Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
A huge thank-you to Matthew and Greg for taking over the website in my absence. I’ve just returned from the Galápagos, and haven’t yet fully absorbed the experience, which exceeded all expectations. I’ll be posting about it over the next week or so, but in the meantime here are a few iconic animals that I snapped (more on these species later). Note: I do not have a zoom lens.
by Matthew Cobb
There has been a lot of argument about how to classify primates, and on what basis. Molecular data have shown that the “haplorhines” (tarsiers, New World monkeys, Old World monkeys and hominoids) are monophyletic – we all share a common ancestor which did not give rise to the remaining primates, the “strepsirhines” (lemurs and lorises). Those of you with a classical training will have guessed that the “rhine” business suggests this classification is to do with the shape of the nose in these animals. Furthermore, haplorhines generally have acute colour vision (they are mostly diurnal), while strepsirhines, which are generally nocturnal, do not.
This has led to the suggestion that, during primate evolution, vision and the sense of smell have been traded, in particular in the human lineage. As we grew to be increasingly visual animals, we came to rely less on our sense of smell. This can be seen, it is claimed, in the number of “dead” olfactory receptor genes (“pseudogenes”) to be found in the human genome compared to that in New World Monkeys, a direct result of our acquisition of full trichromatic vision. But is this actually true? Was there a “trade-off” of one sense against another?
A study by a group of Japanese researchers (Atsushi Matsui, Yasuhiro Ho and Yoshihito Niimura), about to appear in Molecular Biology and Evolution [subscription needed], looks at this widely-accepted suggestion and finds little evidence to support it.
They looked at the olfactory receptor (OR) genes in five primate species (human, chimpanzee, orangutan, marmoset and rhesus macaque) together with two “strepsirhines” – the bushbaby and the mouse lemur, with the tree shrew as a comparison (“outgroup”). Surprisingly, they found no significant differences in the number of functional OR genes between the marmoset (New World Monkey) and the macaque (Old World Monkey) and the hominoids. In fact, humans had the second largest number of intact ORs (396), just behind the chimpanzee (399), and as against only 296 in the orangutan. This suggests that – whatever you might think – you can probably detect a similar number of odours as any of the other primates.
They then looked at how these genes evolved over time. They looked at which genes seemed to be the same in each of the different species (“orthologous” genes). This is particularly difficult in the case of OR genes, which evolve extremely rapidly, for reasons we do not understand. They estimated that the most recent common ancestor of all primates would have had around 550 OR genes. 62 of those genes are still shared by all the species they studied, and 34 of them are present in a single copy in each primate genome. Indeed, when you take into account gene duplication, nearly 77% of the human and chimpanzee OR genomes are common to the two species.
This figure shows how many of those 550-odd genes each species has lost over the last 48 MY or so (in the white bar on the right). Probable gene duplications are shown with a plus sign on the right of the bars, followed by the total number of functional ORs for each species. The number of genes that were lost at each branching event in our evolutionary tree are shown on the left. Strikingly, the same number OR genes were lost at the point we split with the strepsirhines (51 – arrowhead) and when we and the chimps split from the orangutans. This is not what was predicted by the “gain colour/lose smell hypothesis” – we would have expected to see a larger number of OR genes lost when we first parted company with our less-visual primate cousins.
This is not the end of the story, however. We already know that in humans, our OR genes have become “pseudogenized” at a greater rate after we split from the chimps, suggesting a relaxation of selection pressure on (some part of?) our olfactory genome. People have speculated that this may be due to our apparent non-reliance on pheromones for sexual and territorial communication. However, there is no evidence for this, any more than we have any idea as to what the relatively small OR repertoire in orangutans might indicate. For the moment, we cannot take the sequence of an OR gene and say what the corresponding receptor protein detects.
Although this study has not found evidence to support the trichromatic vision hypothesis, the authors point out that more comparisons from more species are needed, in particular because New World Monkeys and strepsirhines show highly variable colour vision systems. We are still far from understanding the effect of evolution on sensory systems, even in the species that are closest to us, including our own.
Matsui A, Go Y, Niimura Y. ( 2010) Degeneration of Olfactory Receptor Gene Repertories in Primates: No Direct Link to Full Trichromatic Vision. Mol Biol Evol. Jan 8. [Epub ahead of print]
[First posted at the Z-letter]
by Matthew Cobb
Despite my impression, it appears that Jerry never blogged on the case of Casper the commuting cat, who lived in Plymouth (UK). Casper, like any self-respecting commuter, would get the bus, as shown on this BBC news video:
Now, Casper is no more, the victim of a hit and run driver. As reported in The Guardian: “A notice appeared at the cat’s usual bus stop saying: “Many local people knew Casper, who loved everyone. He also enjoyed the bus journeys. Sadly a motorist hit him … and did not stop. Casper died from his injuries. He will be greatly missed … he was a much-loved pet who had so much character. Thank you to all those who befriended him.”
