Sea food was good for the mind

by Andrew Farrer

In the 1960s the importance of coastal sites for man living in the Middle Stone Age (250 – 35 thousand years ago) was realised. It seems, from the volume of the remains in human archaeological sites, that shellfish and other marine resources made these locales so appealing. It has been suggested that, more than being just a new food source, shellfish played a role in the evolution of the modern human.

Sea food contains much higher levels of the Omega-3 fatty acids than terrestrial food sources. Omega-3 is famous for being an excellent resource for developing brains; providing some of the building blocks required for maximising brain potential. As a result, living on the coast placed our ancestors in an environment ideal to evolve the complex, organic computer we are now so proud of.

Initially the quantity of Omega-3 consumed would have fulfilled the requirements of our ancestors’ smaller brains but over the generations, as the brain became more expensive, the need for shellfish would have increased. This presents a simple hypothesis: exploitation of marine resources should increase over time. The problem is that Middle Stone Age sites are not described in enough detail to really explore the connection. Worse still, the definition of key criteria varies between sites, making inter-site interpretation virtually impossible.

Hoedjiespunt 1(33° 01’ 42” S 17° 57’ 34” E) is on a peninsula in Saldanha Bay, South Africa. Approximately 68 miles North-West of Cape Town. Images from Google Earth

Figure 1: Hoedjiespunt 1(33° 01’ 42” S 17° 57’ 34” E) is on a peninsula in Saldanha Bay, South Africa. Approximately 68 miles North-West of Cape Town. (Images: Google Earth)

Researchers from the universities of Tuebingen and Cape Town reopened excavations at Hoedjiespunt 1 (see Figure 1 for information) in an effort to set the standard for study and reporting of archaeological data. Will et al. represents the first paper published as a result of this work and focuses on the interpretation of lithics (stone tools) and behaviour. Removing the soil in no more than 3 cm deep layers at a time the researchers found over 3,000 lithic artefacts distributed between three Archaeological Horizons (Archaeological Horizons are layers within the soil, much like strata in rock but formed by human activity). Three unique layers containing archaeologically relevant remains demonstrate that the site was habituated at least three distinct times (See Figure 2). The lithics, dating of shells and consideration of sea levels suggests Hoedjiespunt 1 was utilised 130 – 119 thousand years ago.

The lithics were of four main raw materials: quartz, quartz porphyry, calcrete and silcrete. Only silcrete is considered a good quality stone for knapping (tool preparation) and it is the only material not to be found on site (closest deposits are 6 – 18 miles away). Whilst evidence of all stages of production is found for the other materials, silcrete tools were made off-site. Interestingly the knappers have used different techniques for the differing materials, presumably to get the best results from each stone.

Will et al. suggest that the presence of silcrete shows our ancestors carried tools at all times. They would then have instruments directly available in unexpected situations encountered whilst travelling. Hoedjiespunt 1 seems to have required tool use in quantities that would be impractical to have carried from elsewhere. Poorer quality materials still made adequate tools (quartz forms sharp edges and can be retouched as it goes blunt); so, to me, this seems an economic decision, it was simply more cost effective to use poorer on-site materials than transport good quality ones.

Ocher (a natural pigment) was also found in a modified form. Often used for ritualistic or symbolic drawing it’s commonly seen as a sign of behavioural modernity. It can, however, also be used for hide tanning, insect repellent and as an adhesive. Ocher found at Hoedjiespunt 1 was mainly in the form of pencils though no evidence of design was found.

Figure 2: The three Archaeological Horizons (AH I-III) are clear in the excavation. Topped by a modern humus layer and with shelly sand (SHES) below. (Image: Will et al. 2013)

Figure 2: The three Archaeological Horizons (AH I-III) are clear in the excavation. Topped by a modern humus layer and with shelly sand (SHES) below. (Image: Will et al. 2013)

Whilst comparison between Hoedjiespunt 1 and other sites would reveal the most about changing behaviour at different times and places, this is difficult as the details of other sites are frequently not known in as much depth as Hoedjiespunt 1. However, a lot can be drawn from on-site finds. Data shows that the site was used regularly for short periods (perhaps at specific times of year to coincide with marine resource harvesting) by mobile hunter-gathers. Absolute and relative dating strongly suggests that these were H. sapiens; our direct ancestors. These people demonstrated the ability to plan and appreciate quality; as seen by the non-local preparation and transport of silcrete tools. Connecting lithics to marine resource harvesting is difficult but we can note several factors that support such a conclusion: the shellfish deposits are not natural, shellfish are burned, the three horizons are consistent (the site was used for the same purpose repeatedly) and the locale is best explained by marine resource exploitation as it is neither sheltered from the elements nor a suitable base for terrestrial hunting. In conclusion, our ancestors appear to have had a sustained and stable system that integrated marine resources as a main food source into their diets at Hoedjiespunt 1 and probably elsewhere.

