Archive for the 'Evolution' Category

Of Protostomes and Deuterostomes

Here is a cute cartoon about evolutionary divergence and bittersweet reunion by Abstruse Goose:

Via PZ posting at the Panda’s Thumb.

US public opinion polls dampen my day yet again.

Polls about public science literacy in the US always manage to depress me. We are the richest nation in the world, have outstanding universities, and spend more money on education per capita than any country besides Norway. And yet, we slum it down with Turkey on the public acceptance of evolution.

The discrepancy between public science literacy in the US versus the rest of the first world is jaw-dropping. Here is a new poll from Angus Reid comparing views on evolution between the US, Britain, and Canada. The respondents were asked:

Which of these statements comes closest to your own point of view regarding the origin and development of human beings on earth?

  • Human beings evolved from less advanced life forms over millions of years.
  • God created human beings in their present form within the last 10,000 years.
  • Not sure.

And the results:

U-S-A! U-S-A! U-S-A!

Depressing? Yep. Surprising? Not so much any more.

This poll shows that virtually half of the US population is made up of young-earth creationists. HALF! Were not even talking intelligent design or wishy-washy, God-guided evolution here. Half of the US electorate thinks the universe sprung into unchanging existence less that 10,000 years ago; this is Flintstones creationism.

Only 35% of Americans can tell hard science from a fairy tale. How does this happen? Is it all because of rampant fundamentalist religiosity and anti-intellectualism? Are our schools really that bad at teaching science? Does the media drown human consciousness in insipid drivel, preventing people from being capable of a single fleeting critical thought? The answer is probably a lot of each, and it leaves me feeling overwhelmed at the prospect of ever overcoming it.

Science literacy in the United States of America:


Aphid adornment: Lateral gene transfer from fungi to aphids.

Carotenoids are integral components of animal biochemistry. These organic compounds, characterized by long hydrocarbon chains and loops, are used in photoreception, antioxidation, the immune system, and for ornamental coloration. There are over 800 known carotenoid compounds found in nature. They absorb varying wavelengths of blue and green light, causing tissue containing large quantities of carotenoids to appear green, yellow, orange, or red. This absorptive property is what makes carotenoids crucial for vision and coloration in animals.

However, there is a snag. Animals cannot produce their own carotenoids. Their genomes lack the enzymes necessary to synthesize carotenoids from smaller hydrocarbons, and therefore they must ingest carotenoids from organisms that can. Certain bacteria, archea, plants, and fungi are all capable of producing specific carotenoids. By adding these organisms to their diet, animals can fulfill their carotenoid needs.

One animal that takes advantage of carotenoid coloration is the pea aphid, Acyrthosiphon pisum. There are two primary color morphs of this aphid species, green and red (see below). The green aphid morph has large quantities of greenish-yellow carotenoids: alpha-, beta-, and gamma-carotene. The red aphid has decreased amounts of those carotenoids, and instead has gobs of the red carotenoid, torulene.

Color morphs of the pea aphid, A. pisum, and the carotenoids predominately responsible for the color variation. Adapted from Moran and Jarvik, 2010.

This polymorphism is of great ecological significance for the aphid. Parasitoid wasps prefer to lay their eggs in green aphids, and carnivorous ladybugs prefer to eat red aphids. If there is a spike in wasp parasitism, the red morphs become more predominant. If there is a spike in ladybug predation, then the green morphs become more common. By maintaining the genetic diversity of both color morphs in an aphid population, that population can guard against being wiped out by a temporal increase in parasites or predators.

However, this polymorphic color variation seen in aphids presents an interesting question. Where are the aphids getting their carotenoids? The plant phloem sap that aphids suck out of leaves is low in carotenoids, and the carotenoids produced by aphid host plants do not match those found in the aphids. In addition, the endosymbiotic bacteria within the aphids cannot be the source of the carotenoids, as there are no carotenoid biosynthesis genes in their genomes.

However, researchers were surprised to discover that the aphid’s red-green color polymorphism is inherited in a classic Mendelian autosomal manner (remember your Punnett squares, kids?), with the red allele dominant to the green allele. This indicates that the genes responsible for carotenoid-based colorations in these aphids are located within their own genomes! A search of the newly published pea aphid genome revealed the presence of several carotenoid synthases, cyclases, and desaturases. This suite of carotenoid biosynthesis genes is capable of producing the colored carotenoids necessary for the red and green aphid color morphs. A mutation in one allele of these genes prevents the production of the red carotenoid, torulene, resulting in the green aphid color morph.