Vale, Felix!
by Matthew Cobb
Convergent adaptations form one of the most striking classes of proof for evolution by natural selection. Radically different species, with common ancestors deep in the past, show near-identical adaptations to similar environments. Convergence can even be seen in species that are separated by vast depths of time, such as icthyosaurs (extinct marine reptiles) and dolphins, which show strikingly similarities in their bodily form, a consequence of adaptation to the environment (water) and their predatory role, based on a common tetrapod anatomy and musculature.
However, most examples of convergent adaptation remain at the level of form or function, rather than the genes involved. It’s possible that the same genes are involved in shaping a dolphin and an icthyosaur, but it’s unlikely we’ll ever know. An exception is the recent discovery of convergent mutations in species of sand lizards with white skins, all of which affect the melacortonin-1 receptor. But in a way, that isn’t too surprising – the melacortonin-1 receptor controls skin colour in these animals, and only a restricted number of molecular changes would give rise to an advantageous white form.
Even more striking is the announcement, shortly to appear in the pages of Current Biology, of identical skin toxins produced in two lineages of frogs, but on the basis of two different genes that diverged during the Cambrian, between 488 and 557 MY ago!
Both lineages of frogs – the Australian Litoria species and the Pipidae (which includes the model species Xenopus laevis) – secrete caerulein, a powerful toxin that induces vomiting, diarrhea and pancreatitis, amongst other things. Strikingly, the two sets of amphibians have very different ecologies and are separated by massive distances – the Australian/Papuan Litoria frogs tend to be terrestrial, whereas Xenopus and its African relatives are strictly aquatic. This means that their toxins are used to ward off very different predators, although the assumption is that in all cases the predators are vertebrates, which are all vulnerable to these toxins.
Researchers in Belgium and Australia, led by Kim Roelants, studied the genome of these frogs, and also looked at the proteins they produced, and discovered that although the caeruleins produced by the two sets of species are identical, they use very different genes to get there.
In the case of Xenopus and its relatives, the caerulein gene evolved through duplication of the cholecystokinin gene (cck); in the case of Litoria, the gene involved was gastrin. Both these genes are present in all vertebrates, but diverged during the Cambrian, and subsequently evolved into a series of genes with different functions in different lineages.
In both cases, gene duplication – when a gene gets mistakenly copied through a genetic accident – provided the raw material on which natural selection could work. With two versions of a gene, one is able to maintain the important function that originally led to its presence, will either evolve randomly (and eventually become a pseudogene, no longer functional) or will accidentally produce a product that is in some other way advantageous to the organism that carries it.
In the case of the cck gene, there were several such duplication events, including two within the lineage that led to Xenopus – there are now three cck genes in Xenopus.
The authors explain this striking case of molecular convergence by the fact that the products of both cck and gastrin genes retained a common structure; this meant they could both function in the frog’s physiology and produce a compound that would repel a wide range of vertebrate predator (by affecting the same physiological processes).
In other words, natural selection was able to use gene duplication to maintain one function, and select another, focusing on the same tiny character, but in two very different genes.
[First posted at the z-letter]
by Matthew Cobb
According to The Guardian:
The video, shot in October on the island of Sumatra, shows two, one-year-old cubs and their mother approaching and sniffing the camera before moving on.
WWF’s tiger research team set up four video camera traps along known tiger routes that allow the animals to move between two protected areas in central Sumatra – the Rimbang Baling wildlife reserve and Bukit Tigapuluh national park.
Ian Kosasih, WWF Indonesia‘s forest programme director, said the images showed the need to turn the corridor into a protected area and for paper and palm oil companies in the area to shield what he called high-value forest.
“When these cubs are old enough to leave their mother … they will have to find their own territory,” Kosasih said. “Where will they go? As tiger habitats shrink with so much of the surrounding area having been cleared, the tigers will have a very hard time avoiding encounters with people. That will then be very dangerous for everyone involved.”
Sumatran tigers are on the brink of extinction because of rapid deforestation, poaching and clashes with humans. Their numbers have dwindled to about 400 from about 1,000 in the 1970s, the WWF estimates.
The infrared-triggered camera traps, which are activated upon sensing body heat in their path, have become an important tool to monitor the population and identify which areas of forest are used by tigers, WWF said. WWF operates dozens of cameras throughout the central Sumatran province of Riau.
