Thursday, August 7, 2014

New beginnings

After some time away from blogging I have returned with a new website. Please go and read it:

Thursday, August 8, 2013

Science Week - Citizen Marine Science

This morning I went to the launch of Australia's National Science Week. One of the centerpieces of this year's activities is a citizen science project where volunteers will be able to help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the ocean. If you are interested in helping with these two projects all you need to do is visit Explore the Seafloor.
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:
citizen scientists will help map the location of kelp and sea urchin populations and track how these organisms are responding to changes in the oceans. - See more at:

Tuesday, July 23, 2013

Killing whales for science

Australia has taken Japan to the International Court of Justice over Japan's whaling in the Southern Ocean. There is an interesting series of articles on the Conversation that summarise the court case (in chronological order they are here, here, here, here and here). Australia has argued that Japan is in violation of the International Convention for the Regulation of Whaling and also that Japan's whaling is in contrary to their obligations under the Convention on the International Trade of Endangered Species and the Convention on Biological Diversity.

Japan insists that its whaling activities are for scientific research, which is allowed under the rules set out in the Whaling Convention. Australia case will primarily try to establish that the activities are really a commercial harvest in breach of the International Whaling Commission's moratorium. New Zealand, while not bringing a case against Japan, is set to provide evidence in support of Australia's case. 

It's the worst kept secret in the Universe that Japan is actually engaging in commercial whaling, but establishing it legally seems a bit more tricky. The scientific basis for the hunt has repeatedly been criticised for failing to meet the minimum standards required for science. The major concerns are that very little of the data is published in the scientific literature and most of the hypotheses they claim to be testing are already well established or can be tested without killing whales.

The Institute of Cetacean Research (ICR) is the organisation the undertakes the supposed scientific research involving the lethal sampling of whales. The International Fund for Animal Welfare (IFAW) has recently estimated that the Japanese Government has provided 387 million dollars to the ICR since scientific whaling began in 1988. Since then the ICR has published 150 papers in the literature (according to Web of Science), which is extremely poor output for the amount of money put in (2.58 million per paper!). It is, in fact, poor output had they only received 1% of the IFAW figure.

Another thing to consider is that the 150 published papers are not all on whales and those that are often do not require that the whales be killed to collect the data. Only a tiny minority of the ICR papers present data the require the death of whales and the 387 million dollars has been provided specifically to support the killing of whales. No funding agency would normally continue to provide funding for a research program that has so utterly failed to produce valuable science.

The ICR has stated on several occasions that the output would be better if they didn't have to contend with the Sea Shepherd activists because they prevent adequate sample sizes being taken. Despite these claims the sample size is clearly more than high enough to do some interesting science. In a brief literature search*, I found four papers published since January 2012 that required a total of 37 dead whales. In the same period, the ICR has killed 170 whales in the Southern Ocean alone (notably the lowest two catches since its whaling began) and published just one study in a low quality journal.

It is a hard problem to define exactly what constitutes science. Japan has argued that the International Court for Justice "is a court of law, not of scientific truth", claiming that the Court doesn't have the jurisdiction to determine what constitutes science. But, I think this misses the point. The Court is not being asked to define what constitutes science, but whether the research program is legitimate under the Whaling Convention or veiled commercial whaling. That veil is pretty thin in my opinion and I hope the Court sees it that way too.

*The papers I looked at in the literature search were:
1) Ford T. J., Werth A. J. & George J. C. (2013)
An Intraoral Thermoregulatory Organ in the Bowhead Whale (Balaena mysticetus), the Corpus Cavernosum Maxillaris.
The Anatomical Record 296, 701–708 doi:10.1002/ar.22681

2) Werth A. J. (2013)
Flow-dependent porosity and other biomechanical properties of mysticete baleen.
The Journal of Experimental Biology 216, 1152-1159 doi:10.1242/jeb.078931

3) Pyenson N. D., Goldbogen J. A., Vogl A. W., Szathmary G., Drake R. L. & Shadwick R. E. (2012)
Discovery of a sensory organ that coordinates lunge feeding in rorqual whales.
Nature 485, 498–501 doi:10.1038/nature11135