These are the first carotenoid biosynthesis genes found in an animal. Indeed, no other known animal genome, including several other insect genomes, contain homologues to these genes: so where did they come from?

Carotenoid synthesis genes from various organisms. Adapted from Moran and Jarvik, 2010.

A gene tree containing the aphid carotenoid genes, as well as similar genes from bacteria, plants, and fungi can bee seen to the left. The aphid genes (blue) are completely nested within fungal carotenoid biosynthesis genes (brown). Therefore, at some point in aphid evolution, the genes for carotenoid biosynthesis were transfered from a fungi directly into the aphids genome. It is likely that a similar event occurred from bacteria (black) to plants (green) as well. The possible mechanisms for such gene transfers, especially between two eukaryotes, are poorly understood at this point.

Earlier, I wrote about a similar case of lateral gene transfer from algae to a sea slug. That was the first known transfer of genes between multicellular organisms. This new example in aphids lends support to the notion that these lateral gene transfers are more common in eukaryotes that once though. It may turn out, as genome sequencing increases at exponential rates, that the eukaryotic tree of life actually resembles (to some extent) the interconnected gene web seen in bacteria.


  • Moran, N., & Jarvik, T. (2010). Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Science, 328 (5978), 624-627 DOI: 10.1126/science.1187113

Hat tip to Microecos for tweeting this.

Et tu, Connecticut?

Mark Tangarone, a Weston, Connecticut grade school teacher, came up with an awesome lesson plan to teach his students about evolution by recreating the voyage of the HMS Beagle:

To learn about Darwin, students would have retraced the path of the HMS Beagle, the expedition that inspired a young Darwin’s theory of evolution. Each student would study a stop in the voyage, reporting on the animals and adaptations that Darwin observed.

Now, that sounds like an exciting and engaging way to teach science to children. It presents science as the adventure that it is, while exploring the central theory of evolution that unifies all of biology. The first lesson, in the first biology class should always be about evolution, not a smattering of unconnected nature facts. Mark Tangarone astutely realized this, and for his creative efforts the school administration has twice rejected his lesson plan, driving him to earily resignation.

The administrators squeamishly claimed that they rejected to plan in order to avoid controversy stirred up by religious students and parents. However, the true colors come out in this quote from principal, Mark Ribbens:

While evolution is a robust scientific theory, it is a philosophically unsatisfactory explanation for the diversity of life.

Surprise, surprise. Creationist administrators hiding behind ‘philosophy’ in order to deny their students a proper science education.

Kudos, Mr. Principal, for putting the interest of educating of your students third, behind your religious dogma and spinelessness. In addition you drove a good teacher into early resignation and put you school administration on a pedestal as a shining example of anti-intellectualism, uncharacteristic of New England.

Read more at Wired

Creationists visit awesome museum, intentionally learn nothing

Photo: NMNH

The Raw Story has a rage-inducingly depressing story about a field trip for the biology students at Liberty University to the National Museum of Natural History (NMNH) in Washington DC.

First of all, I love this museum. It hosts an overwhelming diversity of priceless natural treasures arrayed through its halls for your enjoyment and appreciation. It’s hard to imagine that the wealth of displays in the actual museum are only the tip of the iceberg for the Smithsonian’s truly enormous collections; both on-site and at massive off-site warehouses. No trip to the capital is fully complete without checking this gem out.

The NMNH also does a good job of stressing the central importance of evolutionary processes in shaping the full diversity of life on earth over billions of years. It sticks to the science and makes no excuses to appease the faithful; as any honest presentation of evolutionary biology should. However, what do creationist students, rigorously conditioned to believe fairy tales and un-think their way around reasonable evidence, get out of a visit to this very special and enlightening museum?

Apparently nothing.

Let’s take a look at some quotes from the students. Keep in mind these are prospective science graduates: Prepare to be overwhelmed by jaw dropping lapses in critical thinking and logic.

In reference to the date associated with this model of a Morganucodon ‘rat’ Lauren Dunn, 19, authoritatively states,

210 million years, that’s arbitrary. They put that time to make up for what they don’t know.

