Top 5 Misconceptions About Evolution

Happy Darwin Day!

Here's a good little infographic about some of the misconceptions of evolution.

http://molecularlifesciences.tumblr.com/post/75224638930/top-5-misconceptions-about-evolution-a-guide-to

Prey (Shake 'em off)

Co-evolution and predator-prey relationships in a Taylor Swift parody. Still ridiculously catchy.

Swarming Squid Sperm: A Strategy in Sneakiness

Sneaky swarming squid sperm. Yeah, let’s talk about that. ‘Cause you hear that and you gotta know, right? But before all the sperm and the swarming is the amorous squid. Let’s start there.

As you may expect, squid have both a male and a female. Male squid produce spermatophores, packets of sperm that they can transfer to the females. Female squid carry around these sperm packets until they are ready to spawn. That can be quite some time in some species. When they are ready, they will use the stored sperm to fertilize and then release hundreds or thousands of eggs into the water as jelly-like strands. That’s about what we know about squid reproduction, the rest is relatively mysterious.

A newish study in Current Biology sheds some light on the mysterious nature of squid sperm. The study organism is Loligo bleekeri, one of the more common of the pencil squids (Loliginidae) in Japan and southern Korea. It is moderately large (40 cm) with very short arms. It is a polyandrous species, meaning that males only mate with one female, but females mate with many males. It is a good mating system for researchers interested in mate choice and sperm competition (oh yeah, there’s a whole subdiscipline of the science of sperm competition – rethinking your job now aren’t you?). These have been shown to drive sperm evolution (yes, that’s a thing) and morphology to optimize fertilization success. Because in this game, it’s all about how many babies you have.

One of the things that makes this squid species particularly interesting is the dimorphism among males. Large “consort” males do all the work. They compete with other males, court females with colorful body displays, and guard the female until she spawns his offspring. Smaller “sneaker” males are just that: sneaky. They rush in under the nose (or beak, as it were) of the consort male, attach their spermatophore and book it on outta there. The dimorphism in males is reflected in their mating as well as their size. Consort males place their spermatophores inside the female’s oviduct, while the sneaker males just stick it onto the external body surface near to the seminal receptacle near the mouth. It isn’t as close to the eggs, but it must be a successful otherwise why do it? What is it that makes this stick-and-ditch strategy so successful?

To find out, the researchers dissected consort and sneaker males to recover their spermatophores. Then sperm were released into test tubes, diluted and tagged with fluorescent labels (each type with a different label). They observed that when the sperm suspension was drawn into a capillary tube the sneaker, but not the consort, sperm aggregated (or “swarmed”) to form a regularly striped pattern along the tube. And, when sneaker and consort sperm were mixed, still only the sneaker sperm swarmed. The sperm weren’t slowing down or sticking together, so what was causing the swarming? It’s not like the sperm are problem solving. So the next thought was: Maybe it’s a chemical response. So a filter assay was designed where two chambers were separated by a filter so fine that only small molecules could get though. A sperm suspension was put into the lower chamber and then each type of sperm added to the top to see where it swam. Again, only sneaker sperm migrated toward the filter. Okay, so it must be some kind of chemical attractant, but what and how?

Again, labeled sperm suspensions were put into capillary tubes. Then bubbles of different gases were microinjected into the solution. This assay revealed that carbon dioxide (CO2) attracted sneaker, but not consort, sperm. This CO2 is likely generated by the sperm via the carbonate system. Not exactly a super-simple system. To tease apart the mechanism, they developed caged carbonate (you’re thinking Han Solo…me too, but not quite the same) to sculpture gradients of bicarbonate (a basic solution, pH-wise). This system allowed them to determine that swarming depends on acidic (CO2 and/or H+) gradients but not on a biocarbonate gradient. Next, they found that carbonic anhydrases (CAs) are involved in swarming as CO2 sensors in cells.

But let’s go back to the acid thing (as both CO2 and H+ increase acidity). The researchers used a pH-sensitive dye to look at the acid gradient during swarming. They observed that the middle of the swarm acidified first, producing a H+ gradient outwards. When they added a buffer, the swarming disappeared. When they put a pipette of acid (H+) into the suspension, both sneaker and consort sperm moved toward it. But remember that only CO2 attracted the sneaker sperm. Additionally, the pH at which these types of sperm responded was different. They found that only sneaker sperm lowered their intracellular pH with environmental pH. This means that only sneaker sperm have a H+ transport system that allows for the CO2 attraction. And finally, they showed that calcium (Ca2+) influx controls cause the sperm to turn around when they reach the end (weak part) of the gradient.

Whew! That’s a lot of compact information! So let’s put it together in a whole-organism, what-the-heck-is-going-on kind of way. Why does it matter that sneaker sperm like CO2? Remember back to the placement of the spermatophores by each of the males. When the female releases her eggs, the consort male’s sperm has first access because it is in the oviduct. They fertilize a lot of eggs but not all. Then the female holds her eggs in her arms while she swims to a good substrate to release them. Squid arms and mouth are not all that far away from each other. This is when the sneaker male sperm goes to work. The swarming allows the sperm to stay close to the site of egg deposition and may be sensing CO2 released from the eggs; both increase the chances of fertilization. And, in the end, that’s what it’s all about.



Hirohashi, N., Alvarez, L., Shiba, K., Fujiwara, E., Iwata, Y., Mohri, T., Inaba, K., Chiba, K., Ochi, H., Supuran, C., Kotzur, N., Kakiuchi, Y., Kaupp, U., & Baba, S. (2013). Sperm from Sneaker Male Squids Exhibit Chemotactic Swarming to CO2 Current Biology, 23 (9), 775-781 DOI: 10.1016/j.cub.2013.03.040


And for a little more info, here's an earlier study on the same topic:


Iwata, Y., Shaw, P., Fujiwara, E., Shiba, K., Kakiuchi, Y., & Hirohashi, N. (2011). Why small males have big sperm: dimorphic squid sperm linked to alternative mating behaviours BMC Evolutionary Biology, 11 (1) DOI: 10.1186/1471-2148-11-236



(image via MarineBio.org -- Note that this species is Loligo vulgaris, the European squid. It is weirdly difficult to find images of L. bleekeri, but this image gives you some of the characteristics of the genus.)

A Dottyback in Damsel Clothing: Color Mimicking in Fish

I was looking around for a study and stumbled upon one about fish mimicry in Current Biology. What first caught my attention was its use of a video abstract. What a cool idea amped up a few notches by beginning with music reminiscent of Game of Thrones. Then I started to think back about posts I've done on predator-prey relationships and could only come up with 1, the One-Third for the Birds post back in 2012. Clearly it is time to revisit that topic. Oh, and while we’re at it, we’ll throw mimicry into the mix.