4) Yamato M., Ketten D. R., Arruda J., Cramer S. & Moore K. (2012)
The Auditory Anatomy of the Minke Whale (Balaenoptera acutorostrata): A Potential Fatty Sound Reception Pathway in a Baleen Whale.
The Anatomical Record 295, 991–998 doi:10.1002/ar.22459

Friday, July 12, 2013

Squid family planning

ResearchBlogging.orgFemale southern bottletail squid may be able to influence the paternity and quality of their offspring by eating the sperm of males. This behaviour is likely to be the result of the conflict that arises between males and females because of their competing evolutionary interests in reproduction. Both sexes use a variety of tactics to manipulate the outcome of mating into their favour. In southern bottletail squid, Sepiadarium austrinum, males use aggression to coerce females into copulations that they might otherwise avoid. 

A new paper from Ben Wegener, Devi Stuart-Fox, Mark Norman and Bob Wong shows that males don’t have it all their own way. Mating occurs head-to-head and is initiated by the male who lunges at the female and grasps her in his tentacles. The male then transfers packets of sperm, called spermatophores, to the female by sticking them into a cavity just below her mouth where they can survive for up to three weeks. But, the spermatophores often have shorter lives because the females will remove and eat them, sometimes before the male has finished copulating with her.

The authors also determined how females were using the nutrients gained from eating the spermatophores. They fed a group of spermatophore-depleted males on a diet laced with a radioactive marker, which was incorporated into new spermatophores as they produced them. Once the females had eaten the radiolabeled spermatophores it was possible to find where the nutrients were being used by assaying for the marker in tissue samples. 

Levels of the marker were elevated in a number of tissues, including the eggs and reproductive glands. Females, therefore, benefit from consuming spermatophores by gaining some additional nutrition that can be allocated to producing offspring. It’s also possible that spermatophore consumption is a form of cryptic female choice, where the spermatophores of low quality males are eaten preferentially. But, this remains to be demonstrated.

This story is also published on the Australasian Evolution Society website in the Research Highlights section.

Wegener, B. J., Stuart-Fox, D., Norman, M. D., & Wong, B. B. M. (2013). Spermatophore consumption in a cephalopod Biology Letters, 9 (4) DOI: 10.1098/rsbl.2013.0192

Monday, June 10, 2013

Living fossils can evolve quickly

ResearchBlogging.orgThe evolution of living fossils is not unusual. The odd thing about them is that they have ancient origins and are, today, not very diverse groups. Sturgeon are ray-finned fishes in the family Acipenseridae, which are known from almost 200 million year old fossils. Fossils that are recognisably similar to modern sturgeons appear about 100 million years ago. There are 23 (but maybe a few more) modern species in the Acipenseridae, which is probably fairly similar to their historical diversity.

A sturgeon in the genus Acipenser, possibly A. transmontanus (image Wikipedia).
Other families of fish are much more diverse than the Acipenseridae. Some of the most beautiful marine fish are in the families Gobiidae (gobies) and Labridae (wrasses), with over 2,000 and 600 species respectively. And they aren't even the largest families of fish. That honour probably goes to the Cyprinidae (carps and minnows) with over 2,400 species. This pattern raises an interesting question; why are some groups highly diverse while others are not?

The old glory goby, Amblygobius rainfordi (top), the Yellowtail coris wrasse, Coris gaimard, being cleaned by a cleaner wrasse, Labroides phthirophagus (middle), and the cleaning goby, Elacatinus evelynae (bottom). Notice the convergent colour evolution in the cleaner fishes (all images Wikipedia).
One hypothesis is that some groups are more 'evolvable'. These groups are able to change their morphology relatively quickly and are consequently able to form more new species. For this hypothesis to be true, we should see a correlation between the amount of phenotypic change within a group and the amount of speciation. Studies that have looked at this relationship within lineages have failed to detect it.

A new paper by Rabosky and others argues that a fairer test of the hypothesis is to look at the relationship among lineages. They constructed an enormous evolutionary tree containing almost 8,000 species from across the entire spectrum of diversity of ray-finned fishes. They used body size evolution as a proxy for phenotypic change and found overwhelming support for the hypothesis; families with greater diversity in body size typically contained a greater number of species.