The importance of this paper is not that it presents a ground breaking result (it does not) but that it represents a very important part of science that is often glossed over in our media fuelled world; collection of knowledge. All the sensational headlines seen in newspapers and blogs are born from lots of hard work and the building of a huge base of knowledge. Then a hypothesis and (possibly) a theory can be developed. This paper aims to continue the trend for much more in depth archaeological site review. Will et al. have not proved or disproved the Omega-3 hypothesis but they have certainly provided necessary steps to do so.

 

Reference:

Will, M. et al., 2013. Coastal adaptations and the Middle Stone Age lithic assemblages from Hoedjiespunt 1 in the Western Cape, South Africa. Journal of Human Evolution, (64), pp.518–537. Available at: http://www.sciencedirect.com/science/article/pii/S0047248413000924 [Accessed May 31, 2013].

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Eggs can’t run

by Andrew Farrer

Avoiding predation is important. From an evolutionary view being eaten is a poor strategy and I think we can all appreciate the more proximal aversion to being lunch for something else. The world is full of a myriad of strategies to avoid becoming a meal; herding (or flocking), poisonous or foul tasting chemicals, mimicry, camouflage, etc. However, the method that first comes to mind is simple: run. Nothing can beat distance for its defensive capabilities.

The tegu (of the genus Tupinambis) is another lizard who responds to mechanical stimulation, or in this case, tickling.  Credit: Varnyard/YouTube

Eggs, though, are not good at running. If there is no parental care then all they may have at their disposal are camouflage and safety in numbers. For a predator, a clutch of eggs is a nutritious and easy meal. As such, the best strategy for an embryo is to hatch at the earliest possible developmental stage, leave the confines of the egg and become mobile. On the flipside, however, the world can be a harsh place and remaining in the egg as long as possible can protect the embryo. Also, once hatching competence has been reached development does not flat-line. More time developing in the egg could make a hatchling more robust. The solution would seem to be for the embryo to monitor the external environment and adjust its hatching date. Conveniently for them (and this post) that is exactly what they do; it’s called Environmentally Cued Hatching (ECH).

In 2011 J.S. Doody stated that ECH was the “..variation in time, age, or developmental stage at hatching, facilitated by an extrinsic cue..”. It can be divided into three areas: Early Hatching, Delayed Hatching, and Synchronous Hatching (hatching at the same time as other eggs in the clutch). Research is currently scattered and unconnected but in recent years researchers have been drawing together the few papers and the anecdotes that support the ECH hypothesis. The ability to react to environmental cues has been noted in a wide range of organisms. Parasitic flatworm eggs can survive in harsh environments that the larvae cannot, so hatching is delayed until conditions become more favourable. Some molluscs can delay due to food scarcity, and Spitting-spider mothers can trigger early hatching of the eggs clinging to her body so she can better defend herself. There are also examples from nematodes, crustaceans and insects. In the vertebrates, fish may need an extrinsic trigger as well as an intrinsic one to hatch at all and pig-nosed turtle eggs can detect vibrations from hatching siblings, leading to synchronous hatching.

A delicate skink hatches after the egg was touched by a researcher. Vibrations can induce hatching up to 7 days early in this species Taken from (J S Doody, 2011). Credit: N. Pezaro.

A delicate skink hatches after the egg was touched by a researcher.
Vibrations can induce hatching up to 7 days early in this species
Taken from J S Doody (2011). Credit: N. Pezaro.

A recent study by J.S. Doody and P. Paull studied how mechanical stimulation affected the eggs of the Delicate skink (Lampropholis delicate – a lizard native to Eastern Australia). Laboratory experiments showed that mechanical stimulation (in this case, being placed on an orbital shaker for one minute a day) of wild and lab lain eggs resulted in these eggs hatching 3.4 days earlier than a non-stimulated control group. The skink certainly reacted to mechanical stimulations but what about direct threat? Moving to the field the experiments and the results got a bit more interesting.

