlapping ranges but either can’t or don’t interbreed. For the purpose of speciation, interbreeding means producing fertile young.

Allopatric speciation is easy to understand. Most species have a large enough range that they are spread out into definable populations. They may even develop definable characteristics. Populations on the edge of a range, say a prairie species pushing into the desert, will likely develop some adaptions not possessed by the main population. At some point these adaptation may push the population into a range that does not overlap with the parent population. It also may happen that environmental change may doom the parent population to extinction, but the subpopulation’s adaptations allow them to survive as a new species. Sometimes geography simply changes, physically separating species (canyons open up, mountains rise, rivers change their course, land masses move).  Sometimes physical separation may be abrupt, such as when plants and animals find their way to islands and set up a new population, adapting to the new environment (like the Galapagos).

Sympatric speciation has been trickier to understand. Pollen will spread, animals will interbreed. It’s what they do. Research has focused on genetic events that make two populations unable to interbreed, because their offspring would be infertile. This will happen after species diverge sufficiently, but how will they diverge in the first place if they are exchanging genetic material? There must have been some genetic event, even in an individual, that instantly created genetic incompatibility. In plants this is commonly autopolyploid speciation, where the chromosome number is accidentally doubled during reproduction. The offspring cannot interbreed with the parent species because of chromosome number incompatibility. This is why some plants, like potatoes, can have very high numbers of chromosomes.

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Sep 09 2022

Neanderthal Brains

Published by under Evolution

Neanderthals (Homo neanderthalensis) is the closest evolutionary cousin to modern humans (Homo sapiens). In fact they are so close there has been some debate about whether or not they are truly a separate species from humans or if they are a subspecies (Homo sapiens neanderthalensis), but it seems the consensus has moved toward the former recently. They are not our ancestors – humans did not evolve from Neanderthals (anymore than we evolved from modern Chimps). Rather, we share a common ancestor with Neanderthals, about 700,000 years ago.

Neanderthals dominated in Europe from about 400,000 to 40,000 years ago, with their close relatives, the Denisovans, in Asia. They existed alongside modern humans for a long time, but then disappeared. There is probably no single simple reason why this occurred. There were likely many factors – some competition, some interbreeding, and independent reasons for Neanderthal decline that perhaps had nothing to do with humans. But as part of this question is the distinct but related one of – are modern humans somehow inherently superior to Neanderthals? Did we outcompete them because we were better?

This is a difficult question to answer from fossil evidence alone. Neanderthals were more robust than humans, and had brains which were as large (for body weight, meaning they were actually a bit bigger). Perhaps the replacement of Neanderthals by humans was a lateral move. Or perhaps Neanderthals were better adapted to the European ice age, and modern humans had the edge in warmer climates.

But there is a more direct question than ultimate evolutionary forces – were modern humans smarter than Neanderthals?  To answer this question we can use biological evidence or cultural evidence. I will get to the biological evidence second, discussing a recent study that may shed significant light on the question. But first let’s look at the cultural evidence.

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Jul 11 2022

T. rex Arms

Published by under Evolution

The arms of a T-rex are iconic for several reasons. First, they are comically small. T. rex itself is a superstar of the dinosaur world – perhaps the most famous extinct predator. Its jaws are massive and terrifying. Yet just behind those killer teeth there are these tiny arms that seem out of proportion, and scientists struggle to figure out what they are for and why they are so small. In fact, when the first T. rex skeleton was discovered by Barnum Brown in 1902 he did not think the arms were part of the same skeleton, they were just too small. The mystery of the T. rex’s arms remains an enduring scientific question.

There are, in fact, three groups of dinosaurs that are typified by very large heads and jaws and tiny forelimbs, the tyrannosaurids, the carcharodontosaurids, and the abelisaurids. Also, the ancestors of the tyrannosaurids had longer arms, and it appears that these three groups of theropod dinosaurs did not share a common short-armed predecessor. Therefore this feature of tiny arms seems to have evolved independently in the three groups. This deepens the mystery. T. rex is not some quirky evolutionary one-off. This was a trend in the large theropods, which strengthens the conclusion that there was a clear evolutionary pressure for this morphology.