Different prey species employ various options in predator avoidance including mimicry. Generally, mimicry is a strategy of looking, acting, smelling, or sounding like something else as an act of deception to gain protection. But prey species are not the only ones that mimic. Predators use it to get close enough to catch their prey. Blending into the background or looking like something familiar can be very useful in sneaking up on an unsuspecting prey animal. However, in both predator and prey, there is a huge caveat to mimicry - numbers. The mimic must be rare compared to their model. If the mimics are encountered too often then the predator/prey learns of this cunning deception and the mimicry becomes ineffective.

This month Cortesi et al. published a short paper looking at body color and predatory behavior in dusky dottybacks (Pseudochromis fuscus). This small species (8 cm) is a generally solitary and aggressive predatory reef fish native to the southwestern Pacific Ocean and eastern Indian Ocean. The fish are usually found in association with branching corals (e.g. Cauliflower corals [Pocillopora]  and Staghorn corals [Acropora]), setting territories where they love to hunt and eat juvenile coral reef fish, particularly the similar-looking damselfish. Individuals range in color from yellow to a “dusky” purple/brown. The researchers based their experiments on 3 interesting facts: 1) when the dottybacks matched the color of other reef fish they increased their hunting success, 2) dottybacks have been shown to change body coloration within 2 weeks when translocated to a different, dark colored reef and 3) dottybacks aggressively mimic similarly colored adult damselfishes. Does one color work better than another? Are there cues that drive the color change?

Figure 1 (A and B) from Cortesi et al (2015) Current Biology 

To test this, they set up sites at Lizard Island, Great Barrier Reef, Australia. Ya know, given the option, that's probably where I’d do my research too. They collected dottybacks and adult damelfishes and assessed the home ranges of the yellow and brown dottyback color morphs. Then, to look at the genotypes associated with different color morphs, they used microsatellites on fin clips from fish from three lagoon locations. Next, they conducted a translocation experiment. They found an open area and created a small patch reef using pieces of live or rubble coral. A total of 15 yellow damselfish (Pomacentrus amboinensis, P. moluccensis) and 15 brown damselfish (P. chrysurus) of all size classes were placed on the patch reefs. Once the damselfish were adjusted to their new home, the dottybacks (tagged unique fluorescent elastomer markers) were added in a 2 x 2 x 2 design (dottyback color x damselfish color x habitat type, each with 2 levels: yellow/brown dottyback, yellow/brown damselfish, live coral/coral rubble). Once all of the fish were on the patch reef, they were observed for predation and body color (using spectral imaging, skin biopsys for histology, and lots of mathematical models).

The researchers also conducted a very similar experiment using controlled conditions. Damselfish and dottybacks were caught and placed into experimental aquarium tanks containing live and rubble corals. Both juvenile and adult damselfish were acclimatized to a tank before a dottyback morph was introduced. Then strike rates of dottybacks directed at the damselfish were recorded. Then they conducted a prey color choice experiment to examine if dottybacks had a preference for a particular colored prey fish, again in the experimental aquariums. Considering that dottybacks aren't just predators but also prey for larger fish, the researchers tested to see if dottybacks also benefit from matching the color of the habitat using coral trout (the predator) in controlled choice tanks.

Whew! That’s a lot of experiments for one little report paper. In the field, they found that yellow dottybacks associated themselves with live coral and yellow damselfish, and brown dottybacks associated with coral rubble and brown damselfish. The translocation experiment showed how the color of resident adult damelfish induced color change in the dottybacks in patches where their colors were mismatched, independent of habitat type. The skin biopsies showed that unlike other species of fish, the dottybacks did not achieve this change by altering the number of chromatophores (pigment containing cells that reflect ligh) but, rather, the ratio of xanthophores (yellow pigment cells) compared to melanophores (black pigment cells) alters.

In the aquarium experiments, they found that dottybacks were three times more successful in capturing juvenile damselfish when their color matched that of the adult damselfish. This bit of deception works on the fact that the juveniles are less vigilant when they perceive all bigger fish as harmless adult damselfish. The strike rates showed that dottybacks prefer to go after prey fish of the same coloration to themselves, but, when mismatched, brown dottybacks are more likely to have successful strikes than yellow ones. When the dottybacks became the prey species, coral trout were found to strike more often at fish that were color mismatched to the background. This means that the color change has a secondary camouflage benefit and possibly a dilution effect when they are associated with similarly colored damselfish.

Graphical Abstract from Cortesi et al (2015) Current Biology

Collectively, these experiments uncovered a novel mechanism of the mimicry game: phenotypic plasticity. Phenotype is an organism’s observable characteristics (how it looks), and plasticity describes a quality of being easily shaped or molded. Phenotypic plasticity is one of those rare scientific words that means exactly what it sounds like: the ability or an organism to change its characteristics in response to the environment. This plasticity allows the dottybacks to deceive their prey using multiple guises and thereby increase their hunting success with the added benefit of hiding from their own predators.


F. Cortesi, W.E. Feeney, M.C.O. Ferrari, P.A. Waldie, G.A.C. Phillips, E.C. McClure, H.N. Sköld, W. Salzburger, N.J. Marshall, & K.L. Cheney (2015). Phenotypic Plasticity Confers Multiple Fitness Benefits to a Mimic Current Biology, 25 (1-6) : 10.1016/j.cub.2015.02.013


Write-up by the authors on The Conversation: "The dusky dottyback, a master of disguise in the animal world."



(image via the Australian Museum)

Happy Darwin Day!

Happy Darwin Day! Here's another song from the Darwin Song Project.

Not So Simple: Social Evolution in Silk-Weaving Ants

Silk weaving ants. That in and of itself is really neat. Then you see this picture of Polyrhachis shattuck...I mean, look at her! How many cool points can one animal rack up? A new study in Behavioral Ecology and Sociobiology takes a look at these arboreal nesting and silk-weaving ants.

Let's begin with sociality. It is one of those subjects in biology that is considered its own discipline. When you think of social animals you probably think of herds of mammals or maybe schools of fish. Sociality reaches its peak in eusociality, a surprisingly complex and truly social organization. These animals live in groups, cooperatively care for juveniles, divide labor, and overlap in generations. Studies of these social systems has shed light onto broader concepts of collective decision making, even leading to advances in our own technology (traffic flow, communications networks, internet searches, etc.). However, as much as we know about the social mechanics, we know very little about the evolution of such systems.