One group to buck this trend were the sturgeons. The rate of change in body size in sturgeons is amongst the fastest for all fishes. The baluga, Huso huso, is one of the largest ray-finned fishes, growing to over five and a half meters and 1,000 kilograms, while the dwarf sturgeon, Pseudoscaphirhynchus hermanni, grows to just 27 cm and 50 grams. This considerable difference in body size has arisen almost 5.4 times more rapidly than expected and only five of the 172 families in the analysis diverged faster.

These results are in complete contrast to the popular conception of living fossils as slow changing evolutionary oddballs. Indeed, in this analysis sturgeon are outliers because of the speed of their evolution. Clearly some traits in sturgeon are highly conserved over large periods of time, but we should not assume that this means that all of their traits are highly conserved. Living fossils are evolving and can diverge rapidly.

I've also written about living fossils here and here.

Rabosky, D., Santini, F., Eastman, J., Smith, S., Sidlauskas, B., Chang, J., & Alfaro, M. (2013). Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation Nature Communications, 4 DOI: 10.1038/ncomms2958

Friday, June 7, 2013

World Oceans Day

Tomorrow is World Oceans Day, but today you can get a live stream from the Great Barrier Reef. Expert marine biologists are apparently on hand (I can't load the website) to answer your questions and you can even talk to SCUBA divers on the Reef. Check you social media too because it'll be on Twitter, G+ and YouTube.

Wednesday, May 29, 2013

Worm sperm

ResearchBlogging.orgYou may have never thought about what feature distinguishes males from females. After all, in mammals the differences are often clear to us. In other groups too, the differences between male and female traits are often conspicuous. But, there are many species where male and female reproductive organs are both present in the same individual. Even in these species we can tell male parts from female parts.

To distinguish male from female we look at the relative size of the sex cells or gametes. Males produce the smaller gametes (e.g. sperm) and females produce the larger gametes (e.g. eggs). This difference in the size of the gametes is known as anisogamy, which essentially means without ("an") the same ("iso") gametes ("gamy"). 

The converse of anisogamy is isogamy. Species that are isogamous are very rare now, but this is thought to be the ancestral condition. As in anisogamous species where fertilisation only occurs when egg and sperm meet, fertilisation cannot occur in isogamous species unless the gametes of two different mating types meet. In isogamous species mating types are are referred to by various names, such as "+" and "-", in place of male and female.

The origins of anisogamy are unclear, but we have a pretty good explanation for why it evolved. Each gamete an individual produces costs energy and it must be stocked with additional reserves so that the zygote can complete development and start acquiring it's own energy. In isogamy, each member of a pair contributes half the energy to produce a viable offspring. In anisogamy, the cost is overwhelmingly paid by one of the mating types.

Investing almost nothing in individual gametes comes with a huge advantage, vastly more gametes can be produced increasing the number of offspring you can potentially produce. The more gametes an individual has the more fertilisations and individual can potentially achieve. Once one mating type gets far enough down the path of small gametes, its pair can't follow because that is likely to result in a zygote that doesn't have enough resources to survive.

It is relatively clear that fertilisation success has driven the evolution of males that produce more, small sperm. However, there are other aspects of sperm size and shape that appear to contribute to fertilisation success and these are surprisingly variable among and within species. Clear demonstrations that differences in sperm characteristics affect fertilisation success are rare, which makes a new paper in Evolution particularly interesting. 

Darren Johnson of the National Centre for Ecological Analysis and Synthesis, with Keyne Monro and Dustin Marshall of UQ (now both at Monash) looked at sperm traits in the broadcast spawning tubeworm, Galeolaria gemineoa. These worms can occur individually or in huge aggregations, leading to substantial variation in the concentrations of sperm and eggs in the wild. Because they don't leave their tubes, their options for increasing fertilisation success are limited relative to mobile species.

A colony of Galeolaria caespitosa, which are nearly identical to G. gemineoa (photo D. Semmens).
Groups of eggs from multiple females were exposed to the sperm of a single male at six different concentrations and two different ages. Fertilisation success was measured at the proportion of eggs that were undergoing normal development within each treatment. This is not a direct measure of fertilisation success because some embryos may have died very early due to genetic incompatibilities rather than the absence of fertilisation. However, it is a reasonable and practical proxy.

