Watching New Species Emerge

Science Sushi has a great article on new species evolving before our eyes. Evolution deniers may claim that we never see new species in the process of evolving, but that’s simply untrue, and further confirms that the political debate over evolution has nothing to do with science or facts.

Critics of evolution often fall back on the maxim that no one has ever seen one species split into two. While that’s clearly a straw man, because most speciation takes far longer than our lifespan to occur, it’s also not true. We have seen species split, and we continue to see species diverging every day.

For example, there were the two new species of American goatsbeards (or salsifies, genus Tragopogon) that sprung into existence in the past century. In the early 1900s, three species of these wildflowers – the western salsify (T. dubius), the meadow salsify (T. pratensis), and the oyster plant (T. porrifolius) – were introduced to the United States from Europe. As their populations expanded, the species interacted, often producing sterile hybrids. But by the 1950s, scientists realized that there were two new variations of goatsbeard growing. While they looked like hybrids, they weren’t sterile. They were perfectly capable of reproducing with their own kind but not with any of the original three species – the classic definition of a new species.

How did this happen? It turns out that the parental plants made mistakes when they created their gametes (analogous to our sperm and eggs). Instead of making gametes with only one copy of each chromosome, they created ones with two or more, a state called polyploidy. Two polyploid gametes from different species, each with double the genetic information they were supposed to have, fused, and created a tetraploid: a creature with 4 sets of chromosomes. Because of the difference in chromosome number, the tetraploid couldn’t mate with either of its parent species, but it wasn’t prevented from reproducing with fellow accidents…

The apple maggot fly, Rhagoletis pomonella is a prime example of a species just beginning to diverge. These flies are native to the United States, and up until the discovery of the Americas by Europeans, fed solely on hawthorns. But with the arrival of new people came a new potential food source to its habitat: apples. At first, the flies ignored the tasty treats. But over time, some flies realized they could eat the apples, too, and began switching trees. While alone this doesn’t explain why the flies would speciate, a curious quirk of their biology does: apple maggot flies mate on the tree they’re born on. As a few flies jumped trees, they cut themselves off from the rest of their species, even though they were but a few feet away. When geneticists took a closer look in the late 20th century, they found that the two types – those that feed on apples and those that feed on hawthorns – have different allele frequencies. Indeed, right under our noses, Rhagoletis pomonella began the long journey of speciation…

There are a few more really interesting examples and an explanation of how and why speciation can happen; you should check out the article at Science Sushi if you’re interested.

The point is that all kinds of creatures, from the smallest insects to the largest mammals, are undergoing speciation right now. We have watched species split, and we continue to see them diverge. Speciation is occurring all around us. Evolution didn’t just happen in the past; it’s happening right now, and will continue on long after we stop looking for it.

Fantastic. Evolution is not a thing of the past, and it doesn’t happen to some things and not others. I recently read someone’s racist theory about how because the modern human species began in Africa and went outwards, Africans were less evolved than others. That clearly doesn’t make any sense, and this article’s conclusion should make it obvious why (among other reasons): evolution doesn’t stop. Everything currently living is still evolving, and there’s no end goal to evolution that you can point at and say “The closer you are to that, the more evolved you are.” 

If anything, one might say that bacteria are the “most evolved” organisms, since they reproduce so quickly and thus can change their genetic makeup, as a community, far faster than most living things. Though they don’t have the benefit of sexual reproduction to shuffle around their genes, their DNA will still undergo mutation, and they can also exchange DNA with each other using conjugation

In conclusion, there’s a lot of misinformation about evolution, whether through ignorance or bad intentions. It’s too bad that more people don’t know more about it, because the truth of it all is pretty amazing. 

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Archaeopteryx and On Classifying Species

There’s a fantastic article at 10,000 Birds about the classification of Archaeopteryx, usually considered the first species of bird to emerge from dinosaurs, and more generally how biologists figure out how to classify ancient species. It’s a pretty great and easy-to-read insight into how to figure out the evolutionary tree that we often take for granted. Check it out!