The debate over T. rex’s tiny arms comes up every time a new relevant discovery is made, and a recent discovery of a carcharodontosaurid is no exception. The fossil is of a new species, named Meraxes gigas (yes, after one of the dragons in Game of Thrones). Most importantly, it has small forearms, confirming that this lineage also had this strange feature. So what, then is the reason for the tiny arms?

The short answer is that we don’t know, mostly because we cannot observe the behavior of these animals to see how they use them. Also, evolution can be tricky, and we cannot always determine a single use for a feature or cause for its form. Often there is a complex web of reinforcing factors. But here are the main contenders for possibly relevant factors. Evolutionary pressure can come in several forms. One is to avoid a detriment, another is because the feature has a specific use, and a third is sexual selection (a product of the choice of mates). In the case of the reduced forelimbs, focus has primarily been on the first two factors.

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Jun 30 2022

Is Music Universal?

From a neurological and evolutionary perspective, music is fascinating. There seems to be a deeply rooted biological appreciation for tonality, rhythm, and melody. Not only can people find certain sequences of sounds to be pleasurable, they can powerfully evoke emotions. Music can be happy, sad, peaceful, foreboding, energetic or comical. Why is this? Music is also deeply cultural, with different cultures independently developing forms of music that are very different from each other. All human cultures have music, so the question is – to what extent are the details of musical appreciation universal vs culturally specific?

In Western music, for example, there are minor and major scales, chords, and keys. This refers to the combinations of notes or intervals between them. Music in a minor key tends to evoke emotions of sadness or foreboding, while those in a major key tend to evoke happiness or brightness. Would anyone from any culture interpret major and minor key music the same way? Research suggests that major and minor emotional effects are universal, but a recent study casts a little doubt on this conclusion.

The researchers looked at different subpopulations of people in Papua New Guinea, and both musicians and non-musicians in Australia. They chose Papua New Guinea because the people there share a common musical tradition, but vary in their exposure to Western music and culture. The experiment was simple – subjects were exposed to major and minor music and were asked to indicate if it made them feel happy or sad (the so-called emotional “valence”). Every group had the same emotional valence in response to major and  minor music – that is, except one. The one group that had essentially no exposure to Western culture and music did not have the same emotional reaction to music.

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May 31 2022

Were Dinosaurs Warm or Cold-Blooded?

Published by under Evolution

If you haven’t seen the new series, Prehistoric Planet, hosted by David Attenborough, you should see it. The visuals are stunning, the science is updated, and it provides a compelling look into the world of dinosaurs and other animals contemporary to the dinosaurs. While watching an episode last night, depicting a velociraptor leaping around energetically, my wife asked, “Were dinosaurs cold-blooded?” The classic concept of dinosaurs is of large lumbering and slow animals, cold-blooded (ectothermic) like other reptiles. However, scientists have long suspected that some if not all dinosaurs may have been warm-blooded (endothermic) – hence the updated vision of dinosaurs as energetic animals. (The picture is of a baby T-Rex.)

Birds, which are dinosaurs, are very endothermic, even more so than mammals. So the real question is not if dinosaurs were endothermic, but when in their evolution did they become so. One reasonable hypothesis is that the bird clade evolved endothermic metabolism in order to fuel their very high energy lifestyle of flying, so it may be a later development within the bird subgroup. In any case, I gave a short version of that answer, continued to watch the show and vowed to update my knowledge on where the question of dinosaur metabolism lies. By coincidence, a recent study sheds considerable light on this question, possibly settling it, in fact.

Ectothermic vs endothermic metabolism is mostly about how efficiently oxygen is metabolized with fuel in the body to produce energy, which also produces heat as a byproduct. Ectothermic creatures, like modern reptiles, burn oxygen slowly, so that can eat less, breath less, but also are less active. Further, their metabolism does not produce that much heat, so that cannot regulate their own body temperature. They have to use the environment to do so, like basking in the sun. We have a skink as a pet, and you have to provide a warm and cool side to their environment, so that they can use external temperature to regulate their internal temperature.

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Mar 21 2022

Origins of Life From RNA

Published by under Evolution

It is common to observe that one of the greatest unsolved questions of science is how life began. This is a distinct question from how the diversity of the species of living things emerged. It is well established that once life had established a self-replicating system capable of generating some variation, that evolutionary forces would kick in and could, and in fact did, create all life on Earth. But we are a long way from reverse-engineering in any detail how those first organic molecules transitioned from chemistry to life.

