Archive for the 'Evolution' Category

Oct 30 2020

Evolution of Dogs

Published by under Evolution

The evolution of dogs from wolves is a long and complex one. A recent study adds some further information to this tale – as long as 11,000 years ago there were already at least five different distinct breeds of dog. These different breeds partly tracked along with human populations, but not completely. But let’s back up a bit and see where this new information fits into the story.

Experts actually don’t agree on exactly when and where dogs first appeared, or even if it was one event or multiple independent origins. What is clear is that dogs are essentially domesticated wolves. Their likely origin was in Europe sometime between 19 and 32 thousand years ago. This makes dogs the first domesticated animal. I have often considered (being a life-long dog owner myself) how useful dogs would have been to ancient people. They are excellent guardians, sending up an alarm when anything strays too close to camp. My dog will let me know when racoons are poaching the bird feeder at 3am. They are territorial and will keep critters small and large out of the area. And in an emergency they will even fight for their masters. More developed and trained dogs can also do all sorts of jobs, from herding to hunting.

The extreme usefulness, not to mention companionship, of dogs to humans lead to the early hypothesis that humans domesticated wolves, probably by first raising wolf pups. Tamed wolves are more aggressive than dogs, but they can bond with humans and function in the human world. We know from the silver fox experiments that some mammal species can be significantly domesticated in just a few generations. So it would not take long for these tamed wolves to become more docile, loyal, and obedient. But experts now suspect this is not what actually happened.

The history of human and wolf interaction is mainly one of competition and eradications. Humans have always treated large predators as a threat. Wolves specifically have mostly been eradicated where humans flourish, often deliberately. This still does not preclude the exception of tamed wolves, but it did give rise to an alternate hypothesis – perhaps wolves domesticated humans rather than the other way around, meaning that it was the wolves who changed the nature of our relationship first. In this scenario wolf populations living near humans may have learned to poach at the edges of settlements, perhaps eating the bones or other refuse that humans discarded. The more cute and friendly wolves would have had more success at this strategy, while the more aggressive wolves would have been killed or driven off. This could have led to a subpopulation of friendly wolves mostly living off of human refuse. Selective pressures could have then quickly domesticated these proto-dog wolves, who were only later taken as companions by humans. Human selection would then have taken them the rest of the way to modern dogs.

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Sep 28 2020

Y Chromosomes of Humans, Neanderthals, and Denisovans

Published by under Evolution

Recent human ancestry remains a complex puzzle, although we are steadily filling in the pieces. For the first time scientists have looked at the Y chromosomes of modern humans, Neanderthals, and Denisovans, giving us yet one more piece of the puzzle. But first, here’s some background.

The common ancestor of humans (by which I mean modern humans), Neanderthals, and Denisovans lived between 500,000-800,000 years ago. This common ancestor species almost definitely lived in Africa, but we are not sure exactly which species it was. Homo heidelbergensis is a candidate, but it’s not clear if the timeline matches up well enough. In any case, this split probably occurred when the ancestors of Neanderthals and Denisovans migrated from Africa to Europe. They then split from each other, with the Neanderthals remaining in Europe and the Denisovans going to Asia. This split happened around 600,000 years ago, but could be more recent.

Why is there so much confusion about the exact time of the split? There are two main reasons. The first is that these splits were not single events. Populations of early humans became relatively separated from each other, enough so that genetic differences could start piling up. But they also continued to interbreed, sharing genes throughout their history. There is a specimen that is likely the child of a Neanderthal and a Denisovan from just 50,000 years ago. Humans and Neanderthals interbred right up until the end. All non-African humans living today have 2-3% Neanderthal DNA.

The other reason the divide is difficult to pin down is because there are numerous methods for estimating when it occurred, and they give slightly different answers. We can look at teeth, and other fossil bones, and genomic DNA, mitochondrial DNA, or specifically X and Y chromosomes. We can also look at their culture via their tools. We can see when certain tools start appearing in different locations. Culture, by the way, can also be shared among populations, so that picture may be confused as well.