At high sperm concentrations, males that produced sperm with longer average tail length and smaller average head size achieved greater fertilisation success. In contrast, males that produced sperm with longer than average heads were favored at low sperm concentrations and older age. The results suggest that variation in sperm size and shape within a species may be preserved because different fertilisation environments favor contrasting sperm characteristics. 

The logistics of genetically assigning paternity prevented the authors from varying sperm competition environments. Had the sperm of multiple males been in competition to fertilise the eggs, different traits or trait combinations could have been favoured. While it is probably more realistic to pit the sperm of several males against each other, single male experiments still provide useful insights into selection on sperm traits.

An abbreviated version of this post also appears in the Research Highlights on the Australasian Evolution Society website.


Johnson, D., Monro, K., & Marshall, D. (2013). The maintenance of sperm variability: Context-dependent selection on sperm morphology in a broadcast spawning invertebrate Evolution, 67 (5), 1383-1395 DOI: 10.1111/evo.12022

Sunday, May 26, 2013


The Deep Submergence Vehicle Alvin is the best known marine research vessel. It was commissioned by the United States Navy in 1964, but it calls Woods Hole Oceanographic Institution home. For its 49th birthday, it's received a refit that will increase its dive range by two kilometers and give the people inside more room and greater vision. Unfortunately, due to the limitations of its batteries, Alvin won't be able to reach its rated depth for another few years. Lithium-ion batteries are considered to be too great a fire risk at the moment.

Alvin returning to the surface carrying samples (photo Wikipedia)
Alvin sprang to fame in 1977 when scientists inside it made the first observations of hydrothermal vent communities off the Galapagos Islands. These were the first communities of multicellular organisms ever discovered that were able to survive in isolation from the sun. To marine biologists, the discovery of hydrothermal vent communities was more exciting than the moon landings less than a decade earlier. And it was Alvin, like Apollo 11, that made it possible. Unlike Apollo 11, Alvin continues to make discoveries and has contributed more to marine science than any other vehicle.

Thursday, May 9, 2013

Living fossils are evolving

ResearchBlogging.orgCharles Darwin coined the term living fossil in On the Origin of Species. He didn’t use it the same way that it has come to be used. He suggested that living fossils are modern species that can be used to link to groups in the same way that fossils can. One of the examples he gave was the platypus, which lactates and lays eggs, which is evidence that mammals and reptiles share a common ancestor. I don't think he meant it to mean an unchanged relict, as some people interpret his words.

Today, a living fossil is a species that retains many features of their fossil ancestor so that it is recognisably closely related. There are some stunning examples of this, such as orb-weaving spiders. In 2011 a 165 million year old spider fossil was described by Seldon et al., which shared so many features with modern Nephila spiders that it was placed within the same genus. Interestingly, I have never heard of web building spiders being referred to as living fossils despite there being amazing conservation of traits in many groups.

The orb-weaving spiders Nephila clavipes (left) and N. jurassica (right) are separated by 165 million years, but placed within the same genus (image of N. clavipes from Wikipedia and N. jurassica from Seldon et al. 2011).
Unfortunately, living fossil has become synonymous with a species, or group of species, displaying no evolutionary change or very slow change. This is completely wrong. Although the conservation of morphology in Nephila is remarkable, there are more than 150 known species in the genus. Clearly there has been evolutionary diversification within the group. Indeed, whenever living fossils are examined in more than superficial detail it becomes difficult to see them as organisms that evolution forgot.

Horseshoe crabs are one of the most iconic living fossils. There are four living species in three genera. They are placed within the subphylum chelicerata, which makes them more closely related to spiders and scorpions than they are to true crabs, which are placed within the subphylum crustacea. Although there are fewer species of horseshoe crabs than Nephila, that fact that there are four species that are all different from fossil species is a strong indication that evolution hasn't stopped for them.