Objection, your honor! Projection and a baffling lack of critical self-analysis. Just because you choose to believe made up explanations for natural phenomena does not mean that paleontologists operate under the same absence of rigor. The Rhaetic strata where the earliest Morganucodon fossils are found have been accurately dated with a variety of techniques (ICS Upper Triassic timescale PDF).

Regarding the the same Morganucodon model, Nathan Hubbard, a MD hopeful, said,

There is no scientific, biological genetic way that this, this rat, could become you.

Yes there is. It looks something like this (Luo, 2007), and it is supported my mountains of peer-reviewed science. Also, why the revulsion at the prospect of being cousin to ‘this, this rat’? Morganucodons walked the earth for at least 50 million years during truly tough times. I’m proud to know I’m biologically connected to a surviving mammalian lineage whose rat-like progenitors somehow thrived alongside theropod dinosaurs. I wonder how Nathan would feel if I told him we are also related to tapeworms, dung beetles, jellyfish, and Treponema pallidum via ancient common ancestors.

Marcus Ross, a paleontology professor from Liberty says,

In order to be the best creationist, you have to be the best evolutionist you can be… [it can be difficult to convince people to take creationist beliefs seriously]. The attitude is when you are a creationist you are ignorant of the facts.

Please demonstrate otherwise…

He (Ross) says carbon-dating techniques that have been used to suggest the Earth is in fact billions of years old are simply not reliable.

*Facepalm* Carbon dating has nothing to say about billion year time scales; it is only useful on material up to around 60,000 years old. Other methods are used for much older time scales. So yes, my attitude will continue to be that you are ignorant of the facts. It’s either that, or you are lying, delusional, or a little of each.

Beyond the braindead quotes from the Libertines, this article about this field trip is a boatload of fail. It doesn’t challenge a single wild assertion from the creationists, explains evolution (befuddledly) in half a sentence, and states that creationism is, ‘an increasingly popular theory’. This article goes well beyond an equal-time treatment (which itself is useless when comparing science with bullshit) and gives creationism a special pedestal from which to drop their nuggets of inanity onto the The Raw Story’s readership.

The most unfortunate part about all this is that these Liberty University students allegedly have honest career aspirations. They want to be scientists, researchers, doctors, and professors; perhaps because of a true passion for science, or maybe as a means to leverage their faith on society. Regardless, they will be at a disadvantage. Beyond ignorance of modern scientific knowledge, they have not been taught to think critically. The scientific process that these students learn begins with a conclusion and then flails around impotently trying to support it with facts. That is not how research science works, it is antithetical to it.

Evolving a camera eye: Anyone can do it

PBS has a great video up about the evolution of camera eyes, from their documentary, Evolution: ‘Darwin’s Dangerous Idea’. Using a synthetic optical demonstration and examples from nature, Dan-Eric Nilsson describes some of the selectable gradations between a flat patch of photosensitive cells and a fully functional camera eye. Camera eyes, also called simple lens eyes, have a single chamber with a light-sensitive retina on one wall, across from a lens, through which light enters and is focused onto the retina.

Dan-Eric Nilsson holding the lenses of a collossal squid. Photo: Museum of NZ, Te Papa.

Camera eyes are found in most vertebrates; the only exceptions being species that have regressively lost their eyes due to low-light lifestyles. There are other examples of camera eyes in nature, however. The best know among these are cephalopods. Octopus, squid, and cuttlefish all have camera-style eyes that are structurally very similar to vertebrate eyes. This is a classic example of convergent evolution: Despite independent retinal derivation, vertebrates and cephalopods have both hit on a similar eye design solution for seeing their world. There are further examples of lens eyes in jellyfish, annelid worms, and gastropod mollusks; also typifying the concept of convergent evolution.

Less commonly known is that some arthropods have also discovered simple camera eyes. The majority of arthropods have compound eyes, composed of many independent optical units called ommatidia. Each ommatidial facet of a fly’s eye, for example, has its own lens and photoreceptor apparatus. Compound eyes work very well for most arthropods, however their maximum resolution is limited by their structure: The smaller the lens, the greater the light diffraction anomalies it produces; and compound eyes require thousands of very small lenses. Therefore, some arthropods have evolved camera-like simple eyes, with a single chamber in order to greatly increase resolution.