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Mar 12 2020

Smallest Dinosaur Ever

Published by under Evolution

We like extremes, partly because they help define the borders of reality. It helps our mental model of the world when the know the biggest, smallest, hottest, lightest, or fastest of something. It’s also just fascinating to see how extreme some things can get. For this reason there has been a fascination with which dinosaur is the biggest – how big did these animals get. The record is currently held by Argentinasaurus, a long-necked sauropod, weighing between 77 and 110 tons. Meanwhile, the record for the smallest known dinosaur is microraptor, a bird-like dinosaur only 40 cm long. Well, that is until the latest discovery.

Scientists report the discovery of the head of a bird-like dinosaur trapped in amber. The species has been named Oculudentavis khaungraae and is about the size of a bee hummingbird, the smallest living bird. The specimen is trapped in amber from Myanmar, and is dated at 99 million years old. The amber preserved some soft tissue, including its tongue. The specimen is interesting on multiple levels.

First, it reflects the extreme of vertibrate miniaturization. It’s difficult to cram all the sensory organs into a tiny skull, and species that evolve to become so small have to find solutions. In this case the eye socket anatomy appears different than hummingbirds and other tiny birds. Rather than a rim of bone, the socket is more spoon-shaped. The anatomy also suggests a small opening for light, which further implies the species was diurnal.

The mouth sports a surprising number of teeth, making the creature look like a predator. At that size is likely fed on insects. So we have a bird-like dinosaur the size of a tiny hummingbird that hunted insects during the day. The anatomy, such as fusion of the skull, also suggests this was an adult, so not just a juvenile specimen to explain its small size.

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Mar 02 2020

A Claim for Dinosaur Proteins and DNA

Another paper has been published in the simmering controversy over whether or not proteins, and even DNA, can survive millions of years in well-preserved dinosaur (non-avian dinosaurs, that is) fossils. The paper looks at cartilage from a duck-billed dinosaur, a young Hypacrosaurus stebingeri. The authors claim:

“…microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains.”

Let me say right away that these claims are controversial, but what would they mean if true? If we could examine the structure of proteins and DNA from >65 million years ago, in well-preserved dinosaur fossils, then the world of molecular biology would extend back to that era. Molecular examination has had a significant impact on paleontology – but it has limits. So far the oldest DNA sequenced from a fossil is from a 700,000 year old horse frozen in ice. The oldest protein so far confirmed is from a rhino 1.7 million years old. This means that if the current claims are true, DNA can survive in fossils 100 times longer than the current record would indicate.

This is also not the only source of information from which to estimate the lifespan of DNA. Researchers have examined DNA from Moa specimens in New Zealand, over a span of about 8,000 years. This allowed them to estimate the half-life of DNA, the time over which about half the bonds would be broken. Their estimate – 521 years. This means that all the chemical bonds in a DNA molecule would be gone after 6.8 million years, but having any fragments along enough to sequence would be gone after about one million years. This aligns nicely with the evidence from actual fossils. So claiming DNA from >65 million years would be extraordinary, to say the least. This is why most scientists remain skeptical of these claims.

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Nov 07 2019

The Evolution of Bipedalism

Published by under Evolution

The evolution of human bipedalism is one of the great events in the history of life that we still need to flesh out. We tend to focus on big transitions because of their implications for the story of life – the evolution of flight, moving out onto land, and the development of intelligence. There is still much we don’t know about the exact path taken in the development of human bipedalism, because we lack good windows into that time and place of our past.

Scientists have now described a new hominid species, which I’ll get to below, but first some background. The first evidence we have of hominid bipedalism is in Sahelanthropus tchadensis, which lived between 6 and 7 million years ago. For context, the last common ancestor with chimpanzees was between 8 and 6 million years ago, so this is pretty close to the transition. We only have skull specimens, but we can tell the species was bipedal because the foramen magnum, the opening for the spinal cord at the base of the skull, opens below like in humans, rather than toward the back like in all other apes.