Most eusocial animals are found in the phylum Arthropoda, with the order Hymenoptera being the largest and most well-known, and all ants classified as eusocial species. And ants are the focus of today's chosen study. Ant larvae spin individual protective cocoons of silk and, depending on the species, that silk is either allocated to the colony or sequestered for the larvae’s individual needs. Donated silk is used by the worker caste to weave together leaves into nests. The “lowest grade” of arboreal (a.k.a. tree-dwelling) ants, Dendromyrmex, have larvae that produce silk without any interaction or provocation from the worker ants. In “intermediate grade” ants, Camponotus senex and Polyrhachis ?doddi (re-described as Polyrhachis robsoni (Kohout 2006)), the workers hold larvae at the work site and, with simple ritualized behaviors, the workers collect the silk. In the “highest grade” genus, Oecophylla, the larvae donate their silk supply to the colony. A worker ant will use highly ritualized behaviors - bring the larvae to the work site, straddle a leaf seam, use antennae to tap the head of the larva (telling it to extrudes silk from its salivary glands), use silk to glue together the seam, repeat.

A comparison of ant genera in this way, simple to complex, is thought to represent possible evolutionary steps in nest-weaving behavior. However, molecular sequence data suggests that nest-weaving has evolved independently in each of the four genera in which it occurs. This new study focuses on Polyrhachis ants. This genus offers good within-taxa comparison of multiple life strategies as different species vary in their nesting locations, from intertidal to subterranean to arboreal, the presence of nest construction, and even silk sources.

A total of 37 specimens of ants from all 13 currently recognized (*grr*, an often frustrating term in insect taxonomy) subspecies and five outgroup taxa were used for this study. The researchers isolated total genomic DNA and amplified and sequenced DNA from six fragments using specific primers for each gene region. After they collected the sequences, they analyzed and aligned them using computer programs. In their complicated analysis (they used Bayesian…that always makes my eyes cross) they input the gene level data along with variables of nesting preference (ground = soil, logs, stones vs. arboreal = twigs or leaves in trees) and nest construction (silk weaving vs. no silk vs. other silk). All of this allowed them to construct phylogenies (like an evolutionary family tree) and infer relationships among the species and ancestral states for behavior.

Their results showed robust phylogeny with strong support for the monophyly of the genus Polyrhachis, further supported by the inclusions of nesting preference and nest construction.This is good because it provides a nice, solid ancestral reconstruction for the evolution of the different species and their relationships to each other. It also allows for the comparison of the different nesting strategies within the framework of evolution. The investigation turned up some very interesting results. Simply, their results do not support the stepwise evolution of simple to complex. They found that the production of arboreal silk nests is the ancestral state with at least two transitions to subterranean nesting and the loss of silk weaving as species become more derived. There is also some flexibility and reversal in the behavior. Basically, the ants evolve, abandon and then re-evolve the nest weaving practices. The loss of silk nest weaving seems to occur with the transition from arboreal to terrestrial nesting followed by the re-evolution of silk nest weaving. This suggests a strong but flexible link between nesting preference and nest construction.

To illustrate this evolve-abandon-re-evolve point, the researchers present the example of Hedomyrma, a subgenus within a larger clade of subterranean nesters. This larger clade has already lost both arborality and nest weaving. But there are 2 species of Hedomyrma (Polyrhachis argentosa and Polyrhachis fervens) that have reverted to arborality. The re-evolution of this nesting preference has come with the modification of building nests within the hollow internodes of bamboo sans silk. Another reversal pattern is seen in a third species of Hedomyrma (Polyrhachis turneri), which has larvae that retain all of their silk for their own cocoon-constructing needs. Rather, worker ants steal silk from spiders to build nests on the sides of rocks. So the nest construction characteristic is what has re-evolved, just with a different mechanism. Larval cocoons have been lost in 2 of the arboreal nest-weaving species studied, and the allocation of larval silk to colony rather than individual need is considered a more derived but decoupled characteristic of nest construction.

I think that both the flexibility and the rapid evolution (or re-evolution) of this system is what attracted me to this paper. We know that evolution is a complex concept that we often boil down to from-simple-to-complex, and in many cases it is exactly that. This study almost reads like a sequel, a what-happens-next sort of thing.


Robson, S., Kohout, R., Beckenbach, A., & Moreau, C. (2015). Evolutionary transitions of complex labile traits: Silk weaving and arboreal nesting in Polyrhachis ants Behavioral Ecology and Sociobiology DOI: 10.1007/s00265-014-1857-x


(image of Polyrhachis shattuck, Maliau Basin, Sabah via AntWiki via California Academy of Science Ant Course)

Deadbeat Dads: Hatching Plasticity in Glassfrog Embryos

I have recently emerged from the all-enveloping cocoon that is data analysis and presentation writing. Powerpoint, Photoshop, and JMP have been in charge of my waking hours for the past couple of weeks. But now I am free! Is that daylight and springtime I see? If you’ve been following the Facebook page then you will still have received the occasional sciency goodness, but now it’s time for me to get back to blogging.

This week a new paper published in Proceedings of The Royal Society B about baby glassfrogs caught my eye. There are more than 100 species of neotropical glassfrogs (Centrolenidae) and more are being regularly discovered. Glassfrogs are so called because of the transparent skin on their venters which allow for the observation of their internal organs. Dorsally, they tend to be green with various yellow, white, blue or red markings, with some species even reflecting light in the infrared spectrum. These frogs live high in the trees that overhang mountain streams in Mexico, Central, and South America. They make high peeps or whistles, and in some species, a single individual will initiate a chorus.

Glassfrogs are also known for their parenting skills, which seems ubiquitous across the taxon. Females lay small clutches of eggs several meters above the water on rocks or vegetation. The male will then take charge of egg maintenance, sometimes caring for multiple clutches. The male will hydrate the eggs (“hydric brooding”) in order to moderate water balance and prevent dehydration, modifying this behavior in response to weather conditions. When the eggs hatch, the tadpoles fall into the water. But sometimes a new female will show up and the male glassfrog will forget all about his clutches and he’ll take off with her. So what happens to all of his abandoned eggs?

The behavior exhibited by the males offers an excellent opportunity to study parent-embryo interactions. Early life stages in most animals are often the most vulnerable and, as such, parental care of eggs has evolved independently in many species. The term “hatching plasticity” can encompass a wide variety of these survival methods employed by embryos to increase their survivorship such as hatching early to escape danger or delaying hatching to remain in safety. Embryos can alter their rate or sequence of development. The environment and/or parental care than have both direct and indirect effects on these processes.

The authors looked at the brooding behaviors of male Fleischmann’s Glassfrogs (Hyalinobatrachium fleischmanni), specifically how embryos respond when their fathers are no longer around to hydrate them. Nightly, the researchers monitored male territories and egg clutches along stream transects near San Gabriel Mixtepec in Oaxaca, Mexico. They conducted a male-removal experiment where they displaced 40 males from their clutches and then monitored embryo survival, development and hatching time compared to the clutches of 50 attending males.