Delicate skink lay their eggs in narrow, rocky crevices. Doody and Paull located a nest with eggs at the minimum hatching age. To simulate a predator they poked the eggs with the blunt end of a bamboo cooking skewer. Within 10 seconds of being poked 16 of the 19 eggs hatched, the young lizard immediately launching itself from the crevice, falling 1.4 metres to the safety of the leaf litter below (a long way when you’re less than 40 mm long). The remaining 3 eggs also hatched but, being less dare-devilish than their siblings, opted for hiding deeper in the crevice. Simulating an egg being knocked from the nest Doody and Paull pushed 42 eggs out of nest crevices; 36 hatched as result with 12 of those emerging from the egg as it landed. The lizards’ piece de resistance, however, was hatching on open ground; they erupted from the egg and immediately sprinted away. These youngsters could sprint, on average, 41.6 cm (S.D. ±22.76 cm, Range; 5 – 89 cm, n=30) to cover. Not bad for a creature that has never seen the world before, or used its legs.

It’s the explosiveness that indicates an anti-predator response. However, wild skink that hatch early are significantly smaller than those who hatch spontaneously, and their eggs display yolk traces that spontaneous hatchers do not. The loss of energy (and thus body size at hatching) is a smaller cost than death and so worth paying. However the premature hatch could put youngsters at a disadvantage alongside spontaneous hatchers; presumably more so the earlier the hatch was triggered. Still, if you’re going to flee from danger, exploding from your egg beforehand is the way to do it.

 

References

Doody, J S. (2011). Environmentally cued hatching in reptiles. Integrative and Comparative Biology, 51(1), 49–61. doi:10.1093/icb/icr043

Doody, J. Sean, & Paull, P. (2013). Hitting the Ground Running: Environmentally Cued Hatching in a Lizard. Copeia, 2013(1), 160–165. doi:10.1643/CE-12-111

Warkentin, K. M. (2011). Environmentally cued hatching across taxa: embryos respond to risk and opportunity. Integrative and Comparative Biology, 51(1), 14–25. doi:10.1093/icb/icr017

Evolutionary ingenuity often seems a bit weird

by Andrew Farrer

Simultaneous hermaphrodites are fascinating organisms. Unlike the more famous sequential hermaphrodites, such as the clown fish and sea horse (who change sex during their life cycle), simultaneous hermaphrodites are male and female simultaneously. During a single copulation event both partners donate and receive sperm.

C reticulata

Almost all nudibranchs (commonly referred to as sea slugs, despite this term also applying to taxonomic groups not related to nudibranchs) are simultaneous hermaphrodites.  With such an unusual sexual arrangement, our first question would be; why? There are several hypotheses, the most favoured of which is that for organisms living in low population densities and with low mobility it is beneficial to be able to play both roles. Turning that question on its head, we could ask: why not a simultaneous hermaphrodite?

Sex (the “mixing” of DNA between generations) does increase fitness (Lee et al. 2010) but exactly why is contentious. Reversing Muller’s Ratchet (thus preventing mutational meltdown) is commonly cited. However, despite the benefits, there are costs. The “two-fold cost” is incurred because a sexual organism, unlike an asexual organism, must locate a partner (a conspecific) with which to exchange DNA (Otto & Lenormand 2002).

Unfortunately, further problems are caused by mitochondria (and other non-nuclear DNA carrying organelles). Mitochondria with differing genomes do not like being in a cell together and the ensuing war can be catastrophic for the host cell. To avoid this deadly encounter, cells evolved to allow the mitochondria from only one parent into the next generation. The cell who’s mitochondria are passed on are female, the other cell, who’s mitochondria don’t pass on, are male (Lane 2005). Unfortunately, in avoiding the mitochondrial war, organisms have doubled the two-fold cost. Whilst the two-fold cost concentrated on the issue of needing a conspecific partner at all; now only half the conspecifics available are suitable. Two-fold became four-fold.

This leads us neatly back to simultaneous hermaphrodites. Why do it? Well, now all the conspecifics around are potential partners again and they still avoid the mitochondrial death trap. So nudibranchs, as weird as they seem, have solved an evolutionary conundrum quite neatly.

