Tag Archives: evolution

Ancient Ants

An ant so unlike all other living ants that it was given an extraterrestrial name has been discovered in the Amazon rain forest, biologists announced today. The tiny new species is the only known surviving member of an ant lineage that separated from the main family more than a hundred million years ago, DNA analysis revealed.

The pale, eyeless ant appears to be adapted to living underground, possibly surfacing at night to forage. Its long mandibles suggest that the 0.08-inch-long (2-millimeter-long) animal is a predator, most likely of soft-bodied creatures such as termite larvae.

Christian Rabeling, a graduate student at the University of Texas in Austin, found a single specimen of the new species, thought to be a worker ant, in tropical soils near Manaus, Brazil. Rabeling’s team named the new creature Martialis heureka—”Martialis” means “of Mars
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The new species’ genes suggest that it broke away from the main ant family before the origin of all other living ant groups, which include 20 subfamilies that together contain more than 12,000 species.

8 Percent of the Human Genome is Old Virus Genes

In Our Genes, Old Fossils Take On New Roles

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

The thousands of human endogenous retroviruses, or HERVs, sketch a history of rough times during the 550 million years of vertebrate evolution. The best-preserved one, HERV-K113, probably arrived less than 200,000 years ago, long after human beings and chimpanzees diverged from a common ancestor.

But these retroviruses are more than just curiosities. They are some of the most important enemies we ever had. They helped mold the immune system that is one of the evolutionary marvels of life on Earth.

I must say there is tons of amazing stuff I learn about but I still find retroviruses amazing.

Superbugs – Deadly Bacteria Take Hold

Superbugs by Jerome Groopman, New Yorker:

“My basic premise,” Wetherbee said, “is that you take a capable microÃ¶rganism like Klebsiella and you put it through the gruelling test of being exposed to a broad spectrum of antibiotics and it will eventually defeat your efforts, as this one did.” Although Tisch Hospital has not had another outbreak, the bacteria appeared soon after at several hospitals in Brooklyn and one in Queens. When I spoke to infectious-disease experts this spring, I was told that the resistant Klebsiella had also appeared at Mt. Sinai Medical Center, in Manhattan, and in hospitals in New Jersey, Pennsylvania, Cleveland, and St. Louis.
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Unlike resistant forms of Klebsiella and other gram-negative bacteria, however, MRSA can be treated. “There are about a dozen new antibiotics coming on the market in the next couple of years,” Moellering noted. “But there are no good drugs coming along for these gram-negatives.” Klebsiella and similarly classified bacteria, including Acinetobacter, Enterobacter, and Pseudomonas, have an extra cellular envelope that MRSA lacks, and that hampers the entry of large molecules like antibiotic drugs. “The Klebsiella that caused particular trouble in New York are spreading out,” Moellering told me. “They have very high mortality rates. They are sort of the doomsday-scenario bugs.”

Great article. Related: Bacteria Survive On All Antibiotic Diet – Bacteria Can Transfer Genes to Other Bacteria – New Yorker on CERN’s Large Hadron Collider – posts on health related topics

How Humans Got So Smart

Cooking and Cognition: How Humans Got So Smart

For a long time, we were pretty dumb. Humans did little but make “the same very boring stone tools for almost 2 million years,” he said. Then, only about 150,000 years ago, a different type of spurt happened — our big brains suddenly got smart. We started innovating. We tried different materials, such as bone, and invented many new tools, including needles for beadwork. Responding to, presumably, our first abstract thoughts, we started creating art and maybe even religion.

To understand what caused the cognitive spurt, Khaitovich and colleagues examined chemical brain processes known to have changed in the past 200,000 years. Comparing apes and humans, they found the most robust differences were for processes involved in energy metabolism.

The finding suggests that increased access to calories spurred our cognitive advances, said Khaitovich, carefully adding that definitive claims of causation are premature.

Nice example of scientific discovery in action. The direct link from cooking to brain development is far from proven but it is interesting. I also like “the same very boring stone tools for almost 2 million years” – maybe that is because I am too cynical (but while evolution is amazing – sometimes it is amazing how slow progress is).

World’s Smallest Snake Found in Barbados

photo of Leptotyphlops carlae

The world’s smallest species of snake, Leptotyphlops carlae, with adults averaging just under 4 inches in length, has been identified on the Caribbean island of Barbados. The species — which is as thin as a spaghetti noodle and small enough to rest comfortably on a U.S. quarter — was discovered by Blair Hedges, an evolutionary biologist at Penn State.

Hedges determined that the Barbados species is new to science on the basis of its genetic differences from other snake species and its unique color pattern and scales. He also determined that some old museum specimens that had been misidentified by other scientists actually belong to this new species.

Scientists use adults to compare sizes among animals because the sizes of adults do not vary as much as the sizes of juveniles and because juveniles can be harder to find. In addition, scientists seek to measure both males and females of a species to determine its average size. Using these methods, Hedges determined that this species, is the smallest of the more than 3,100 known snake species.

According to Hedges, the smallest and largest species of animals tend to be found on islands, where species can evolve over time to fill ecological niches in habitats that are unoccupied by other organisms. Those vacant niches exist because some types of organisms, by chance, never make it to the islands. For example, if a species of centipede is missing from an island, a snake might evolve into a very small species to “fill” the missing centipede’s ecological niche.

In contrast to larger species — some of which can lay up to 100 eggs in a single clutch — the smallest snakes, and the smallest of other types of animals, usually lay only one egg or give birth to one offspring. Furthermore, the smallest animals have young that are proportionately enormous relative to the adults. For example, the hatchlings of the smallest snakes are one-half the length of an adult, whereas the hatchlings of the largest snakes are only one-tenth the length of an adult. The Barbados snake is no exception to this pattern. It produces a single slender egg that occupies a significant portion of the mother’s body.