About 6 million years ago we have Orrorin tugenensis, from which we have a thigh bone which suggests bipedalism. But the earliest human ancestor with extensive evidence of bipedalism is Ardipithecus ramidus, dating to 4.4 million years ago. We have several specimens, the best of which, “Ardi”, contains foot and limb bones. Ardi has clear adaptations to bipedalism, but also for tree climbing.

Keep in mind, we did not evolve from chimpanzees – chimps and humans share a common ancestor. Chimps have diverged from that common ancestor as much as humans have. We don’t have any specimens that are candidates for that common ancestor, so we don’t really know what it was like. Chimps can walk on two legs part of the time, but they are not adapted to it. Chimps (and gorillas) knuckle walk – the walk on four limbs with their forelimbs resting on their knuckles.

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Oct 31 2019

Tracing Human Origins

Published by under Evolution

When and where did fully modern humans first emerge? That is an interesting question that paleontologists have been chasing for decades. Now a new genetic study claims to have pinpointed that origin to northern Botswana 200,000 years ago. The claim is already getting some pushback from other experts, but the new data does add to our understanding of human origins.

The study looks at mitochrondrial DNA, a technique that has been used before. This is DNA outside the nucleus, in each mitochondria of the cell (the power factories). They are almost exclusively passed down through the maternal line, because the egg provides all the mitochondria to the embryo, while sperm generally contribute none (although one may sneak through from time to time). You can therefore use mDNA to trace maternal lines.

When this type of analysis was first done researchers found that all humans have a common female ancestor going back to about 200,000 years in Africa. This result was widely misinterpreted in the press, not helped by the fact that this alleged ancestor was deemed the “mitochondrial Eve.” If you go back far enough, everyone is related to everyone. Therefore we all have many common ancestors. What the analysis shows really is a couple of things. First, that only one mitochondrial line from this time survived to the modern day. That doesn’t mean we only have one common female ancestor. But every time a woman has only sons, her mitochondrial line dies out. This finding does suggest, however, that the human population when through a relative bottleneck at this time. Our ancestors were not spread around Africa or the world, because then each region would have its own mitochondrial lineage.

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Oct 03 2019

Developmental Biology Reveals Evolutionary History

Published by under Evolution

The notion that ontogeny (development from a fertilized egg to adult) recapitulates phylogeny (evolutionary history) is an outdated notion that has been scientifically rejected. That does not mean, however, that evolutionary history is not reflected in developmental pathways. Creationists often conflate the two in order to create a strawman of the current scientific position.

The difference is interesting and makes sense. What does not happen (and why should it) is stages of embryonic development passing through adult forms of ancestral species. What does happen is stages of embryonic development passing through embyronic forms of ancestral species. This about evolution and development this way – evolution often occurs through altering developmental pathways. But this alteration can occur anywhere along the developmental timeline.

What evolution cannot do is rewrite the genetic code from the ground up. It can only alter the existing code. As evolutionary history gets longer and longer, therefore, the developmental pathway of living creatures gets more and more convoluted and tortuous. At no point can evolution “clean up” the code. So contemporary animals do not develop in a straight line to their mature form. They take a twisting and winding course that reflects their past history. But of course this path does not pass through the adult form of their ancestors, because development doesn’t follow those old pathways all the way to their conclusion. They are diverted along the way.

As the technology to perform high definition 3D scans of embryonic anatomy improve, we are finding more and more examples of this phenomenon. A recent paper gives a dramatic example –  Development of human limb muscles based on whole-mount immunostaining and the links between ontogeny and evolution.

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Jan 25 2019

Rethinking Neanderthals

Published by under Evolution

Old ideas die hard. The first extinct hominids found were Neanderthals, and our cultural conception of them was formed in the 19th century, a time rife with parochial attitudes toward “primitive” peoples. The first Neanderthal skeleton also happened to suffer from crippling arthritis, giving it a hunched over posture.

The cultural notion that our closest relatives were brutish and primitive became deeply embedded. Certainly, this idea has been moderated significantly in the last century, but not completely expunged. Meanwhile, paleontologists have discovered more and more evidence that Neanderthals were just a different breed of human. They were fully bipedal, so their gait was modern. They were more robust than Homo sapiens, because they were adapted to Europe’s Ice Age. But robustness should not be confused with brutishness.