However, a Japanese team (Sekizawa et al. 2013) have observed a behaviour which places one nudibranch, Chromodoris reticulata, back in the realms of weird. This nudibranch is a simultaneous hermaphrodite which, after copulation, disposes of its penis and replaces it with a new one.

Around 20 minutes (20.57 ±7.04 min.) after copulation ends the penis is severed from the body. Within 24 hours (approximately) a new penis is formed from a spiral structure of undifferentiated tissue in the body. Indeed, the individual generally absconds from sex for this period, although on occasion it will play the female role.

C reticulata

The discarded penis is barbed and is sometimes found with sperm clinging to it. The authors hypothesised that this is either a sperm replacement technique, removing sperm from a previous mating, or excess sperm from the mating. They point out that a DNA test is needed to resolve this. I would suspect it is sperm replacement; it is wasteful of an individual to create such excess sperm that it is so clear post-copulation. Also, unless the barbs evolved to remove the individual’s own excess sperm (which seems unlikely), this hypothesis doesn’t explain their presence. The difficulty in removing the penis from the vagina of the partner is also noted as a reason for the discarding. Perhaps damage to the non-muscular penis results in a decreased effectiveness in later copulations. It also seems a risk to insert a penis covered in another individual’s sperm into a partner: the barbs are less effective against any sperm to be removed and there is the possibility of insemination by the trapped sperm.

There is little doubt that the severing of the penis is beneficial to Chromodoris reticulata; that it outweighs the costs of producing a replacement and the loss of mating potential during that period. That’s the beauty of evolution; in context it always makes sense. That doesn’t stop the idea sounding quite “unusual”. I think it keeps the nudibranchs in the bizarre category for now.

Lane, N., 2005. Power, Sex, Suicide. Mitochondria and the Meaning of Life, Oxford University Press.

Lee, S.C. et al., 2010. The evolution of sex: a perspective from the fungal kingdom. Microbiology and molecular biology reviews : MMBR, 74(2), pp.298–340. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2884414&tool=pmcentrez&rendertype=abstract [Accessed August 4, 2011].

Otto, S.P. & Lenormand, T., 2002. Resolving the paradox of sex and recombination. Nature reviews. Genetics, 3(4), pp.252–61. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11967550 [Accessed June 13, 2011].

Sekizawa, A. et al., 2013. Disposable penis and its replenishment in a simultaneous hermaphrodite. Biology Letters, 9(February).

Toxic science gets a thorough decontamination by Rosie Redfield et al

Extraordinary claims require extraordinary evidence, as the great Carl Sagan once said.  And they don’t come much more extraordinary than Wolfe-Simon et al’s highly publicized claim that bacteria can incorporate arsenic into their DNA instead of phosphate, and hence that the six fundamental elements of life (carbon, hydrogen, nitrogen, oxygen, sulphur and phosphorus) are not so fundamental after all.

The claim was met with a resounding outcry by the wider scientific community, with extensive methodological criticism highlighting many errors which could have introduced the illusion of arsenate incorporation.  However, Rosie Redfield and colleagues went the whole hog by replicating the study in its entirety, modifying it to include rigorous checks for contamination, the absence of which caused such a negative reaction to the original paper.  The results of this replication were published in Science Express on July 8th.

Wolfe-Simon et al had claimed that their growth medium contained no phosphate, and hence that growth when arsenic was added was a result of arsenate incorporation into the DNA of the bacteria (which was a strain called GFAJ-1).  However, Redfield et al refute this claim by pointing to the large body of literature cataloguing bacterial growth at the level of phosphate (3-4 uM) remaining in this ‘phosphate-free’ medium.  Conclusion: growth of GFAJ-1 when arsenate was added could have been caused by trace levels of phosphate in Wolfe-Simon et al’s medium.

It was also reported by Wolfe-Simon et al that GFAJ-1 cells grew very slowly in the medium, but grew faster when arsenic was added.  This was refuted by Redfield et al, who replicated the level of phosphate in Wolfe-Simon et al’s ‘phosphate-free’ medium, and observed significant growth.  Conclusion: GFAJ-1 doesn’t need arsenic to grow quickly at low levels of phosphate.

