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.

Saturday, April 27, 2013

Cooperative hunting between species

Cooperative hunting among individuals of the same species is common. But, cooperative hunting between different species is incredibly rare. Ed Yong has an interesting story on cooperative hunting between moray eels and grouper. Although this behaviour was first documented in 2006, there is a new study that describes a previously undocumented behaviour that the grouper uses to recruit its hunting partners.

Thursday, April 18, 2013

Why fund science research?

It's an easy question to answer. Science is economically and culturally important. 

As Phil Plait discusses on Bad Astronomy, Stephen Moore of the Wall Street Journal says that we shouldn't fund basic research because it is innovation in industry that brings the economic returns. That is nonsense. Industry innovation would come to a shuddering halt without basic research. It's curiosity-driven research that provides the fuel that industry uses to produce new products.

Funding science provides more than a return on investment. It's also about understanding the natural world. The Universe is a fascinating place and we humans (with exceptions like Stephen Moore) are deeply interested in finding out about it. To me, the accumulation of knowledge should be viewed as the primary goal of science. Commercialisation of that knowledge is just a welcome side effect.

Monday, April 15, 2013

The resilience of coral reefs

ResearchBlogging.orgMany people are justifiably concerned with the potential impacts of climate change and ocean acidification on coral reefs. But, coral reefs have been declining for at least the last 25 years and probably much longer, overwhelmingly due to threats that are unrelated to climate change. If we do not address these impacts we will continue to lose coral cover and reefs will be more vulnerable to climate change and ocean acidification.

A coral outcrop on the Great Barrier Reef (photo Wikipedia)
A new paper serves as an illustration of how resilient coral reefs are to climate impacts when they are isolated from other anthropogenic impacts, such as overfishing and agricultural runoff. James Gilmour and other researchers from the Australian Institute of Marine Science and some from the Centre of Excellence for Coral Reef Studies followed the recovery of the Scott Reef system after a catastrophic bleaching event in 1998 that reduced coral cover from 50% to 10%. There was great concern for the reef system because it was isolated from other reefs that could supply coral larvae to fuel recovery.

The Scott Reef system. The crescent shaped reef at the bottom is Scott Reef South, the small reef above the left arm of the crescent is Scott Reef and the pear shaped reef is Scott Reef North (photo Wikipedia).
It turns out that, on balance, the isolation was a good thing. The supply of coral larvae reaching the reef was less than 6% of what it was prior to the bleaching event for six years. But, the reef was also isolated from chronic anthropogenic pressures, particularly overfishing. The number of herbivorous fish was already high at the time of the bleaching and jumped afterwards. As coral cover increased the numbers of herbivorous fish declined back to what they were prior to the bleaching.

The daisy parrotfish, Chlorurus sordidus, is an important herbivore on coral reefs (photo Dennis Polack, EOL).
The herbivorous fish kept seaweed and other organisms that compete with coral from taking over. Remnant corals that survived the bleaching were able to grow quickly and the small numbers of coral larvae reaching the reef had unexpectedly high survival. The fast growth of existing coral drove the initial recovery of the reef. Once young corals became established and began reproducing the supply of larvae increased and the recovery of coral cover accelerated.

Ten years after the bleaching event the supply of coral larvae had returned to the levels seen before the bleaching. Two years later the amount of coral cover and community structure on the reef had largely been restored. The rate of recovery is made more remarkable by the occurrence of a second more moderate bleaching event, two cyclones and a disease outbreak.

The study highlights just how resilient coral reefs can be to the effects of climate change and other disturbances if chronic anthropogenic stress is low. Overfishing, sedimentation and pollution are causing severe declines in coral cover right now. If we can control these threats, coral reefs might be able to survive in a warmer, more acidic ocean.