The Origin of Walking

From New Scientist:

A lungfish that uses its fins for walking could help to unravel the steps our distant relations took in order to move from water to land.

The African lungfish (Protopterus annectens) has lobe-shaped fins similar to those seen in the ancestors of the first vertebrates to walk on land.

Anecdotal evidence suggested that the fish use these to walk along lake beds. Now Heather King of the University of Chicago in Illinois has filmed the lungfish in motion and found that they do indeed walk using their two pelvic fins.

This suggests fins were used for walking before they evolved into specialised limbs, says King.

New Scientist has a video of this but it’s rather brief. This is pretty cool – an idea of one step in the path species took from single-celled aquatic organisms to land animals.

The Possible Birthplace of Life on Earth

I wanted my 100th post on this blog to be about something suitably epic; this article should do. It’s about the identification of a group of volcanoes in Greenland that may have had the right conditions for creating life 3.8 billion years ago, something that hasn’t been found anywhere else. 

From Science Daily:

The mud volcanoes at Isua, in south-west Greenland, have been identified as a possible birthplace for life on Earth by an international team headed by researchers from the Laboratoire de Géologie de Lyon: Terre, Planètes et Environnement (CNRS/Université Claude Bernard Lyon 1/ENS de Lyon). Almost four billion years ago, these volcanoes released chemical elements indispensable to the formation of the first biomolecules, under conditions favorable to life. It is the first time that such an environment, meeting all the requirements for the emergence of life, has been identified by scientists in 3.8 billion year-old formations…

Mud volcanoes are cooler than igneous volcanoes, and don’t eject lava. According to Wikipedia, “Ejected materials are often a slurry of fine solids suspended in liquids which may include water, which is frequently acidic or salty, and hydrocarbon fluids.” Sounds nasty. 

Serpentinite is a dark green mineral used in decoration and jewelry. In nature, it is formed when sea water infiltrates into Earth’s upper mantle, at depths that can reach 200 km in subduction zones. According to the scientists, this mineral, often found in the walls of hydrothermal sources, could play a major role in the appearance of the first biomolecules…

The team of scientists publishing this article focused their studies on serpentinites from Isua, in south-west Greenland, which date from the start of the Archean [4 to 2.5 billion years ago]. Dating back some 3.8 billion years, the rocks of Isua are some of the oldest in the world. Using isotopes of zinc as indicators of the basic or acid nature of an environment, the researchers highlighted the basic character of the thermal fluids that permeated the Isua serpentinites, thus demonstrating that these minerals formed a favorable environment for amino-acid stabilization…

Nearly four billion years ago, at a time when the continents only occupied a very small part of the surface area of the globe, the oceanic crust of Isua was permeated by basic hydrothermal fluids, rich in carbonates, and at temperatures ranging from 100 to 300°C. Phosphorus, another indispensable element to life, is abundant in environments where serpentinization takes place. As this process generates mud volcanoes, all the necessary conditions were gathered at Isua for organic molecules to form and be stable. The mud volcanoes at Isua thus represent a particularly favorable setting for the emergence of primitive terrestrial life.

So that’s pretty cool. However, as fun as it may be to point at a specific place as the origin of life, we have to of course keep in mind that this is just one possibility. Life is generally thought to have originated near hydrothermal vents, so those are still a possibility. It’s also hard or impossible to say that this location at Isua is more likely than others, since, as they say, those are some of the oldest rocks in the world; there’s no way to compare them to equally old rocks everywhere else.

Could still make for a good tourist attraction though…

On the Origins of Viruses

Wired has an interesting article from Ars Technica on the questions raised by recent discoveries of some huge viruses (“huge” relative to other viruses of course). The characterization of viruses themselves challenged biologists’ definition of life, and these giant viruses do so even more. They’re as large as some bacteria, contain genes previously thought to be specific to cells, and one virus (mamavirus) even gets infected by a small virus – the first known virophage, a virus that infects a virus.