The Atlantic horseshoe crab, Limulus polyphemus, mating (photo Wikipedia)
The general shape of modern horseshoe crabs is strikingly similar to the fossils that date from about 450 million years ago. Close examination, though, shows that parts of their shape, their legs in particular, have changed over time. Briggs et al. 2012 looked at a fossil horseshoe crab from 425 million years ago, which is relatively early in their evolution. They found that modern horseshoe crabs are missing an entire set of limbs that were present in their ancestors.

All modern chelicerates, including living horseshoe crabs, have unbranched limbs; each limb is a single series of segments. Most crustaceans have limbs that branch at the base into two series of segments. Branched limbs, like those in crustaceans, are the ancestral condition and unbranched limbs are thought to have evolved several times among the arthropods. Indeed, Briggs et al. found that the fossil horseshoe crab had branched limbs, which have been lost in their descendents. 

Like horseshoe crabs, tadpole shrimp have a broad semi-circular carapace protecting their heads and are considered living fossils. There are 11 recognised species in two genera, Lepidurus and Triops. The two genera probably diverged about 180 million years ago, but there are fossil tadpole shrimp dating from about 250 million years ago. That's not as long as the really iconic living fossils, like horseshoe crabs and the coelacanths, but it is still an impressive amount of time to retain enough features to be easily recognised as related.

The tadpole shrimp, Lepidurus apus (photo Wikipedia)
The problem with relying on features that preserve in the fossil record is that it underestimates the actual amount of evolutionary change because generally only hard parts are preserved. A recent study of tadpole shrimp highlights this point. Mathers et al. 2013 used genetic analyses to construct the evolutionary relationships among the 11 species of tadpole shrimp. They found that there are actually 38 species and that these species arose relatively recently. This shows that rather than evolutionary stasis, there is likely to be high species turnover in the group.

There are many reasons why some features may be conserved over long periods of time. None of these have to do with natural selection taking a break. In fact, if natural selection did cease we should expect to see features wander under random genetic drift, as has been hypothesised for eyes in cave dwelling animals. Conserved features are much more likely to be the result of developmental constraints or stabilising selection.


Briggs, D., Siveter, D., Siveter, D., Sutton, M., Garwood, R., & Legg, D. (2012). Silurian horseshoe crab illuminates the evolution of arthropod limbs Proceedings of the National Academy of Sciences, 109 (39), 15702-15705 DOI: 10.1073/pnas.1205875109 

Mathers, T., Hammond, R., Jenner, R., Hänfling, B., & Gómez, A. (2013). Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’ PeerJ, 1 DOI: 10.7717/peerj.62

Selden, P., Shih, C., & Ren, D. (2011). A golden orb-weaver spider (Araneae: Nephilidae: Nephila) from the Middle Jurassic of China Biology Letters, 7 (5), 775-778 DOI: 10.1098/rsbl.2011.0228

Monday, April 29, 2013

The aquatic ape hypothesis is still wrong

An article in the Guardian says that at a conference next week, David Attenborough will voice his support for the aquatic ape hypothesis. I grew up watching Attenborough documentaries. I am a huge fan and would credit him with helping to ferment my interest in biology. But, I am no fan of the aquatic ape hypothesis because it  is adaptationist and fails to provide parsimonious explanation for human evolution.

The aquatic ape hypothesis tries to force large number of human traits together under one umbrella explanation, that our ancestors had a close association with water. But no time period in the history of our evolution is specified and the fossil record shows that the traits claimed to have evolved in association with water appeared at widely different times. Without good fossil evidence demonstrating a strong association with water the hypothesis is dead... in the water.

The hypothesis is driving the evidence presented, not the other way around as it should be in science. A mish-mash of highly derived and rudimentary adaptations to water are used as evidence. Few of these are consistently associated with aquatic animals, such as hairlessness, which is present in several terrestrial mammals and absent in the majority of aquatic mammals. There are also a number of features that we humans have that are inconsistent with aquatic ancestry, such as internal testicles. 

I am at a loss to explain how the aquatic ape hypothesis keeps getting coverage in popular press given how weak it is as an explanation. I get that human evolution is interesting, but it is such a bad explanation on the basis of both evidence and the methodology of its proponents. It's the phlogiston of explanations for the evolution of human traits. Fortunately, the recent coverage has spawned some well deserved ridicule, which has had a strong response on Twitter.