Arachnids, and specifically jumping spiders, possess the prime examples of simple eyes among the arthropods. They make use of a corneal simple eye. In a corneal simple eye there is no crystalline lens and the refractive focusing of light is carried out solely by the curved cornea. Using simple corneal eyes, jumping spiders achieve the greatest visual resolution among arthropods. In addition, some tiny copepod crustaceans have been found to have simple eyes with lenses. Among these, certain genera even have multiple lenses, producing telescoping optics.

Adapted from Land, 2005. Photos: jurvetson, George Grall, Thomas Shahan

Simple camera eyes are a spectacular example of convergent evolution. They can be found in at least five of the major animal phyla; Cnidaria (jellies), Arthropoda, Chordata (including vertebrates), Annelida (worms), and Mollusca. These phlya represent a tremendous diversity of creatures separated by vast eons of deep evolutionary time. This demonstrates the ability of a useful design to reveal itself through evolution in disparate lineages; built from whatever components are available.


Happy 201st Birthday Charlie!

Unraveling Arthropoda

This post was chosen as an Editor's Selection for ResearchBlogging.orgA new paper, published online in Nature this week, aims to resolve long-standing disputes within Arthropod phylogenetics. This work offers strong evidence for, and opens new, perplexing questions about, the deep evolutionary history of arthropods.

The phylum Arthropoda consists of four major subphyla:

  • Chelicerata – Arachnids, horseshoe crabs, sea spiders.
  • Myriapoda – Centipedes, millipedes.
  • Crustacea – Crabs, lobsters, shrimp, copepods, ostracods, barnacles, pill bugs, brine shrimp, water fleas, remipedes, ect.
  • Hexapoda – Insects, silverfish, springtails.

All known arthropods are included in these subphyla. However, the interrelation of the subphyla has long been in contention. Up to now, a series of morphological and molecular-based classification paradigms have been employed to parsimoniously resolve the deep phylogeny of arthropods; with mixed results. Two of the competing hypotheses of deep arthropod phylogenetics are the Paradoxopoda and Mandibulata models.

Both Mandibulata and Paradoxopoda propose a Pancrustacean clade consisting of Hexapods and Crustaceans as closely related sister groups. They differ in their treatment of the Myriapods and Chelicerates. Paradoxopoda has Myriapods and Chelicerates as closely related sister groups. Mandibulata, on the other hand, has Myriapods as a sister group to Pancrustaceans, and Chelicerates as a distant, early-branching clade of arthropods. While Mandibulata is supported by taxonomy (Crustaceans, Hexapods, and Myriapods all have mandibles, where as Chelicerates have chelicerae for mouthparts), Paradoxopoda is primarily supported by recent mitochondrial molecular pylogenetics.

Also under contention is the relationship between Crustaceans and Hexapods within the increasingly well supported Pancrustacean clade. It has not yet been settled if the two are distinct sister groups, or if the Hexapods are nested within the Crustaceans. If the latter is true, researchers have not been able to determine which branch of the Crustaceans gave rise to the Hexapods.

In the present study, researchers at University of Maryland, Duke, and the Natural History Museum of LA have dramatically improved on previous molecular approaches for inferring deep arthropod phylogenetics. They did this by increasing the number and diversity of arthropod species included, as well as the type and amount of genetic sequence characters used. Whereas previous approaches used mitochondrial genetic sequences, resulting in the morphologically perplexing Paradoxopoda model; the researchers in this study instead used nuclear protein-coding genes. Nuclear genes have been increasingly used to resolve deep evolutionary relationships in animals.

The researchers included in their molecular phylogenetic analysis 75 arthropod species. The 75 arthropod taxa were chosen to encompass the broadest spectrum of known arthropod groups. From each of these species, they sequenced 62 nuclear genes; totaling 41 thousand bases of DNA sequence per species. These sequence data sets from the 75 different arthropods were compared to one another, producing this phylogenetic tree:

Maximum likelihood phylogenetic tree of arthropods. Adapted from Regier et al., 2010.

This tree further supports a Pancrustacean clade consisting of Hexapods and Crustaceans. In addition, this work supports the Mandibulata model of deep evolutionary relationships within Arthropoda. Pancrustacea is sister to the Myriapods, forming the Mandibulata clade; which is then sister to the early-branching Chelicerates. This reconstruction strongly refutes the mitochondrial Paradoxopoda model.