The researchers found that removing fathers significantly reduced the amount of time until hatching, with no effect on embryo survival. They found that, on average, there was a 21.2% reduction in the duration of the embryonic period for the male-removal group. This early hatching appeared to be a response to the deteriorating conditions without the fathers rather than the parent directly altering hatching time. These unmaintained eggs lost thickness (a measure of hydration) but not integrity (the egg capsules did not degrade over time) or rate of development. The neglected embryos simply hatched at a less mature stage of development. However, hatchlings from the male-removal group were significantly smaller and had fewer, less developed gut coils, the latter illustrating that age had a significant effect on development. The observed hatching plasticity was found to be due to embryos actively hatching at different developmental stages; the neglected embryos hatched at a less mature stage.

This is one of the first studies to demonstrate that embryos can time hatching to cope with variation in parental care, employing adaptive strategies to cope with these variations. The embryos are responding to their deteriorating egg environment, a dehydration-induced hatching if you will. They increase their likelihood of surviving by responding to their changing environment. A nice example of within-species coevolution.


Delia, J., Ramirez-Bautista, A., & Summers, K. (2014). Glassfrog embryos hatch early after parental desertion Proceedings of the Royal Society B: Biological Sciences, 281 (1785), 20133237-20133237 DOI: 10.1098/rspb.2013.3237


And a nice little write-up over at Science called "When Dads Go Missing, Frogs Start Hatching"


(image via Tropical Herping)

Fun with Fundulus: The Evolution of Pollution Resistance in Killifish

(credit to Evan D'Alessandro, Rosenstiel School of Marine and Atmospheric Science)

In honor of Mr. Charlie Darwin’s birthday I thought I would read an evolution paper. Put that together with the turn my career has taken into ecotoxicology (and the associated steep learning curve), I was steered towards a study about adapting to pollution.

Let me start by introducing you to today’s study organism: The mummichog (Fundulus heteroclitus) is a species of non-migratory killifish found along the Atlantic coast of North America. They can be found in the brackish waters of tidal creeks, saltwater marshes, and estuaries. These fish are remarkably hardy, adaptable, and easy to study. Throughout the decades, a great deal of knowledge has been gathered about their life history, genetics, behavior, and endocrinology. They have also been used to study embryological processes and responses to chemicals and toxins. The mummichog’s adaptability to varying temperature, salinity, and oxygen along with their ability to survive in highly polluted areas has made them a popular subject in toxicology.

We know that animal populations adapt to environmental stressors through genetic and epigenetic (heritable changes in gene activity that are not caused by changes in the DNA sequence) changes. Changes that, in turn, affect gene expression and/or protein function. In this way, toxic chemicals can drive selection. A big part of the field of toxicology is understanding the molecular basis of these changes as natural populations adapt to altered environments. The mummichog’s ability to live in grossly contaminated waters has been used to better test and understand the molecular mechanisms by which natural populations adapt to long-term, multi-generational exposure to pollution.

Toxicologists, like geneticists, seem to love acronyms. And once you start reading chemical names, you know why. So let’s get some chemical terminology out of the way first. There are several chemicals that are under the umbrella of “dioxin-like compounds” (DLCs) which are by-products of various industrial processes and are all highly toxic. Aromatic hydrocarbons such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), and polycyclic aromatic hydrocarbons (PAHs) all cause toxicity similar to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and DLCs. This toxicity manifests as interference in embryonic development, reproductive problems, immune impairment, and other not-so-pretty consequences.

A new study in BMC Evolutionary Biology takes a look at the Fundulus of New Bedford Harbor, Massachusetts. This 18,000 acre estuary and seaport is one of the EPA’s Superfund sites. It is highly contaminated with PCBs and heavy metals. Through their various stages of development and into adulthood, the killifish of these waters are less sensitive and/or resistant to the effects of the toxins. The researchers took a candidate gene approach to investigate the molecular basis of this adaptation to DLCs. To do this, they went to New Bedford Harbor and other polluted sites to collect fish. They also collected from reference sites where the PCB sensitivities of the killifish have been characterized and measured. Their methods included a lot of genetic work that, for the sake of space and sanity, I’m not going to detail. Let’s just skip along to the results shall we?

The researchers found a repeated evolution of resistance to DLCs in widely separated populations of Fundulus along the east coast of the U.S. There is strong evidence that this adaptation involves altered sensitivity of the aryl hydrocarbon receptor (AHR). Genes encoding proteins in the (AHR)-dependent signaling pathway are a master regulator of responses to many of the most toxic DLCs. The AHR is a ligand-activated transcription factor that exhibits high affinity for DLCs, regulates the expression of a large set of genes in response to DLC exposure, and is required for TCDD or PCB toxicity in fish (and mammals too). Two paralogs (or clades) of the AHR pathway have been identified in mummichog, AHR1 and AHR2, as well as an AHR repressor (AHRR). The loci (gene locations) for these three genes were found to contain a large number of polymorphisms, many of which encoded changes in amino acids. Perhaps most interesting was AHR2, the predominant form expressed in many fishes which has 951 amino acids whose variants lead to 26 different forms of the protein. The genetic diversity at these the three loci was not significantly different between contaminated and reference sites except in the case of AHR2. This paralog had significant FST values (the fixation index that measures population differentiation due to genetic structure) and showed very low nucleotide variability (0.1%).

So what's happening here? When polluted sites are compared to reference sites there is similar genetic diversity. However, when you look at specific nucleotides you see a story start to emerge. AHR1, AHR2, and AHRR are resistance genes that mediate toxic effects, and populations of killifish exhibit strong genetic structure at all three of these loci. The selection observed at AHR1 and AHR2, specifically the latter, at the highly polluted New Bedford Harbor site suggests an adaptation to the PCBs present there. AHR2 seems to be one of the genes, possibly the major one, involved in this resistance and may be one of the recurring targets for selection during local adaptation to DLCs. This adaptation allows the mummichog to survive in a really polluted environment. These results are consistent with several lines of evidence from similar studies both in the field and the lab.

Witnessing, quantifying, and mapping these mechanisms greatly advances our understanding of the consequences of environmental toxins. Overall, this is a very interesting example of adaptation in an ever changing environment.


Adam M. Reitzel, Sibel I. Karchner, Diana G. Franks, Brad R. Evans, Diane Nacci, Denise Champlin, Verónica M. Vieira, & Mark E. Hahn (2014). Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats BMC Evolutionary Biology, 14 (1) DOI: 10.1186/1471-2148-14-6


Read more about this study in the Woods Hole Oceanographic Institute's New Release "Solving An Evolutionary Puzzle New Bedford Harbor Pollution Prompts PCB-Resistance in Atlantic Killifish"
(also the source of the above image)

EPA's New Bedford Harbor Superfund Site page

And you can learn more about how the mummichog became a model organism here:
Atz, J. W. 1986. Fundulus heteroclitus in the Laboratory: A History. Amer. Zool. 26(1): 111-120. DOI: 10.1093/icb/26.1.111 (LINK)

Photographing the Bare Bones of Evolution

Patrick Gries is a photographer with a reputation in luxury goods, design, and contemporary art. In his series Evolution, his atypical approach to the collection of vertebrates at the Muséum d'Hisorie Naturelle has garnered attention from a different sphere, scientists. Evolution captures over 250 of the museum's skeletons as sculptures that straddles the line between art and science. The exhibition has been in France and Denmark, and there are plans for a show in Tokyo. But no need to buy a plane ticket, you can get all the work from his coffee table format book.