Gilmour, J., Smith, L., Heyward, A., Baird, A., & Pratchett, M. (2013). Recovery of an Isolated Coral Reef System Following Severe Disturbance Science, 340 (6128), 69-71 DOI: 10.1126/science.1232310

Friday, April 12, 2013

In the cave of the blind, the no-eyed crab is king

ResearchBlogging.orgCave dwelling creatures are often blind. The prevailing view is that, in such species, mutations in the visual system have little or no effect on fitness and vision is lost as these mutations gradually accumulate. There are several other types of characters that we can be reasonably confident are adaptations to life in caves, such as elaboration of structures for touch or smell. However, it is often hard identify which population cave adapted species are descended from and, therefore, how long ago they invaded caves. Without this information it has been hard to test ideas about the evolution of traits associated with life in the dark.

A cave form of the fish, Astyanax mexicanus, which is eyeless and unpigmented, traits typical in caves. It is a commonly used model species in studies of adaptation to cave environments (photo Wikimedia Commons).
Sebastian Klaus and colleagues from the National University of Singapore and Goethe University examined five species of freshwater crab in the genus Sundathelphusa, which occur on Bohol Island in the Philippines. Four species are only found in caves and the other has established several populations in caves. The repeated invasion of caves by the crabs has led to varying degrees of adaptation to life in the dark within the group. 
Freshwater crabs in the genus Sundathelphusa from Bohol Island. Thy are arranged from least cave adapted (top) to most cave adapted (bottom). From top to bottom the species are Sundathelphusa boex, S. vedeniki, S. urichi, S. sottoae and S. cavernicola (from Klaus et al. 2013).
The team used genetic data to estimate the time at which each species and population last shared a common ancestor. They then compared several features of cave-adapted crabs with their closest terrestrial relatives. Reductions in the visual system were just as pronounced as changes in cave-adapted features, indicating that evolution occurs at similar rates. The authors argue that this is a clear sign that eye loss is under directional selection because changes should appear more slowly if they are a result of selectively neutral mutations. 
They don’t speculate at all about what might favour eye-loss in the Bohol crabs, but hint in the introduction that it could be due to trade-offs between vision and other sensory systems. Trade-offs occur where increasing one aspect of fitness necessarily requires the reduction of fitness in another. If eyes are energetically costly to build and maintain then retaining functional eyes might prevent greater investment in other senses. Trade-offs are ubiquitous in biology and have been implicated in the loss of eyes in other cave dwelling species.
While I was doing research on this study I came across several creationist websites that argue cave adapted creatures are strong evidence that evolution is false because a trait is lost. According to them this shows evolution progressing in the wrong direction to what is predicted. They argue that evolution should progress towards more information and greater complexity. This is incorrect and shows, yet again, that creationists typically have a poor understanding of evolutionary theory.
The 'logic' of this argument is similar to the idea of a "Great Chain of Being", which pervaded early thinking about biology. This type of thinking is where we get several antiquated, but persistent terms, such as "missing link" and "highly evolved". It continues to dog evolution in the way that evolutionary information is often presented, such as the placement of organisms more closely related to us at the right or top of phylogenetic trees and at the end of textbooks.
The phylogeny of primates with humans at the top and less related groups at the bottom (from Wikipedia).
Linear descent was never part of Darwin's theory, nor was an increase in information ever a necessary assumption on which evolutionary theory rests. When you look at an evolutionary tree (like the primate tree above), all of the living species at the branch tips have an equally long evolutionary history. They are not descended from each other, they are descended from a common ancestor. You could say that they are equally evolved.

The first evolutionary tree drawn by Darwin over 20 years before the publication of On the Origin of Species.
Evolution doesn't prevent information from increasing, but contrary to the creationist claims it does predict that there will be strong limits on it. Both single trait and multi-trait trade-offs are thought to prevent organisms from becoming perfectly adapted. Single trait trade-offs occur where elaboration of a structure increases fitness in one environment, but reduces it in others. Multi-trait trade-offs occur where two or more structures are dependent on a shared finite resource.