Prof Clive Finlayson, director of the Gibraltar Museum, has a recent commentary on BBC’s website in which he punctures this outdated view of our closest cousins. He points out that this biased view of Neanderthals affects not just public perception, but scientific thinking. There have been many assumptions of Homo sapiens superiority, and that Neanderthals were essentially replaced by us through direct competition.

So this also reflects a common misconception about evolution itself, that “survival of the fittest” is always what determines which species endure, and is all about being more advanced and superior. Finlayson points out that we cannot neglect the factor of luck, which may, in fact, often be dominant. Homo sapiens may not have been objectively superior to Neanderthals in any specific way, but were simply better adapted to a changing environment. Neanderthal robustness, an advantage during glacial periods, may have been a hindrance during a warming climate. Sapiens may simply have inherited a better trade-off of features for that period in time.

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Nov 20 2018

Possible New Branch of Eukaryotes Defined

Scientists report in Nature the indentification of two new species of Hemimastigophora, a predatory protist. What makes the paper newsworthy is that the authors are arguing that their genetic analysis suggests Hemimastigophora, currently categorized as a phylum, should instead be its own suprakingdom.

To make sense of this let’s review the basic structure of taxonomy, the system we use to categorize all life. All known life is divided first into three domains, the bacteria, archaea, and eukaryotes. Bacteria and archaea do not have a nucleus, while eukaryotes are larger and have a nucleus which contains most of their DNA.

Eukaryotes are divided into kingdoms, including plants, animals, fungus, protozoa, and chromista (algae with a certain kind of chlorophyll). Kingdoms are then divided into phyla, which are essentially major body plans within that group.

This is a simplified overview, because there is a lot of complexity here, with suprakingdoms, subkingdoms, and further breakdowns. Further, there is a lack of consensus on how to exactly divide up these major groups. Even in the cited paper, the authors say there are 5-8 “suprakingdom level groups” within the domain eukaryotes. The number of kingdoms depends on which scheme you use, and how you interpret the existing evidence.

The reason for uncertainty is that we have not yet done a full genetic analysis on every known group. Further, when we discover new species that lie outside of the existing scheme, we have to rethink how different groups are actually related.

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Oct 26 2018

Laser Scanning Archaeopteryx

Published by under Evolution

My favorite fossil is the Berlin specimen of Archaeopteryx lithographica, for several reasons. First, it is straight-up a beautiful fossil, well-preserved, and just a natural work of art. But this is no object of human creativity – it is also a wonderful transitional fossil, catching evolution in the act of transforming theropod dinosaurs into birds. There is a cast of the Berlin specimen at the Peabody museum in New Haven, and it is capable of capturing my attention even in the middle of the hall of dinosaurs.

Recently I was able to visit the Natural History Museum (NHM) in London – where they have the original fossils of the first Archaeopteryx specimen found in 1861 (before the Berlin specimen), making it the type specimen. It too is beautiful, showing both the plate and the counterplate – the limestone that contains the fossil was cracked open, revealing impressions and fossils on both sides.

You can clearly see the feather impressions surrounding what at first looks like a small theropod dinosaur. On closer inspection, however, there are bird-like features as well, but retaining things like teeth and a long bony tail not seen in birds. Again – a dramatic transitional fossil, clearly connecting birds to what are now called non-avian dinosaurs (because birds are dinosaurs).

Creationists have long tried to argue that Archaeopteryx is not transitional, just a weird bird, but the evidence is undeniable. It has as close to halfway features between walking theropods and modern birds as you can get. But to be clear, Archaeopteryx is not on the direct line to birds. It is a side branch from a period in time when small feathered dinosaurs were undergoing adaptive radiation, only one branch of which would lead to modern birds. This is always going to be the case, however, and does not diminish the transitional significance of this species. Also, in recent decades a number of feathered dinosaurs have been discovered, fleshing out much of the evolutionary pathways between theropods and birds.

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