This is not a scientific question that will be meaningfully resolved with a single experiment or discovery. Answers will slowly yield over time, as they already are, and it will take decades and perhaps centuries for something approaching a complete picture to emerge. But this progress will be built one study at a time, and Japanese scientists have recently contributing a significant piece to the puzzle.

Researchers at the University of Tokyo published a study in Nature Communications in which they establish that an RNA system can spontaneously evolve complexity. RNA molecules are one of the primary candidates for the first prebiotic molecules that lead to life. RNA is a single-stranded version of DNA, a self-replicating molecule built from four bases forming two pairs. The idea is that life started with the formation of a “replicator” – a molecule that could make copies of itself. RNA is a leading candidate for being the first replicator, but DNA and proteins are also candidates. So far we have not yet been able to connect an “RNA world” with a later world comprised of DNA and proteins. It is this gap that the new research helps fill in.

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Mar 15 2022

Why Is Life Symmetrical

Published by under Evolution

There is an inordinance of symmetry in living structures. Perhaps this is why humans have an aesthetic predilection for symmetry – but why does life have a probabilistic predilection for symmetry? Of all the possible forms that exist, symmetrical ones are a minority, and yet evolution seems to prefer them. We might hypothesize that there is a functional advantage to symmetry, but this is not obvious, at least not as a general principle. Specific forms likely function better when symmetrical. For example, forces need to balance, when walking or flying, and symmetry achieves that. Imagine a bird with one wing much bigger than the other, or with the wings placed at different positions along the body.

There appears, however, to be symmetry in excess of function, and this symmetry exists as all levels of biology, down to the molecular level. There are exceptions, of course, but symmetry is the rule. Further, some symmetry is baked into evolutionary designs long before any adaptive use. Therefore we need another, non-adaptive, hypothesis to fully explain symmetry. I have long felt that there is probably a mathematical reason, although could not state it in rigorous terms.  The DNA genetic code for a living organism is not a detailed blueprint. Rather it is a set of instructions to be followed. Think of it like a honeycomb beehive. There is no blueprint for the beehive, and no bee knows what it is supposed to look like. The bees follow simple rules over and over again, and the complex honeycomb pattern emerges. That is where the answer must lie.

Researchers have already put a lot of flesh on this skeleton of an idea, and a recent paper adds some further mathematical rigor. The key does lie in the use of simple algorithms to produce the complexity of life. Imagine having to describe to someone else how to create a pattern, such as with tiling a floor. You are not going to tell them where each tile exactly goes. Rather you will explain a technique or pattern that then gets repeated over and over until the space is filled. That, of course, only works if there is a simple pattern. If the ties are laid out in a mosaic creating a complex landscape, then yeah, you may need to describe where each tile goes.

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Feb 03 2022

Chromosomal Elements Conserved for 600 Million Years

Published by under Evolution

In evolutionary parlance, “conserved” means that some feature has remained relatively unchanged through some period or within a specific clade. Generally features will change over evolutionary time, either through direct selective pressures or genetic drift through random mutations. Therefore, in order for a biological feature to be conserved there must be selective pressure that keeps it from changing. The longer and more tightly that feature is conserved, the more fundamental it must be to biological function. Histones, for example, are proteins that help manage the long strings of DNA in cells – an extremely basic function for all life. Histones are also one of the most conserved proteins in all of biology.

It is therefore highly interesting that researchers recently found that chromosomal elements are highly conserved in virtually all animal groups over 600 million years – which is basically as long as animals have existed. Chromosomes are the organizing units of DNA. Humans, for example, have 23 pairs of chromosomes. Each chromosome contains a number of genes, and humans have about 20,000 functional genes.

Biologists have long known that sequences of genes tend to sort together – they always occur next to each other on the same chromosome, even across species. However, different clades have different numbers of chromosomes and different gene clusters on different chromosomes. Genes, it seems, get shuffled around during evolutionary history. Scientists and the University of Vienna and the University of California were working together to see if they could make more sense out of this chaos, and that’s what they did.

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