This article, though, is about their origins; when did these giant viruses originate, and are they the ancestors or descendants of cellular life?

The unusual size and gene content of the virus led one scientist to suggest that viruses could explain the origin of DNA-based life. If viruses carried all these genes, then it’s possible to imagine that one could set up shop in a cell and simply never leave, gradually taking over the remaining functions once performed by its host’s genetic material. This would explain the origin of DNA, which would distinguish the virus from its host’s genetic material, a holdover from the RNA world. It could also explain the existence of a distinct nucleus within Eukaryotic cells.

Eukaryotic cells (like those found in plants and animals) have a nucleus; prokaryotic cells (like bacteria) do not. The “origin of DNA-based life” is a reference to the fact that it’s theorized that life used to rely on RNA as its chief genetic code, the job DNA does now. And the idea of a virus “setting up shop” in a cell and forming a nucleus is similar to mitochondria and chloroplasts, organelles (cellular compartments) in eukaryotic cells that used to be bacteria, and still have their own DNA and everything. 

A paper is being released today, however, that argues that this scenario has things exactly backwards. Giant viruses, its authors argue, have all these genes normally associated with cells because, in their distant evolutionary past, they were once cells…

And what they find supports the view that the virus started out with a much larger complement of genes… Both viruses share an identical set of genes involved in transcribing their DNA into RNA, and use an identical set of signals to indicate where the transcripts should start and stop…

Clearly, the common genes suggest that the viruses share a common ancestor. This leaves two possibilities for the novel ones: either the ancestral virus had a larger collection and its descendants have lost different ones, or each virus picked up different genes from its hosts through a process called horizontal gene transfer. The authors favor the former explanation, because most of the genes specific to one of the two viruses don’t look like any gene present in their hosts (or any other gene we’ve ever seen, for that matter).

So, when did the common ancestor exist? The authors line up a few of the conserved megavirus genes (including those of a more distantly related giant virus, CroV) with the equivalents in other eukaryotic species, and find that they branch off right at the base of the the eukaryotic lineage. In other words, the viruses seem to have had a common ancestor with eukaryotes, but it split off right after the eukaryotes diverged from bacteria and archaea…

To the authors, this suggests that the viruses are the evolutionary descendants of an ancient, free-living eukaryotic cell. Various genes and structures from that organism have gradually been lost over its long history as a parasite, leaving something that propagates like a virus, but belongs to a distinct lineage from all other viruses that we’re aware of.

The authors make a reasonably compelling case against the megaviruses getting their complex genomes via horizontal gene transfer, although it would be good to see a similar analysis for a lot more of the shared genes. What they don’t do, however, is rule out the initial alternative: it’s still technically possible that the megaviruses and eukaryotes share an ancient common ancestor because all eukaryotes are descendants of the virus’ genome. At the moment, I’m not sure it’s possible to distinguish between these alternative explanations.

If this is true, that would mean we’re more recently related to these viruses than to bacteria or archaea. It’d also imply that a living species evolved into non-life. I bet Darwin wasn’t counting on that.

On the Other Hand… Epigenetic Changes May Have Less Effect On Evolution Than We Think

I love this: I posted a TED talk about the potent future of genetic sequencing in medicine, then posted an article about the importance of epigenetic changes in a model plant, and made an offhanded comment about how that reined in my enthusiasm about the TED talk. Now Science Daily brings us an article from researchers who’ve monitored epigenetic changes in that same model plant over the course of several generations, and found that while the epigenome changes rapidly, those changes don’t necessarily stick – so they’re not necessarily an important factor in evolution, or at least not as important as that last article would’ve had you believe. 

Why do I love this? Because, in a sense, it’s science at its best: constantly re-evaluating and self-correcting. Clearly Science Daily had no problem juxtaposing these articles within a few days of each other, because it’s not its agenda to push one view or another (as far as we can tell, anyway); just to advertise the truth, or rather the closest thing we have to it.