Karmila Parakkasi, the leader of WWF Indonesia’s Sumatran tiger research team, said her crew first captured still images of the tigress and a cub in July 2009 using still camera traps. The photos, however, were not clear. Video camera traps were then installed in September at the same location.
by Matthew Cobb
Over at The Guardian, Ben Goldacre’s excellent “Bad Science” column deals with the issue of “coincidence”. If such rigour were applied to religion…
Every now and then you have to salute a genius. Both the Daily Mail and the Metro report research analysing the positions of Britain’s ancient sites, and the results are startling: primitive man had his own form of satnav.
Researcher Tom Brooks analysed 1,500 prehistoric monuments, and found them all to be on a grid of isosceles triangles, each pointing to the next site, allowing our ancestors to travel between settlements with pinpoint accuracy. The papers even carried an example of his map work, which I have reproduced here.
That this pattern could occur simply because one site was on the way to the next was not considered.
Brooks has proved, he explains, that there were keen mathematicians here 5,000 years ago, millennia before the Greeks invented geometry: “Such is the mathematical precision, it is inconceivable that this work could have been carried out by the primitive indigenous culture we have always associated with such structures … all this suggests a culture existing in these islands in the past quite outside our expectation and experience today.” He does not rule out extra terrestrial help.
In the Metro Tom Brooks is a researcher. To the Daily Mail he is a researcher, a historian, and a writer. I hope it’s not rude or unfair for me to add “retired marketing executive of Honiton, Devon”.
Matt Parker, his nemesis, is based in the School of Mathematical Sciences at Queen Mary, University of London. He has applied the same techniques used by Brooks to another mysterious and lost civilisation.
“We know so little about the ancient Woolworths stores,” he explains, “but we do still know their locations. I thought that if we analysed the sites we could learn more about what life was like in 2008 and how these people went about buying cheap kitchen accessories and discount CDs.”
The results revealed an exact and precise geometric placement of the Woolworths locations.
“Three stores around Birmingham formed an exact equilateral triangle (Wolverhampton, Lichfield and Birmingham stores) and if the base of the triangle is extended, it forms a 173.8 mile line linking the Conwy and Luton stores. Despite the 173.8 mile distance involved, the Conwy Woolworths store is only 40 feet off the exact line and the Luton site is within 30 feet. All four stores align with an accuracy of 0.05%.”
Parker used an ancient technique: he found his patterns in 800 ex-Woolworths locations by “skipping over the vast majority, and only choosing the few that happen to line up”.
With 1,500 locations, Brooks had almost twice as much data to work with, and on this issue Parker is clear: “It is extremely important to look at how much data people are using to support an argument. For example, the case for global warming covers vast amounts of comprehensive evidence, but it is still possible for people to search through the data and find a few isolated examples that appear to show otherwise.”
by Greg Mayer
No, it’s not a reptilian hors d’oeuvre. It’s pictures of a Galapagos land iguana, Conolophus subcristatus, to whet your appetites for those Jerry will have when he gets back. I toured the Galapagos 20 years ago, and took loads of pictures, but they’re Kodachromes (which I haven’t scanned), so the pictures of our saurian friend below are from my colleague and fellow evolutionary biologist Joe Balsano, who visisted in 2007, and then kindly regaled my Darwin class with tales and pictures of his adventure. (More Galapagos reptile photos, at the Galapagos Conservancy, here.)
The Galapagos land iguana, Conolophus subcristatus (Joe Balsano).
The first link above for the Galapagos land iguana, from the Galapagos Conservation Trust (the UK companion to the US-based Galapagos Conservancy) is slightly out of date when it says there are two species of Galapagos land iguana: there are three. The common, or just Galapagos, land iguana, Conolophus subcristatus, is shown above. The Barrington land iguana, C. pallidus, occurs only on the island of Santa Fe (also known as Barrington). The two species differ fairly subtly in color and scalation (pallidus being less colorful, with a more distinctive crest of spines; see the original description by Edmund Heller here [go to Proceedings of the Washington Academy of Sciences in the left sidebar], and the classic paper by van Denburgh and Slevin on Galapagos iguanid lizards from the California Academy Expedition here [go to Proceedings-California Academy of Sciences 4th series in the left sidebar]). These subtle differences are the sort of differences between allopatric populations (i.e., populations inhabiting distinct, nonoverlapping, geographic areas) that can lead to long and inconclusive arguments as to whether the populations should be recognized as species, or subspecies, or not named at all. These arguments are a common, and not at all unexpected, issue when dealing with organisms living on islands. (The evolutionary process issues involved, although not the taxonomic issues, are dealt with comprehensively in Jerry’s and Allen Orr’s Speciation.) But the newly discovered species the pink land iguana of Volcan Wolf on Isla Isabela (Albemarle), Conolophus marthae, is not one of these wishy-washy, is-it or is-it-not-a-species, cases: it’s a new species, alright.