Blind crabs are not evolving in the wrong direction. There is no wrong direction, they're just evolving under the constraint of trade-offs. Eye reduction and loss of pigmentation are not the only evolutionary changes that are occurring either. Other traits are becoming more elaborated, such as the length of their legs and the hairs on their claws, suggesting a multi-trait trade-off. This result is not only consistent with evolutionary theory, but expected.

An abbreviated version of this post is published on the Australasian Evolution Society website in the Research Highlights section.

Klaus, S., Mendoza, J., Liew, J., Plath, M., Meier, R., & Yeo, D. (2013). Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs Biology Letters, 9 (2), 20121098-20121098 DOI: 10.1098/rsbl.2012.1098

Sunday, April 7, 2013

Research Highlights from the Australasian Evolution Society

I have been asked by the Australasian Evolution Society to provide some 'Research Highlights' for their newly launched website. The Research Highlights promote interesting recent research by evolutionary biologists in Australasia. To get more diversity in the types of research covered there will be two or three others writing too. My stories will go up every few weeks and I will endeavor to publish them here as well, probably with some additional comments. My first piece went up a few weeks ago and I've submitted my second, which should go up shortly. I'll post here as soon as it is.

Wednesday, April 3, 2013

My favourite science books

I've been talking to a few people recently about good science books. My favorite books that deal with similar topics to this blog are in descending order:

Mapping the deep - Robert Kunzig
The World without us - Alan Weisman
The wavewatcher's companion - Gavin Pretor-Pinney
Trilobite - Richard Fortey
At the water's edge - Carl Zimmer

Books outside the topic area of this blog that I found to be excellent are:

The demon-haunted world - Carl Sagan
The elegant universe - Brian Breene
Chaos - James Gleick

Neil Shubin's "Your inner fish" is sitting on my bookshelf just waiting to be read. I hear it is very good and will probably make it onto my list. Several books by Dawkins and Gould are also among my favorites, but I liked them less than the ones above. The ancestor's tale (Dawkins) and Wonderful life (Gould) are probably the best I've read of their books.

Monday, April 1, 2013

China's thirst for development

China is noted for its rapid development often at severe cost to the environment. The Australian newspaper reports that more than half of the rivers in China are missing. In the 1990s there were over 50,000 rivers on maps of China, but in a recent national water census surveyors were only able to locate 22,909 of them. Destruction of the environment due to rapid development and the unsustainable use of underground water supplies are thought to be among the main culprits. The government though, is blaming climate change and cartographers mistakes for the missing rivers.

Thursday, March 28, 2013

Are there really plenty of fish in the sea?

ResearchBlogging.orgWe started trying to manage fisheries using science-based principles more than 150 years ago. Today, despite great improvements, we are still struggling to manage fisheries well. Perhaps the greatest missing piece in our understanding is an ability to accurately link the number of spawning adult fish with the number of their offspring that survive to replenish the population. Recognition that individual differences play a role in the dynamics of natural populations promises to greatly improve fisheries management.

A classic example of our inability to effectively manage harvested fish populations is the collapse of the northwest Atlantic cod fishery. Despite being managed using best practices, in 1992 the number of cod had collapsed to less than 1% of the number present in 1977. A moratorium was declared to allow the fishery to recover. It was predicted to rebound within a decade, but twenty years on and cod stocks are still at less than 5% of their previous levels and some authorities suggest the fishery may never fully recover.

An Atlantic cod, Gadus morhua (photo Wikipedia).
Most fishes are highly fecund, releasing tens to hundreds of thousands or even millions of eggs. Mortality during the early life of fish is incredibly high, often with fewer than one in a thousand surviving the first few days. But, because of the shear number of offspring, small changes in the mortality rate can lead to enormous differences in the number of fish that survive to replenish the population. The great difficulty has been to determine which factors contribute to changes in mortality rate.

Predation and starvation are the two greatest sources of mortality for fish eggs and larvae. Neither of these is random. Bigger, better provisioned eggs are more likely to produce larvae that survive the larval period and replenish the adult population. There are also characteristics of the parents that effect the survival of their offspring, such as when and where they choose to spawn, and how big or old they are.