I also love it for my own educational value, because suddenly I was like “Wait – I just swallowed that last article uncritically. Now I feel kind of silly.” The thing is, individual scientific findings are rarely interesting on their own – they’re interesting in terms of the implications and applications, which is why any of these articles will probably have less to say about the actual study conducted than about what the researcher thinks this means for the future. And this latter part, unfortunately, will always be conjecture. We’ll just have to absorb and move along with the actual findings, and try not to get too attached to the hypothetical implications 🙂

Onwards: I briefly explained epigenetics in the last post on the topic, but here’s Science Daily’s superior background briefing, and more about the study:

Jean-Baptiste Lamarck would have been delighted: geneticists no longer dismiss out of hand his belief that acquired traits can be passed on to offspring. When Darwin published his book on evolution, Lamarck’s theory of transformation went onto the ash heap of history. But in the last decade, we have learned that the environment can after all leave traces in the genomes of animals and plants, in form of so-called epigenetic modifications…

Using Arabidopsis, the workhorse of modern plant genetics, the researchers determined how often and where in the genome epigenetic modifications occur — and how often they disappear again. They found that epigenetic changes are many orders of magnitude more frequent than conventional DNA mutations, but also often short lived. They are therefore probably much less important for long-term evolution than previously thought.

A team led by Detlef Weigel, director of the Department for Molecular Biology, focused on one of the most important epigenetic marks, methylation of DNA. Tiny chemical building blocks, methyl groups, are thereby attached to individual letters of the DNA, mostly to cytosines. The genetic information itself in form of the four different letters or nucleotides that make up the genetic code remains unchanged in this process…

“Our experiments show that methylation changes are often reversible.” In other words: New epimutations are often not maintained over the long term. “Only when selection wins out over reversion can these epimutations affect evolution,” says Hagmann. A new epimutation thus must have a strong evolutionary advantage so that it can become established before being lost again. Because reverse mutations do not necessarily happen in the next generation, it is still possible that epigenetic differences contribute to inheritance of traits between parents and their children or grandparents and their grandchildren…

What makes epigenetics interesting for human health is the fact that some epigenetic changes can be triggered by external factors. There is evidence that nutrition or the bond between children and their parents can leave traces in the genome that can be passed on to the next generation. The limited stability of DNA methylation implies, however, that such differences do not necessarily last forever, which is probably not a bad idea because a famine might not last forever. It also means that altered DNA methylation often cannot become subject to natural selection.

I wonder if epigenetics will ever take as prominent a role in students’ education as genetics? I don’t think I ever heard of an “epigenetics class” in university… Quick, to the future!

Epigenetic Evolution in a Model Plant

Science Daily brings us a study showing that epigenetic code potentially evolves much more rapidly than genetic code, which could take even more emphasis away from genes as the final determinant of phenotype. This sort of cancels out the optimism of Richard Resnick’s TED talk, though, doesn’t it? Merde. That’s how science goes though. 

(Epigenetic code: a term for modifications of the genome that affect how DNA is read and translated, without actually changing the genetic code. For example, all of our cells (except for some immune cells) have identical DNA, but they have vastly different properties and behaviour, thanks to the different ways that the same DNA is read.)

The study, published September 16 in the journal Science, provides the first evidence that an organism’s “epigenetic” code — an extra layer of biochemical instructions in DNA — can evolve more quickly than the genetic code and can strongly influence biological traits.

While the study was limited to a single plant species called Arabidopsis thaliana, the equivalent of the laboratory rat of the plant world, the findings hint that the traits of other organisms, including humans, might also be dramatically influenced by biological mechanisms that scientists are just beginning to understand.

“Our study shows that it’s not all in the genes,” said Joseph Ecker, a professor in Salk’s Plant Molecular and Cellular Biology Laboratory, who led the research team. “We found that these plants have an epigenetic code that’s more flexible and influential than we imagined. There is clearly a component of heritability that we don’t fully understand. It’s possible that we humans have a similarly active epigenetic mechanism that controls our biological characteristics and gets passed down to our children. “

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