The photographs were shot with strong directional light and are accompanied with text by scientist, documentarian, and professor emeritus at Paris’ Museum of Natural History, Dr. Jean-Baptiste de Panafieu.

“New forms have evolved from old ones. Stubby amphibian feet have been transformed into hooves, bird wings and whale flippers. Yet many of the bones in those original limbs have not changed their relationship to the rest. They have just been stretched, flattened or reduced to vestigial knobs. Along the paths of evolution, the vertebrate skeleton has been transformed into similar forms many times over — aardvarks in Africa and anteaters in South America.”

My quote on the topic is "evolution is beautiful." Here are a few of my favorites:

You can find more information and pictures here:

Patrick Gries Website

NY Times "Skeletons Flesh Out Life's Past"

Unknown Editors

The Guardian "A bone to pick"

Beautiful Decay "Patrick Gries’ Photographs Of Skeletons Combine Art and Scientific Inquiry About Evolution"

Socialite in the Dark: Do Eyes Really Matter When It Comes To Schooling?

It has been a while since I've visited the topic of blind fish. I know, I know! What took me so long, right? Well, I was browsing for fish papers, ‘cause I take care of lab fish now (I’m working my way up to Fish Whisperer status), and I came across a paper in Current Biology about the schooling behavior of cavefish, specifically the effects of eyesight loss on this behavior.

There are two main types of social “collective behavior” in fish: shoaling and schooling. Shoals are defined exclusively by social attraction, simply being near each other in a group. To form a school, individuals must also maintain coordinated body position with their schoolmates, showing polarized orientation and synchronized movement.

In a 2011 post, The Sleep of the Blind Fish, I introduced you to Astyanax mexicanus, commonly known as the Mexican cavefish or Mexican tetra. I’ll let you visit that post for more details on this species, but for today know that it has two, interfertile forms: the normal or surface form is pigmented, sighted, and has a natural photoperiod, and the blind form is albino, has no eyes, and lives in dark caves. The normal form actively groups into schools and shoals while the cave form has reduced this behavior. A study by Johanna Kowalko et al. looked to quantify this schooling behavior. To do this they made a sort of fish mobile attached to a motor. As the grouped plastic model fish on the mobile moved, the live fish had the option to join, orient with, and follow the group or not. Images and videos allowed the researchers to measure the position of the fish, average and proportion of time each fish spent with the school, and nearest neighbor distances. They found that surface fish followed the model school while cavefish did not. The surface fish swam significantly closer together than did the cavefish. Also, the cavefish showed a loss of the tendency to swim oriented to one another, or school, as well as a decreased tendency to shoal.

Greenwood et al. (2013) Fig. 1

Okay, so why is this? What do you need to do (or have) to form a group? Some type of sense, right? I mean, you need to find others of your species, be able to sense your place in the group, and be able to respond to others in your group. As we know, the cavefish have adapted to a dark environment and so have no eyes. However, they do have a increased number and distribution of taste buds and cranial superficial neuromasts (mechanoreceptors that detect movements and pressure changes in surrounding water, think lateral line or “touch”). Kowalko’s group found that surface fish have significantly fewer and smaller cranial neuromasts than do cavefish, likely an adaptation to cave life. However, they did not find this adaptation to have a large effect on the evolutionary loss of schooling. I’ll bet that your brain is jumping to the next logical conclusion: vision is important. And you would be correct. The researchers did a series of tests where they tested both types of fish in various light conditions. The surface fish actually preferred the dark, but when they were in the dark they swam farther apart and lost schooling behavior while the cavefish were unaffected by the lighting conditions.

Let’s take the next step: Is this a learned behavior or is it dependent on having eyes? It is known that cavefish develop eyes, which undergo apoptosis and degenerate. So if a surface fish were to lose its vision early in development, would it then behave like a cavefish? To test this, the researchers removed one, two, or no lenses/eyes in surface fish larvae (with some awesome microdissection skills I’m sure!), allowed them to grow up, and then tested their schooling behavior. They found that the removal of both lenses caused the fish to swim farther apart than partially-sighted (one lens) or control fish. The partially-sighted fish could follow the model school but still shoaled farther apart than did full-sighted controls.

Next, Kowalko's group wanted to see what was going on in the brain. Recent research has shown that surface and cavefish have different levels of monoamine neurotransmitters (signaling chemicals in the nervous system).  They used inhibitors to alter serotonin and monoamines. Then they ran their schooling tests. They found that serotonin levels make no difference, but preventing the breakdown of monoamines decreases schooling behavior and results in significantly greater distances between fish in the shoaling tests. These results are consistent with other evidence that a molecule involved in the synthesis of dopamine (a monoamine) affects schooling behavior in cavefish.

Finally (whew!), they performed quantitative trait locus (QTL) analysis. Basically, this is a statistical method that links the phenotype (trait) measurements and the genotype (molecular markers) to explain a genetic basis for a complex trait. They found homozygous cave alleles at a marker underlying linkage group 27 that results in a decrease in schooling behavior and a dark preference. They also found schooling QTL that does not fall in the same place as the QTL for dark preference, eye size, pupil size, or neuromast number. This means that there is are both vision-dependent and vision-independent genetic contributions to the evolution of schooling behavior. Interesting.

Is there a story here? Well, sure. Perhaps when the sighted, cavefish ancestors arrived in their new, dark homes they couldn't school because of the lack of light. Their new cave environment also had a different ecology than their surface habitat. For one, it had a lack of big predators. Schooling equals protection in numbers, so a lack of the need of protection equals a lack in the need to school. For another, caves have scarcer food. Groups eat more and eat together. When there is less food and it is more spread out it is advantageous to find and eat it alone. Put together, this relaxed the selective pressure on schooling behavior causing multiple genetic changes, only some of which are vision-dependent.