The most contentious claim in the original paper was that as much as 4% of the phosphate in the DNA backbone of GFAJ-1 was replaced by arsenate (Wolfe-Simon et al, 2011).  Redfield et al checked for the presence of arsenate bonds after three serial washes of the DNA with distilled water, and found arsenate present at a level of 5 x 10-8 M, 50-fold lower than the 4% claimed by Wolfe-Simon et al.  Incidentally, they found a similar level in their water blank, suggesting that even this low level is a result of remaining contamination.  Conclusion: high arsenate levels in the original paper were most likely a result of contamination, introduced by insufficient washing of DNA.

Logically, one would not expect arsenate bonds to exist, because they have previously been reported to be unstable, quickly breaking down by hydrolysis.  Wolfe-Simon et al had claimed that internal proteins or compartmentalization may protect arsenate bonds from this hydrolysis.  Unfortunately, this claim was also refuted by Redfield et al, who showed by gel migration that GFAJ-1 DNA is not associated with hydrolysis-protecting proteins.  They also compared the size of DNA fragments seen before and after removal of any potential hydrolysis-protecting proteins, and found no difference in the fragment size.  Conclusion: there is no hydrolysis-protection mechanism active in GFAJ-1 DNA, and hence arsenate bonds are not even logically possible in this bacterium.

So it would appear that there is no evidence (extraordinary or not) for arsenic incorporation.  I don’t think I can improve on the conclusion by Redfield:

 

“The end result is that the fundamental biopolymers conserved across all forms of life remain, in terms of chemical backbone, invariant.”

 

I suppose there are two ways to look at this.  The first is positive: after all, Redfield et al have ruthlessly employed the scientific method not only to highlight an erroneous claim, but to specify and quantify the source of the error.  But one can’t shake the negative perspective: valuable time has been spent disproving something that should never have been published in the first place.

 

 

References

Wolfe-Simon, F. et al (2011) A bacterium that can grow by using arsenic instead of phosphorus.  Science 332: 1163-1166.

Reaves, M.L. et al (2012) Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells.  Sciencexpress 8 July: 1-4

Recurrent evolution of sticklebacks shown to be due (very broadly) to the same genes each time

Threespine sticklebacks (Gasterosteus aculeatus) have shown a recurrent and relatively predictable pattern of evolution.  Their ancestral home is marine, where they have long spines and a heavily armoured body; however, on numerous occasions they have moved into freshwater, and every time they do they lose their spines and armour.  This is due to a difference in predation pressure.  When in marine habitats, the main predators of the stickleback are birds and fish, which can only eat them if they can swallow them whole.  Long spines make it more difficult for something to swallow you, and armour makes it more likely you will survive a spell in the beak of a bird before being spat out.  But when in freshwater, the main predators of sticklebacks are insects, which grab hold of their prey instead of swallowing them in one.  With this kind of predation, spines and armour are a twofold disadvantage: they give your predator something to grab hold of, and they cost energy to produce, inhibiting body growth and therefore increasing predation risk.

The consistency of stickleback evolution is truly remarkable.  There are many instances worldwide of them moving from marine to freshwater environments, and in every one the same reduction in spines and armour is seen.  However, questions still remain regarding the genetic basis of this recurrent evolution.  How many genes are involved?  Is it mainly changes to protein coding or regulatory genes that enable this recurrent evolution?  And is there a set of “freshwater” genes in the genomes of all populations of sticklebacks, which are repeatedly selected for when they move from marine waters, or are different mutants selected for each time?  These are the questions that a recent open-access Nature paper by Jones et al set out to answer.

The authors took a whole genome approach to the problem, sequencing many different marine-freshwater pairs from across the globe and comparing them to a stickleback reference genome.  This avoided two limitations of previous studies.  The authors could look at every stickleback gene and assess its contribution, rather than deciding a priori to focus on a single gene.  And they stood more chance of detecting patterns of interaction between genes (epistasis), and whether a single trait was being affected by more than one gene (a polygenic trait).