Speciation of Dendroica Warblers

Speciation for Dendroica Warblers

They developed a mathematical model that attributed patterns of speciation to the way that closely related species divide up their environment. According to this model, when there are few relatives around to compete for resources, such as when an environment is first colonized, species differentiate rapidly.
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This model is robust: even when the authors assumed that their phylogenetic tree contains only 25 percent of all Dendroica species, they found that their Î³ test was still valid, indicating that this genus experienced an explosive bout of adaptive radiation before settling down to a “more normal” rate of speciation.

This mathematical model provides an incisive tool to gain a clearer understanding of the pattern and rate of speciation for groups of closely related species, even in the absence of a fossil record, simply by analyzing their DNA.

Lancelet Genome Provides Answers on Evolution

Lancelet genome shows how genes quadrupled during vertebrate evolution by Robert Sanders

“If you compare the 23 chromosomes of humans with the 19 chromosomes of amphioxus, you find that both genomes can be expressed in terms of 17 ancestral pieces. So, we can say with some confidence that 550 million years ago, the common ancestor of amphioxus and humans had 17 chromosomal elements.”
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Each of those 17 ancestral segments was duplicated twice in the evolution of vertebrates, after which most of the routine “housekeeping” genes lost the extra copies. Those left, totaling a couple thousand genes, found new functions that, Putnam said, make us different from all other creatures.

“These few thousand genes have been retooled to make humans more elaborate than their simpler ancestors. They are involved in setting up the body plan of an animal and differentiating different parts of the animal,” he said. “The hypothesis, pretty strongly supported by this data, is that the multiplication of this particular kind of gene and differentiation into different functions was important in the formation of vertebrates as we know them.”

“The most exciting thing that the amphioxus genome does is provide excellent evidence for the idea that Ono proposed in 1970, that the human genome had undergone two rounds of whole-genome duplication with subsequent losses,”

A great example of the scientific method in action. It often isn’t a matter of developing a theory one day, testing it the next and learning the outcome the next. The process can take decades for complex matters.

How Humans Evolved Allergies

Ancient antibody molecule offers clues to how humans evolved allergies

The chicken molecule, an antibody called IgY, looks remarkably similar to the human antibody IgE. IgE is known to be involved in allergic reactions and humans also have a counterpart antibody called IgG that helps to destroy invading viruses and bacteria. Scientists know that both IgE and IgG were present in mammals around 160 million years ago because the corresponding genes are found in the recently published platypus genome. However, in chickens there is no equivalent to IgG and so IgY performs both functions.

Lead researcher, Dr. Rosy Calvert said: “Although these antibodies all started from a common ancestor, for some reason humans have ended up with two rather specialised antibodies, whereas chickens only have one that has a much more general function.
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Professor Brian Sutton, head of the laboratory where the work was done said: “It might be that there was a nasty bug or parasite around at the time that meant that humans needed a really dramatic immune response and so there was pressure to evolve a tight binding antibody like IgE. The problem is that now we’ve ended up with an antibody that can tend to be a little over enthusiastic and causes us problems with apparently innocuous substances like pollen and peanuts, which can cause life-threatening allergic conditions.”

Bacteria Evolutionary Shift Seen in the Lab

Bacteria make major evolutionary shift in the lab

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait. And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.
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sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species.
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The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

Still Just a Lizard

Still just a lizard by PZ Myers

in 1971, scientists started an experiment. They took 5 male lizards and 5 female lizards of the species Podarcis sicula from a tiny Adriatic island called Pod Kopiste, 0.09km2, and they placed them on an even tinier island, Pod Mrcaru, 0.03km2, which was also inhabited by another lizard species, Podarcis melisellensis. Then a war broke out, the Croatian War of Independence, which went on and on and meant the little islands were completely neglected for 36 years, and nature took its course. When scientists finally returned to the island and looked around, they discovered that something very interesting had happened.

The original population of P. sicula was still present on Pod Kopiste, so we have a nice control population. These lizards are small, fast, insect-eaters in which the males defend territories. Sadly, P. melisellensis on Pod Mrcaru had been extirpated. So we had a few innocent casualties of the experiment.

The transplanted P. sicula thrived and swarmed over the island of Pod Mrcaru, but they were different, and they had evolved in multiple ways.

The original P. sicula were insectivores who occasionally munched on a leaf; approximately 4-7% of their diet was vegetation. The P. sicula of Pod Mrcaru, though, had adopted a more vegetarian diet: examining their gut contents revealed that 34% of their diet was plants in the spring, climbing to 61% in the summer…and much of this diet was hard-to-digest stuff, high in cellulose. This is a fairly radical shift.

There were concomitant changes. The lizards’ skulls were wider, deeper, and longer, and they had stronger bites — a necessity for chomping off bits of tough plants, instead of soft mosquitos. Instead of chasing bugs, they’re browsing stationary plants, and their legs are shorter and they are slower. Population densities are higher. The Pod Mrcaru lizards no longer seem to defend territories, so there have been behavioral changes.

Still just a lizard, I know.

Now here’s something really cool, though: these lizards have evolved cecal valves. What those are are muscular ridges in the gut that allow the animal to close off sections of the tube to slow the progress of food through them, and to act as fermentation chambers where plant material can be broken down by commensal organisms like bacteria and nematodes — and the guts of Pod Mrcaru P. sicula are swarming with nematodes not found in the guts of their Pod Kopiste cousins.