Predators of fish eggs and larvae are numerous. Jellyfish, like Aurelia aurita, are among them (photo Wikipedia).
Early hypotheses about what regulated survival in the larval period focused on starvation. Hjort's 'critical period' hypothesis (1914) proposed that food resources must be present when larval fish were switching from using their yolk reserves to feeding. Cushing's 'match-mismatch' hypothesis (1975, 1990) recognised that as larvae grow they need progressively larger prey and timing of prey requirement needs to be a match with the timing of prey availability.

Good evidence to support these hypotheses has only emerged recently, with the arrival of technology that can provide long-term measurements over large spatial scales. Platt et al. (2003) combined data from remote-sensing satellites with long-term population surveys of haddock, Melanogrammus aeglefinus. Their data showed that when the peak of spawning occurred after the peak in the spring plankton bloom, survival of larval haddock was much higher.

A haddock, Melanogrammus aeglefinus (photo Wikipedia).
Beaugrand et al. (2003) used data from continuous plankton sampling devices that are opportunistically attached to merchant ships. The devices gave them not only plankton abundance data, but allowed them to measure the size of prey species. Data on cod, Gadus morhua, were obtained from two largely overlapping population surveys. Like Platt et al., they found that the timing of the plankton bloom was important for larval survival, but they also found that the abundance and average size of prey species were important too.

Predation was recognised early on as an important factor influencing the survival of fish larvae. However, research into its effects on fish populations didn't begin in earnest until the 1970's. The research showed that bigger, faster growing larvae were more likely to survive that larval period. Several, subtly different mechanisms were proposed to explain this pattern and are often combined into the 'growth-predation' hypothesis. 

Testing the growth-predation hypothesis in the wild has proved tricky. But, fish have structures in their ears called otoliths that lay down growth rings a bit like the growth rings in a tree. Because the growth rings in otoliths are laid down daily in many fish species they can be used as proxy measurements of size and growth. Several studies have used otoliths to calculate size and growth rates and have universally supported the growth-predation hypothesis (e.g. Hare & Cowen 1997, Meekan et al. 2006).

The otolith of a black rockfish, Sebastes melanops, showing the light and dark bands of yearly growth increments. Smaller daily increments are visible under higher magnifications (photo Vanessa von Biela, USGS).
Mothers are one of the most important influences on the size and growth rate of larval fish, particularly early in life when mortality is highest. The time that mothers spawn determines the match between hatching and the availability of food resources. The amount that mothers invest in their offspring also influences their survival. Bigger eggs typically hatch into bigger larvae that grow faster and are more resistant to starvation Spawning time and investment can depend on the characteristics of mothers.

It's widely documented that larger, older mothers produce more offspring. Fecundity typically increases with the volume of the body cavity, which is roughly proportional to the cube of female length. Berkeley et al. (2004) also showed that larger, older female black rockfish, Sebastes melanops, invested more into their offspring, resulting in faster growing larvae that were more resistant to starvation. 

The blue rockfish, Sebastes mystinus, looks similar to the black rockfish (photo Wikipedia)
The Berkeley et al. paper became frequently cited to make the case that larger, older females needed better protection (e.g. Palumbi 2004, Birkeland & Dayton 2005). Harvesting large females might be much worse for the population because they produce more offspring that have a greater chance of surviving the larval period. Most fisheries remove the larger, older individuals, even when they are not targeted, which might explain why collapsed stocks struggle to recover faster than expected, like the Atlantic cod.

Marshall et al. (2010) argued that it was unjustified to conclude that larger females produce larvae that greater chance of survival. Decades of empirical and theoretical work has shown that the only time mothers should produce larger eggs is when they are releasing offspring into a poorer quality environment. Berkeley et al. tested larvae in common conditions and, therefore, they didn't expose larvae to the conditions that they would have experienced in the wild. 