The pink land iguana, Conolophus marthae. From Gentile, G., et al. 2009. An overlooked pink species of land iguana in the Galápagos. Proceedings of the National Academy of Sciences 106:507-511.
It is amply distinct, both morphologically and genetically, from the other two species, including in coloration and form of the nuchal crest, as you can see from the pictures above. But, more importantly, it is also sympatric (i.e., living together in the same place) with the common land iguana. This is important because the truest test of species status is the test of sympatry: whether two forms interbreed when they co-occur in nature. In this case, the two species live together side by side, and reproductive isolating barriers, such as differences in male behavior (see the original species description by Gabriele Gentile and Howard Snell), keep them genetically isolated from one another. (Gentile and colleagues did find a single individual which showed evidence of some genetic mixing, but it is evidently insufficient to breakdown the genetic isolation of the forms.) This is a really remarkable and exciting discovery, given how many scientists, park rangers, and even just tourists, have traversed these islands. (I have been to Isabela, not far, at least as the crow flies, from where the new species was discovered.)
Although I think it’s fair to say that interested scientists have been delighted by the discovery of the pink land iguana, a number have been disturbed by what Gentile and Snell did, or rather didn’t do, in naming the species: they did not collect a specimen to document the species, but relied upon blood samples and photos. Usually, when a new species of animal is described, a particular specimen is designated the holotype, and preserved and deposited in the collection of a museum that will make the specimen available for study by other scientists. The specific identity of the holotype fixes the application of the name, and study of the holotype helps resolve any questions or confusions concerning the status or identity of the species, as well as contributing to further knowledge of the species’ biology. But if there is no holotypic specimen, then other scientists are unable to check the describer’s claims, or test their conclusions, or advance the study of the species in any way. Gentile and Snell were aware that what they were doing was problematic, and addressed the question in their paper. They even designated a particular iguana as the holotype, but left it in the wild, hoping that at some later time it might be retrieved using a radio tag they put in it. They did not collect it out of concern that loss of even a single individual might drive the species extinct.
Alain Dubois of the Museum nationale d’Histoire naturelle and Andre Nemesio of the Universidade Federal de Minas Gerais, Brazil, have led the criticism of Gentile and Snell, while acknowledging that there may be times when it is not wise to collect a specimen. See papers by them here, here, and here; Thomas Donegan of Fundacion Proaves supports what Gentile and Snell did. In the bad old days of systematic zoology, species were often named without holotypes, and this led to much confusion. Lately, there have been several species named for which holotypes have not been collected, for the same reasons advanced by Gentile and Snell, and this has led to much controversy; many of the key papers are cited in the woks of Dubois, Nemesio, and Donegan, or in works cited therein.
Some people might ask, what’s wrong with a photo? Well, I think it should be evident that there are many things you can’t determine from a photo, but perhaps a mention of the most famous species named on the basis of a photograph will make some of the problems clear: that species is the Loch Ness monster, Nessiteras rhombopteryx (abstract only without subscription). To put it only a bit too simply, specimens are what separate zoology from cryptozoology, science from pseudoscience. More on this in a later post.
by Matthew Cobb
I promise I’m not making any of this up, but this afternoon, paleontology PhD student Holly Barden came to my office with a present from my colleague, dino-man Phil Manning. Phil was moving office and came across a great Lego construction toy that you could make into a Stegosaur (for reasons that I won’t go into, I have a huge collection of toy Stegosaurs). So far, so ordinary. Except… the Lego kit could also make A PTEROSAUR. And furthermore, LOOK AT THE NAME OF THE KIT. SIGNATURE ON THE LID!
Furthermore, this afternoon my kids were watching defunct UK prehistoric drama Primeval, in which PTEROSAURS came through the anomaly into modern day Britain. I rest my case. FOUR TIMES in TWO DAYS the divine pterosaur (yet again a Pteranodon – no coincidence I think) has spoken to me.
The fact that the Lego box could equally be a message from a Stegosaur god is neither here nor there:
In fact, my daughter Evie (11) and I are making the Stego kit right now – not an easy task! But just like real Stegosaurs, it does have eyes that flash red when you press a button at the back of its head, and great big carnivorous teeth. Eh? Oh.