Johanna E. Kowalko, Nicolas Rohner, Santiago B. Rompani, Brant K. Peterson, Tess A. Linden, Masato Yoshizawa, Emily H. Kay, Jesse Weber, Hopi E. Hoekstra, William R. Jeffery, Richard Borowsky, & Clifford J. Tabin (2013). Loss of Schooling Behavior in Cavefish through Sight-Dependent and Sight-Independent Mechanisms Current Biology, 23, 1874-1883 DOI: 10.1016/j.cub.2013.07.056

See also:

Alison M. Bell (2013). Evolution: Skipping School Current Biology, 23 (19) DOI: 10.1016/j.cub.2013.08.022

Anna K. Greenwood, Abigail R. Wark, Kohta Yoshida, & Catherine L. Peichel (2013). Genetic and Neural Modularity Underlie the Evolution of Schooling Behavior in Threespine Sticklebacks Current Biology, 23 (19), 1884-1888 DOI: 10.1016/j.cub.2013.07.058


(images via Seriously Fish)

The Festival of Bad Ad Hoc Hypotheses

Do you live in or near Cambridge, Massachusetts? Did you know that there is a Festival of Bad Ad Hoc Hypotheses (BAH!) over at MIT?

"The Festival of Bad Ad Hoc Hypotheses (BAH!) is a celebration of well-argued and thoroughly researched but completely incorrect evolutionary theory. It is put on by Zach Weinersmith (cartoonist of SMBC), breadpig (publishers of SMBC and XKCD), and MIT's Lecture Series Committee. It is sponsored by the EvoS Consortium and This View of Life magazine (Editor-in-Chief David Sloan Wilson)," and it is part of the Cambridge Science Festival. Ben Lillie, director of Story Collider, will be the emcee for the evening (and I am hoping that he will record it for his podcast!).

The event was initially inspired by this comic:

BAH! will be held in MIT's Kresge Auditorium (48 Massachusetts Ave., Cambridge MA, USA) on the evening of October 6th, 2013. Doors will open at 6:15 PM and the event will start at 7 PM. There will be 7 speakers presenting their bad theories in front of a live audience and a panel of geeky judges. These judges will determine who presented the best theory who will together determine who presented the best theory according to the following criteria:

1. Force of Science - how much “scientific” information was brought to bear (graphs, real citations, “research” etc.)
2. Artistry - how unexpected and clever the idea and presentation are, and how well the presentation is delivered.
3. Parsimony - the simplest theory that explains the most data is best.
4. Strength of Defense - how well did you defend your views to the judges. 
• Note - being funny is not a good defense.

Unfortunately, submissions for this BAHFest closed on March 10th. But they might do another one in the near future, so keep thinking up bad hypotheses and maybe you can present.

Tickets for this event are $5 for students (valid student ID needed) and $10 for non-students.

Visit the BAH! website for tickets and more information. Oh, and if you go, leave a comment to tell us all about it!

Avast Me Hearties! It's International Talk Like a Pirate Day!

Ahoy, Matey, it be that wonderous of days where even th' weakest of landlubbers can spout the talk o' the pirate! Arrrr!! What? Now, don' go tellin' me ye havenna been practicin' yer pirate-slang, ya scurvy scum! The Cap'n'll be havven ya swab the decks for that'un. Scurry on over to me past page to brush up on yer pirate-talk and plunder some information on ITLAPD beginnins:

Happy International Talk Like a Pirate Day! (2011 post)

For the rest of ye ole salty sea-dogs and saucy wenches that have been sailin' with me for a while, here be some ITLAPD booty to enjoy! Yarrr!!

Pyrates! be a sea faring band from the shores of the Olde Lowlands of Holland. They be a notorious band of buccaneers who be playin' pirate themed folk music!




This bein' the modern age ye must be knowin' how to rap like a pirate too!




We ARR Who We ARR, a Ke$ha parody just for ITLAPD!



Tom Mason and The Blue Buccaneers be singin' "Talk Like a Pirate"!






Here be yer home ports for ITLAPD...

The Official Site for International Talk Like a Pirate Day

Talk Like a Pirate Day UK Headquarters


...and some articles for ye to gaze at...

Zerve's "How to Celebrate International Talk Like a Pirate Day"

Huffington Post's "Talk Like A Pirate Day 2013: Avast Me Hearties"


...and because ye twisted me arm, some more videos on how to talk like a pirate...

Real Pirates' Guide to "Arrrgh!" Volume 1

Real Pirates' Guide to "Arrrgh!" Volume 2

Real Pirates' Guide to "Arrrgh!" Volume 3

Eating and Evolution: Are Prey Preferences Causing the Evolution of Killer Whales?

When I was an undergrad, a lowly freshman who just knew she wanted to study biology, I took an internship at SeaWorld Orlando. I was excited that I got to participate in a real research project doing actual sciency stuff. The project was on the nursing behaviors of captive baby killer whales. Really cool right? Little did I know that actual science is composed of hours upon hours of tedious observation and documentation (2:00pm – melon bumping, 3:00pm – melon bumping, 4:00pm – melon bumping…). Despite that (or, who knows, maybe because of it), it was an neat project that boosted my interest research biology. And I got to watch killer whales for hours every week. So when I came across the paper for today’s post it really reminded me those times.

A new study published in the Proceedings of the Royal Society B, Biological Sciences looks at niche variation within sympatric killer whale populations in the North Sea. Those of you familiar with the terminology I just used might want to skip to the next paragraph. Otherwise, let’s hit a few terms first. We’ll start with the niche variation hypothesis. In the simplest terms, a niche describes where a species lives and the roles it plays in its habitat. The niche variation hypothesis describes differences within a species that are correlated with the variety of foods and habitats that are used by various populations. For example, why do island birds of the same species have different bill sizes? Likely because their bills adapt to the food items they are exploiting on their own island. It conveys a competitive advantage which results in a reproductive advantage that will lead, eventually, to an evolutionary change. This change will likely be a speciation event. This is a lineation-splitting event that produces two or more separate species from one (think about the branching on the tree of life). Usually we think of speciation as occurring via a geographic isolation (birds on different islands, populations separated by a mountain range, etc.), but the niche variation hypothesis allows for sympatric speciation because the exploitation of different resources splits a population within the same habitat. Admittedly, this type of selection would need to be really strong and stable over a long period of time to cause speciation. Now on to the study!

Killer whales (Orcinus orca) are actually members of the dolphin family (Delphinidae). They are the most widely distributed cetacean species in the world and are top marine predators. Males typically live about 30 years on average, and females about 50 years. The diet of killer whales is often geographic or population specific. Populations of orcas are usually defined as either “residents” or “transients.” As the name suggests, residents tend to stay in a more localized area whereas transients travel over large distances, sometimes overlapping with the ranges of resident populations. It has been documented that these different types of populations vary greatly in their diets, each consuming a narrow range of prey. Residents feed primarily on fish while transients feed nearly exclusively on other marine mammals. Considering this, and what we know of how the niche variation hypothesis cause speciation, have or are killer whales branching in to two species?