First they generated a reference genome by sequencing one freshwater female, giving them a standard against which to compare the rest of their genomes.  They then chose 10 sites which showed the two characteristic morphs (assessed by morphometric analysis), encompassing both the Pacific and Atlantic Oceans, and sequenced one freshwater (spineless, no armour) and one marine (spiny, armoured) stickleback from each site.  To identify genomic regions under positive selection which would have driven the divergence between the two morphs, they used two methods.  The first was a Hidden Markov Model: this splits the genome into regions, calculates a phylogenetic tree for the 21 individuals at each of these regions, and groups these trees according to similarity.  This method identified 215 regions (90 after filtering) which separated marine individuals from their freshwater counterparts; the authors inferred that these were the regions likely to be under different selection pressures in either habitat.  The second method was a genetic distance approach: this again splits the genome into regions, and calculates for each region a cluster separation score (CSS), to quantify the level of marine-freshwater divergence at that region.  The number of divergent regions recovered by this method was 174 with a 5% false discovery rate (FDR, equivalent to a p value of 0.05), and 84 with a 2% FDR.  Without being overly clear about which filtering they are accepting, the authors conclude that 242 regions (0.5% of the genome) have been identified by either method, and 147 regions (0.2% of the genome) have been identified by both.

The authors therefore regard as settled the question of whether the same variation is reused, or new variation is continually produced: 0.5% of the genome is an incredibly small proportion for recurrent evolution on this scale, and can only be explained by these relatively few genomic regions being used again and again to produce the same evolutionary pattern.

They next looked for what these regions did, by analysing 64 of the most divergent regions.  41% of these regions were non-coding and therefore regulatory, whereas only 17% were coding and showed non-synonymous differences (i.e. produced different protein products in the different environments).  The other 42% were either coding or non-coding, but did not show any non-synonymous differences between the environments.  The authors therefore concluded that regulatory changes account for a large majority of adaptive change.

And here I must confess some puzzlement with the execution of their next step.  The authors chose to test how many regulatory differences existed between the two morphs by sequencing RNA (no problems so far) from a marine and freshwater morph “born and raised under identical laboratory conditions.”  IDENTICAL LABORATORY CONDITIONS.  They found significant differences in the expression of 2,817 genes out of a total of 12,594 (around 22%).  One wonders how many differences would have been seen had they also compared RNA from fish in their natural habitats, the environments under which those regulatory differences have evolved.

So they had found the portions of the genome that differ between freshwater and marine sticklebacks, and had an idea what their function was.  However, answering this question only raises another: if these genes are constantly used during freshwater-marine divergence, how do they avoid being recombined during sex, which would produce an individual with some “freshwater” variants, and some “marine” variants?  As the authors say, “When adaptive divergence occurs in hybridizing systems, theory predicts that selection can favour molecular mechanisms that supress recombination between independent adaptive loci” (Jones et al, 2012).  So these mechanisms are what they looked for next.

To do this they sequenced the genome of a marine and a freshwater morph in a hybrid zone in the River Tyne in Scotland.  Here, even though the two morphs are recombining their genes during mating, only the two distinct morphs survive, with any intermediates selected against.  They then looked for regions which had high CSS scores, and sharp transitions in their CSS scores at their boundaries.  This would act as a signature of an inverted region, which doesn’t undergo recombination and so passes through the generations as either a “freshwater” or “marine” complex.  They found three such regions, on chromosomes I, XI and XXI.  They then cloned these regions into bacteria, more reliably to compare them with the reference genome, and more easily to sequence their surrounding regions.  When clones were compared with the reference, only chromosomes I, XI and XXI were anomalous, further confirming their status as inversions.  Inverted repeats were also found in the sequence of their surrounding regions, a signature of inversion generation.  Cluster separation scores for the regions confirmed that marine and freshwater sticklebacks carry different forms of the inversions.  Finally, they looked for functional significance of these regions.  They found that the inversion on chromosome XXI contains “separate QTLs controlling armour plate number and body shape, traits that differ between marine and freshwater fish” (Jones et al, 2012).

So how successful have the authors been in answering their questions?  The first has been an undeniable success: that such a small fraction of the genome is consistently found to produce such large phenotypic changes is convincing evidence that the same genes are used repeatedly, rather than new mutations being required every time freshwater is invaded.  However, regarding the function of genes and the relative importance of coding and regulatory change, valuable initial data has been produced here, but no strong conclusions can be drawn from them.  The data here allow hypotheses to be made and candidate genes to be identified; however, experimental manipulations and data from multiple generations will be needed before conclusions can be drawn with any validity.