Larger mothers might provide their offspring with a poorer quality environment in a number of ways. They might expose their offspring to greater competition with their siblings because they release far more larvae. Female size can predict the timing of spawning, and does in the black rockfish, which exposes larvae to different environmental conditions. Therefore, the larger offspring produced by larger mothers might have similar chances of surviving the larval period under natural conditions.

There is some evidence that the decades of theoretical and empirical work might not have captured the whole picture. If all larvae have roughly the same chance of making it through the larval period you would expect that the diversity of surviving larvae would be roughly proportional to the numbers released. Hedgecock et al (2007) estimated that in one cohort of the Pacific oyster, Ostrea edulis, only 10 - 20 individuals produced all of the surviving offspring.

Beldade et al. (2012) conducted a similar study to Hedgecock et al., but they were able to link surviving larvae with adults. They found that larger mothers contributed disproportionally more to the number of larvae that returned to the same population and that greater fecundity alone did not account for the disparity. It's not entirely compelling because it is possible that smaller mothers are producing larvae that preferentially disperse away. It is a tantalizing hint that larger, older mothers really matter more for population replenishment.

Most fisheries models currently do not account for the differences in the survival chances of larvae or the potential differences in the contribution of mothers to the next generation. They treat the survival of all larvae as equally likely, or ignore the larval period altogether. Such models are failing to produce accurate predictions of future stock numbers. Greater understanding of mortality processes in the larval period and the rise of individual based models promise to greatly improve the way fisheries are managed.

Beaugrand, G., Brander, K., Alistair Lindley, J., Souissi, S., & Reid, P. (2003). Plankton effect on cod recruitment in the North Sea. Nature, 426 (6967), 661-664 DOI: 10.1038/nature02164

Beldade, R., Holbrook, S., Schmitt, R., Planes, S., Malone, D., & Bernardi, G. (2012). Larger female fish contribute disproportionately more to self-replenishment. Proceedings of the Royal Society B: Biological Sciences, 279 (1736), 2116-2121 DOI: 10.1098/rspb.2011.2433

Berkeley, S., Chapman, C., & Sogard, S. (2004). Maternal age as a determininant of larval growth and survival in a marine fish, Sebastes melanops. Ecology, 85 (5), 1258-1264 DOI: 10.1890/03-0706

Cushing, D. (1969). The Regularity of the Spawning Season of Some Fishes. ICES Journal of Marine Science, 33 (1), 81-92 DOI: 10.1093/icesjms/33.1.81  

Cushing, D. H. (1990). Plankton production and year-class strength in fish populations - an update of the match mismatch hypothesis. Advances in Marine Biology, 26, 249-293 DOI: 10.1016/S0065-2881(08)60202-3  

Hare, J., & Cowen, R. (1997). Size, Growth, Development, and Survival of the Planktonic Larvae of Pomatomus saltatrix (Pisces: Pomatomidae). Ecology, 78 (8) DOI: 10.2307/2265903

Hedgecock, D., Launey, S., Pudovkin, A., Naciri, Y., Lapègue, S., & Bonhomme, F. (2006). Small effective number of parents (N-b) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Marine Biology, 150 (6), 1173-1182 DOI: 10.1007/s00227-006-0441-y

Hjort, J (1914). Fluctuations in the great fisheries of northern Europe viewed in the light of biological research. Reun. Cons. Int. Explor. Mer, 20, 1-228

Marshall, D., Heppell, S., Munch, S., & Warner, R. (2010). The relationship between maternal phenotype and offspring quality: Do older mothers really produce the best offspring? Ecology, 91 (10), 2862-2873 DOI: 10.1890/09-0156.1   

Meekan, M., Vigliola, L., Hansen, A., Doherty, P., Halford, A., & Carleton, J. (2006). Bigger is better: size-selective mortality throughout the life history of a fast-growing clupeid, Spratelloides gracilis. Marine Ecology Progress Series, 317, 237-244 DOI: 10.3354/meps317237

Platt, T., Fuentes-Yaco, C., & Frank, K. (2003). Spring algal bloom and larval fish survival. Nature, 423 (6938), 398-399 DOI: 10.1038/423398b