One of the problems in answering this question is the long-lived nature of these animals. It’s difficult to see a long-range change on a long-lived species. Most evolutionary studies use either comparisons at a single point in time or over timescales representing one to a few generations. Okay, that’s pretty good, and these snapshots have been very informative, but to get a real-time view in a long-lived species you really need to go small. And by that I mean molecular. Ancient DNA (aDNA) and stable isotope data from subfossil (remains that have not completed the fossilization process) specimens can be used to track niche and evolutionary history. The scientists in this study used these methods to look at the evolution in sympatric killer whale populations in the North Sea. First, they sampled 23 subfossil killer whale bones and teeth recovered by dredging or trawling the Southern Bight of the North Sea or from archaeological sites in Southern Scandinavia. Then they dated their samples using radiocarbon techniques or archaeological context. Next, they used stable isotope ratios to provide a long-term measure of what the animals ate during their lifetimes and thereby estimate the orcas’ niche width (it is argued that populations in wider niches are more variable than populations in narrower niches). Additional evidence of these dietary habits was gathered from examining the wear-patterns on the teeth (for example, feeding heavily on herring badly wears down the teeth). Then mitochondrial DNA (mtDNA) sequencing was used to determine the degree of linage sorting (separate populations carry their genetic diversity with them) based on isotopic (prey) niche. And finally, they biopsied the skin of modern orcas, sampling either while the animals fed on fish or on stranded remains with known stomach contents. From this they were able to extract high-quality DNA and conduct an individual-based analysis of population structure. This, combined with the aDNA data, effectively gave them a map of the evolutionary outcome of niche variation.

This is one of those studies where the results are all variable. *sigh* ‘Tis science. From the isotopic analysis, the researchers found  a lot of overlap in the results, mostly likely explained by among-individual differences. Because this type of analysis represents what an animal ate over its lifetime, differences in prey items within the diets of individuals are not apparent. This and the analysis of tooth wear suggests some overlap either in the diet and/or foraging method of the specimens studied. The result is consistent with the observations of the modern whales. Fish eating pods are often found with mammal remains in their stomach contents. Lineage sorting of mtDNA sequences based on the isotopic values revealed that there “has been multiple diversifications [sic] in isotopic niche” and “an indication there was relatively stable transmission of isotopic niche along matrilineal lines within some clades, in particular those that were dominated by samples from Norway.” The incomplete lineage sorting they found seems to be consistent with relatively recent divergences in niches, and their models indicate panmixia (random mating) between at least some groups that feed on fish and some groups whose diet includes seals.

To sum up, we know that there is niche variation in populations of killer whales. But all of that variation and overlap that the researchers found suggests that any speciation is still at an early stage in this system. And while the results of this study seem to be all over the place, it does add more information to the story while providing a useful long-term evolution study methodology. It also strengths the argument that sympatric speciation is difficult to achieve.

Also check out this great presentation on this study!



Foote, Andrew D., Newton, Jason Newton, Ávila-Arcos, María C., Kampmann, Marie-Louise, Samaniego, Jose A., Post, Klaas, Rosing-Asvid, Aqqalu, Sinding, Mikkel-Holger S., & Gilbert, M. Thomas P. (2013). Tracking niche variation over millennial timescales in sympatric killer whale lineages Proceedings of the Royal Society B, Biological Sciences, 280 (1768) DOI: 10.1098/rspb.2013.1481

Science's article "North Atlantic Killer Whales May Be Branching Into Two Species"

For more information and explanation of some of the evolutionary terms discussed this post see:
Understanding Evolution via Berkeley, particularly the page on sympatric speciation
and for a nice description and examples of niche variation see
Soule, M. and Stewart, B.A. (1970) The "Niche-Variation" Hypothesis: A Test and Alternatives. The American Naturalist, 104(935): 85-97. (LINK)

Some useful resources for information on killer whales:
NOAA Fisheries Office of Protected Resources page on Killer Whales
National Marine Mammal Laboratory's page on Killer Whales
Cascadia Research Collective's "Studying the diet of fish-eating killer whales"


(image via National Geographic, photo credit Gerard Lacz/Animals Animals—Earth Scenes)

They're All Alike: The Giant Squid Conundrum

I wasn’t going to post on another paper this week but then two things happened: I saw the video of the first giant squid filmed in its natural habitat (those scientists get so excited!), and I saw the study about giant squid diversity. I posted the first above and now we'll take a look at the second.

The giant squid (Architeuthis spp.) is one of the largest invertebrates and lives in the deep sea. It was first described as Architeuthis dux in 1857 by Danish naturalist Japetus Steenstrub, but since then, as many as 21 nominal species of Architeuthis have been described. The descriptions of this creature have primarily come from remains found washed up on beaches, found floating on the ocean surface, caught by deep-sea trawling activity, or in the stomachs of sperm whales (Physeter macrocephalus). It wasn’t until 2004 that a live specimen was observed in its natural habitat, and earlier this year that the first video footage was published (although not the in-the-natural-habitat version above). It is estimated that female squid reach a total length of 18m (59ft) and males reach slightly smaller sizes. The giant squid is globally distributed, with the exception of polar regions. They feed primarily on fish and smaller cephalopods. Studies of carbon and nitrogen isotope profiles of the upper beaks suggest ontogenetic diet shift earlier in life (smaller to larger prey items), and carbon isotope composition remains constant in food sources indicating that the squid inhabit relatively small, well-defined and productive areas. The predation of adult squid by sperm whales suggests that squid population size must be large enough to support such a large whale population, although this has never been proven.

There are some rather obvious difficulties in studying giant squid using conventional, observational techniques. So other techniques must be utilized. Enter, DNA. Recent advances in DNA sequencing techniques have made it easier, quicker, and more economical to sequence long stretches of DNA. The role of DNA sequencing is becoming more and more important in phylogenetic and population biology studies. It allows you to assess the number of species, examine the amount of genetic variation, and describe population structure.

In a new paper in the Proceedings of the Royal Society B: Biological Sciences, researchers collected 43 Architeuthis soft tissue samples from the carcasses of dead animals across their known range. They extracted DNA samples from the specimens to analyze the mitochondrial genomes (mitogenomes) and levels of nucleotide variation. They generated mitogeome datasets using several strategies, depending on the quality of the DNA in each sample. I’m not going to go into their sequencing methods – if you are a molecular biologist then you already know them, and if you aren’t then I’ll just bore you. To look at the population level of the genetic variance, they wanted to compare their samples with the fossil record of coleoid cephalopods. This is challenging considering the extremely limited fossil record for these organisms. So they used four different mutation rates to tentatively estimate a time of expansion and upper and lower bounds for the time of divergence of Achiteuthis from other squid families.