 

P.S. This paper was published as an open-access article, meaning an institutional login or massive payout is not required to read it, and that figures and content can be reproduced with a citation.  Let’s hope this soon becomes the norm (and that in the future, authors are not required to foot the bill to make their work open access).

 

 

References

Jones, F. et al (2012) The genomic basis of adaptive evolution in threespine sticklebacks.  Nature 484: 55-61

Peichel, C. and Bougham, W. (2006) Quick Guide: Sticklebacks.  Current Biology 13: 942-943

Marchinko, K. (2009) Predation’s role in repeated phenotypic and genetic divergence of armor in threespine stickleback.  Evolution 63: 127-138

Reimchen, T. and Nosil, P. (2004) Variable predation regimes predict the evolution of sexual dimorphism in a population of threespine stickleback.  Evolution 58: 1274-81

Vamosi, S. and Schluter, D. (2004) Character shifts in the defensive armor of sympatric sticklebacks. Evolution 58: 376-85

Palaeontology and genetics in perfect harmony

It is easy for geneticists to feel superior about their methods: any organism’s genome can be fully sequenced in a matter of hours, providing a wealth of data that seem near-infinite in potential. In contrast, more traditional branches of natural history such as palaeontology can seem a lot of work for very little return. However, far from new techniques in one area leaving another discipline redundant, a recent paper in Science demonstrates how complementary both traditional and modern methods can be, and the startling results that can be produced by employing both together.

The authors investigated the diversification of mammals from a few basal ancestors to the roughly 5,400 species alive today.  They produced two important results: a phylogenetic tree of every family (the third most specific taxon, after species and order) in the mammals; and dates for the major radiations (splitting into different taxa) of basal mammals.  The tree was calculated by sequencing and aligning 26 DNA sequences (21 coding for genes, 5 non-coding) from every one of the insert mammalian families. Previous trees had grouped families based on morphological similarities, and so were vulnerable to mistakes or distortion caused by convergent evolution (when two distantly related species (or families) adapt to an environment in a similar way, producing similar traits and thus giving the illusion that they are closely related). Using DNA sequence data allowed the authors of this study to look beneath such misleading facades: even rapid, dramatic evolution will not mask the genetic similarities two families share in other areas of their genome.

However, DNA alone does not reveal how recently different families split apart from each other. Gene sequences reveal how families are grouped within a tree, and which branches connect one family to another, but other data are needed to tell us how long these branches are in terms of years. And this is where the fossil evidence comes in. By looking at the ages of fossils of the outgroups (distantly related species which are used to provide a sense of “scale” when constructing a phylogenetic tree), the authors were able to date the overall length (age) of the tree. With the branch lengths known, important moments in the evolution of the mammals could be given a concrete date.

This produced two main results. The first reveals more detail about the pattern of evolution before and after the Cretaceous-Palaeogene (K-Pg) extinction event (formerly known as the K-T extinction event, caused by asteroid hits 65 million years ago which led to the eventual demise of the non-avian dinosaurs, along with many other groups). A large increase in the formation of new orders was seen during the Cretaceous, before the asteroid hit; and most mammalian crown-group orders were already established by the end of the Cretaceous, before the asteroid hit. The authors credit the extinction event with “opening up of ecospace”: the crown-group order ancestors could then diversify into their current broad range of species. This has important implications for future palaeontological research: as the authors say, “we are unlikely to find crown rodents or primates in rocks that are much older than the latest Cretaceous”, thus helping to direct the hunt for fossils into the correct stratum.

The second result produced by this dated tree is a refutation of the “delayed rise of present-day mammals” theory: this states that mammalian diversity remained relatively constant after the K-Pg extinction event, and diversified during the Eocene, 10 million years later. The authors of the present study found no such Eocene increase, but instead more diversification soon after the K-Pg border, lending weight to the more traditionally held belief that the extinction of so many groups left the mammals with many empty ecological niches to fill.

What I like most about this paper is its demonstration of the great potential of combining such seemingly disparate fields: palaeontologists now have a more reliable phylogeny to aid in fossil location, identification and analysis; and evolutionary geneticists can place their sequence data in the context of the ecological conditions and events that may have driven the evolution of those sequences.

References

Bininda-Edmonds et al (2007) The delayed rise of present-day mammals.  Nature 446: 507-512

Meredith, R.W. et al (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on mammal diversification.  Science 334: 521-524