The most notable results of this study are in regard to the internal structure of the Pancrustacean clade. Instead of a distinct separation between Crustaceans and Hexapods, we see four resolved clades within Pancrustacea. The Hexapod clade is upheld and nested completely within Crustacea. In addition Crustaceans are split into three paraphyletic clades; Vericrustacea, Oligostraca, and Xenocarida. Vericrustacea (‘true crustaceans’) includes the decapods (crabs and lobsters), mantis shrimp, barnacles, copepods, and branchiopods; most of the critters commonly thought of as crustaceans. Oligostraca is a strange and early branching crustacean group that includes ostracods, tongue worms, and branchiurans. Xenocarida (‘strange shrimps’) includes remipedes and cephalocarids.

It turns out that, according to this analysis, the Xenocarids are the long sought-after sister group to Hexapods. Together they form the new clade Miracrustacea (‘surprising crustacean’). The Miracrustaceans are sister to the Vericrustaceans, forming a clade that is in turn sister to the Oligostraca, rounding out Pancrustacea.

This study causes some serious upheavals in the Pancrustacean clade; breaking Crustaceans into three paraphyletic clades, placing remipedes as close sister taxa to Hexapods, and nesting the Hexapods completely within the Crustaceans. At the same time it presents new and exciting questions to morphologists and evolutionary-developmental biologists.

Further morphological, genetic, and evolutionary study is required in order to understand the full implications of these newly resolved arthropod relationships. However, this research represents a robust step forward towards unraveling Arthropoda.


  • Regier, J., Shultz, J., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J., & Cunningham, C. (2010). Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences Nature DOI: 10.1038/nature08742

Samurai Crabs: Transmogrified Japanese warriors, the product of artificial selection, or pareidolia?

I’m going to share with you two stories about the Samurai Crab, Heikea japonica; one is a ancient Japanese legend, and the other is a modern piece of scientific folklore. First, the historical background of the Japanese myth…

April of 1185 was the end of the line for the Heike Empire in Japan. Their rival clan, the Genji, swept across the southern Inland Sea of Japan and annihilated the final, desperate armada of the Heike at the battle of Dan-no-ura. The defeated Heike child-emperor and his samurai, refusing to surrender, committed suicide by throwing themselves from their boats to drown.

The battle of Dan-no-ura represented a massive cultural and political shift in Japanese history. It was the end of the imperial Age of Courtiers, and the beginning of the Feudal Era of Japan, lasting from 1185 to 1868. During this time, the majority of Japan was ruled by a powerful military dictator, the shogun, and his samurai warriors. Naturally, such geopolitical upheaval has strongly ingrained itself in the culture of Japan, and folklore stemming from the battle of Dan-no-ura survives today.

Popular legend alleges that, following the battle Dan-no-ura, the souls of drowning Heike samurai warriors were transformed into crabs. These crabs are distinguished by having the faces of the fallen samurai on their backs. To this day the Heike crabs roam the depths of the oceans around Japan, searching for the lost heirlooms of their empire.

The ghost of the Heike general Taira no Tomomori (bottom left) at the bottom of the ocean with the anchor he used to drown himself following defeat at Dan-no-ura. He is joined by Heike crabs bearing the faces and souls of his comrades. By artist Utagawa Kuniyoshi, 17th century. Click to embiggen.

Samurai crab, H. japonica and stylized Kabuki samurai face (inset). Click to embiggen.

Continue reading ‘Samurai Crabs: Transmogrified Japanese warriors, the product of artificial selection, or pareidolia?’

We contracted crabs from gorillas

And you were probably thinking that people only got crabs from coeds on spring break in Cancun!

Seriously though, I apologize for the sensationalist title, but this story is a really neat demonstration of the application of phylogenetic comparison and evolutionary divergence time estimation. (For a primer of phylogenetics see this post.)

The venereal affliction known as “crabs” is an infestation of lice that specifically reside in the pubic region of humans. Pubic lice, Pthirus pubis, are of a genetically and morphologically distinct genera of lice from the head louse, Pediculus humanus. If you compare the evolutionary history of primates with the history of the lice that parasitize them, an interesting picture emerges.

Phylogenetic cladograms, assembled from morphological and genetic characters, for primates and parasitic lice. Dotted lines indicate parasite-host relationships. Figure from Weiss, 2009; after Reed et al., 2007.

Continue reading ‘We contracted crabs from gorillas’

I have moved.
Arthropoda can now be found here.

Michael Bok is a graduate student studying the visual system of mantis shrimp.

Flickr Photos