They were able to complete 37 complete and 6 partial mitogenome sequences. Remember up at the top of the post where I said “21 nominal species of Architeuthis have been described?” One pretty strong conclusion of this study is that there is only one species of Architeuthis that exists, namely Architeuthis dux (Steenstrub, 1857). The researchers found the haplotype diversity of these giant squid to be high at the mitogenome level, but the level of nucleotide diversity in these sequences was found to be extremely low, with only 181 segregating sites of a 20,331 base pair long sequence. Only the basking shark (Cetorhinus maximus) has a similarly low diversity, which is the result of a recent bottleneck. This diversity for giant squid is much lower than is seen in other squid, 44 times lower than Humboldt squid (Dosidicus gigas) and 7 times lower than the recently restricted population of oval squid (Sepioteuthis lessoniana). The high haplotype to low nucleotide diversity relationship is interesting because it shows that out of a very diverse phyla of animals, the giant squid is the odd one out. Looking at the species across its range, there was no evidence of any phylogeographic structure, which is odd considering the global distribution.

So how do you explain the low genetic diversity in comparison to the global distribution (and potentially large population size)? The authors hypothesize that it could be a low rate of mitochondrial DNA evolution, something that has been observed in other marine organisms. But a low mutation rate does not explain why mitogenome duplications maintain near 100 percent identity. The authors suggest that “perhaps the duplicated sequences form stable secondary structures, which are somehow selectively beneficial, thereby causing mutations to be under negative selection,” which would lead to “a decreased rate of divergence in the duplicated regions relative to the rest of the genome, which does not appear to be the case.” Alternatively, it could be a recent selective sweep such as a bottleneck. Bottlenecks are events that greatly reduce the size of a population, usually resulting in a large reduction in the genetic diversity of that group. If this bottleneck were followed by an expansion in the number of individuals in that population then you would see that low diversity spread amongst a large population. Modeling and analysis of data support the latter hypothesis over the former.

Unfortunately, genetic data alone can’t provide an answer as to why this might have happened. Whatever event it was, climatic or biological, it would have had to been wide ranging enough to affect a global population. Perhaps it was a sudden inflation of a population that was historically smaller. It is known that cephalopods tend to be subdominant predators, and as such, are affected by the changes in population of predators and competitors. If this small size was due to restraints on predators and/or competition and that restraint were released then you would expect such an inflation in squid numbers. Considering the effect of industrialized whaling in the 1700s to late 1800s, this is a likely explanation, but still too recent to explain it entirely. This change in predators and/or competitors could have been the result of climatic effects such as the last ice age changing. Such changes could have altered the abundance and distribution of competitors such as predatory fish. Or perhaps, rather than a bottleneck, A. dux existed historically as a single, small, geographically isolated population that then expanded globally. This expansion would have had to been in a non-ordered fashion with either nomadic adults or dispersing juveniles and small pelagic paralarvae capable of using currents to travel long distances. But if they can disperse really far then why would they have been restricted historically? The authors hypothesize that a global population existed for a considerable time, and that an average of just one individual exchanged between two populations per generation will be enough to prevent genetic differentiation between them. They believe that the wide ranging dispersal of paralarvae and juveniles on the currents of the upper layers of the oceans could achieve this. These young life stages float along with the currents feeding on zooplankton and such until they reach a sufficiently large size, after which they descend to the closest nutrient-rich deep habitat where they remain until maturation.

I think that’s a pretty good explanation. What about you?


Winkelmann, I., Campos, P., Strugnell, J., Cherel, Y., Smith, P., Kubodera, T., Allcock, L., Kampmann, M., Schroeder, H., Guerra, A., Norman, M., Finn, J., Ingrao, D., Clarke, M., & Gilbert, M. (2013). Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species Proceedings of the Royal Society B: Biological Sciences, 280 (1759), 20130273-20130273 DOI: 10.1098/rspb.2013.0273


ScienceNOW article: "Giant Squid Worldwide Are One Species"
ScienceDump: "The search for the giant squid"
Vido via Nature's: "Giant squid filmed in its natural environment"

Snakes, An Origin Story

Quite honestly, I should have been reading a plant paper for my upcoming lab meeting. But then I stumbled across a really cool snake paper and, well, that won out. I regret nothing. As with most people, I will most likely read the plant paper right before the meeting anyway.

A paper published online today in Biology Letters takes a look at the phylogeny of squamate reptiles (lizards and snakes). This group of reptiles is one of the most diverse and well-known vertebrate groups including approximately 9000 species among 61 families. As with many groups, taxonomists and geneticists are trying to reconcile morphology and molecular analysis. This paper is taking the molecular approach, specifically looking at sister groups and interrelationships of major snake clades and iguanian families. Being a well-studied group, molecular analyses have been conducted in the past. These studies have suggested that squamate molecular phylogeny results differ quite a bit from morphological ones. This study takes one gigantic step forward, increasing the sampling of taxa dramatically and doubling the number of genes studied.

The researchers sampled 161 squamate species and 10 outgroup taxa, including mammals (Homo, Mus, Tachyglossus), crocodilians (Alligator, Crocodylus), birds (Dromaius, Gallus), turtles (Chelydra, Podocnemis) and a rhyncocephalian (Sphenodon). Then they sequenced portions of 44 nuclear genes, targeting single-copy genes evolving at appropriate rates. The nucleotide sequences were then translated into amino acids to aid alignment. This alignment consisted of 33,717 base pairs! I’m not going to go into all of the bootstrapping, likelihoods, and Bayesian analyses that were used (even the word Bayesian makes my brain shut down in protest). But suffice it to say that the different analysis techniques that were used yielded similar phylogenies, providing strong support for the relationships found.

The results of this molecular analysis were found to be consistent with other, recent, similar studies. However, there were some interesting relationships discovered. The first of these was that dibamid (legless lizards found in tropical forests) and gekkotans (geckos and the limbless Pygopodidae) are together the sister group to all other squamates. They also found strong support for paraphyly of scolecophidian snakes (blind snakes). Scolecophidians have reduced eyes and are specialized burrowers. Considering these traits, the paraphyly of this group suggests that it is the ancestral form, that other snakes may have been burrowers ancestrally. This makes sense if you compare the morphology of snakes to other burrowing species such as limb-reduced lizards. They both have short tails and elongate trunks. Very good for tunneling their way through the earth.

Overall, a really interesting study that was huge in its scope. I look forward to more of these kinds of studies in the future.


John J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, Jack W. Sites Jr., & Tod W. Reeder (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species Biology Letters, 4 (11) DOI: 10.1098/rsbl.2012.0703

If you are a non-scientist and I used too many biology-jargony words for you or you just need a refresher on phylogeny, then I recommend looking through these sites:
Fullerton’s Biology 261 course page on Interpreting Cladograms
Berkeley’s Understanding Evolution page on reading phylogenetic trees

Here is some more information on blind snakes:
ScienceBlogs article Scolecophidians: seriously strange serpents

Also:
ScienceShot article: Snakes' Slitherin' Subterranean Kin


(images from  Encyclopedia of Life and Neoseeker, respectively)