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Tuatara tuesday – sex determination in a warming world Hilary Miller Nov 09

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Seeing as reptile reproduction seems to be a bit of a hot topic right now, I thought it was time to talk about sex determination in tuatara.

Tuatara do things a little differently to other reptiles when it comes to sex determination – not because they have temperature-dependent sex determination (thats common to lots of reptiles), but because their pattern of temperature-dependent sex determination (or TSD) is different from most other reptiles.  For tuatara, incubating eggs at higher temperatures (over 22°C) produces males, while lower temperatures (under 21°C) produce females.  In other reptiles with TSD, you generally either get a pattern of females being produced at high temperatures and males at low temperatures, or females being produced at both high and low temperatures, and males produced at intermediate temperatures.

Tuatara hatchling

Dr Nicola Nelson at Victoria University has experimented with switching tuatara eggs between male and female-producing temperatures in an effort to determine which part of the incubation period temperature is critical for sex determination.  She found that sex is set early on – by the time the incubation period is about one third of the way though.  However, incubating eggs in captivity at constant temperatures only tells part of the story, as of course temperatures are not constant in the wild, where eggs are laid in shallow burrows in the soil.  Nelson and colleagues have also collected temperature data from natural nests and found that warmer nests produce males and cooler nests produce females, but what isn’t known is how long eggs have to remain above or below the critical temperature in order to produce males vs females.  Its possible that the critical period for sex determination is actually quite short – for example an egg may actually only need to spend a few days above 22°C in order to turn out male.

A partially buried tuatara nest on Stephens Island

Having more males produced at warmer temperatures could be bad news for tuatara in the light of global warming.  Some tuatara populations, like the small, genetically distinct population on North Brother Island, already have more males than females.  A recent study by Nicola Mitchell of the University of Western Australia predicted that, under current “worst-case” global warming scenarios, populations like North Brother Island will produce all-male clutches by the mid 2080s.

Of course, tuatara have survived changes in climate in the past, but this time around the climate is changing faster than ever before – perhaps too fast for a species like tuatara with its long generation times and low levels of genetic variation to be able to evolve to compensate.   Tuatara may be able to adapt behaviourally to the higher temperatures by nesting earlier, digging deeper nests, or choosing cooler nest sites.  However, on many islands the choice of nest sites is limited, and as tuatara are now confined to offshore islands or ringed in by predator-proof fences on the mainland, they will be unable to simply move south to seek cooler temperatures. It seems likely that tuatara will need our help if they are to survive the threat of global warming.

Further reading:

Mitchell NJ, Kearney MR, Nelson NJ, Porter WP (2008) Predicting the fate of a living fossil: how will global warming affect sex determination and hatching phenology in tuatara? Proceedings of the Royal Society B-Biological Sciences 275: 2185-2193

Huey RB,Janzen FJ (2008) Climate warming and environmental sex determination in tuatara: the Last of the Sphenodontians? Proceedings of the Royal Society B: Biological Sciences 275: 2181-2183

Mitchell NJ, Nelson NJ, Cree A, Pledger S, Keall SN, Daugherty CH (2006) Support for a rare pattern of temperature-dependent sex determination in archaic reptiles: evidence from two species of tuatara (Sphenodon). Frontiers in Zoology 3: 9

 

Tuatara tuesday – an iconic parasite for an iconic species Hilary Miller Oct 26

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As you might expect from an animal that is so evolutionarily distant from its nearest relatives, the tuatara also has some unique parasites to call its own.  One of these is the tick Amblyomma sphenodonti (sometimes also called Aponomma sphenodonti), pictured here.

Tuatara ticks Amblyomma sphenodonti

Like many ticks, A. sphenodonti are host-specific, spending all three of their life stages feeding on tuatara but dropping off into the soil in between stages.

So why should you care about tuatara ticks?  Well, these ticks are evolutionarily distinct in their own right, and are actually quite rare – far rarer than the tuatara themselves.

The taxonomic history of the tuatara tick is a little complicated, so bear with me for a minute.  The tuatara tick is “hard” tick in the family Ixodidae, and was originally named in the genus Aponomma, a group of ticks that predominately parasitise reptiles.  However, a revision of the Aponomma genus placed some of the these species into a new genus Bothriocroton, and moved the rest, including the tuatara tick, into the existing genus Amblyomma. A few years ago, with the help of a keen undergraduate student, I did a small genetics study comparing the tuatara tick with both Bothriocroton and Amblyomma ticks and found that it’s actually not particularly closely related to either group (see the tree below – click on it to enlarge).   The tuatara tick should probably actually be in its own genus, highlighting the fact that it has likely had a long evolutionary relationship with its evolutionarily distinctive host.

Phylogeny of hard ticks, based on 18S rRNA sequences. A. sphenodonti is shown in bold. Other members of the Amblyomma genus group in the top part of the tree, while Bothriocroton ticks form a group in the lower half of the tree.

Surveys carried out in the late 80s-early 90s found A. sphenodonti on only 8 out of 28 natural tuatara populations, and the Department of Conservation lists it as “Range Restricted” in its Threat Classification System. They are also virtually absent from populations established by translocations.  This is partly because up until recently, the ticks were removed when animals were translocated.  However for recent translocations, such as into the  Zealandia wildlife sanctuary in Wellington, the ticks have been left on, but disappeared naturally within the months after the translocation.  The most likely cause of the disappearance is the low density of tuatara in the new location, meaning that when a tick drops off a tuatara at the end of one of its life stages, finding a new host for the next life stage is difficult.  This inability to find new hosts when they are at low densities may have also contributed to the demise of tick populations in the wild.

The case of the tuatara tick highlights how, when populations become endangered, their natural “flora and fauna” are also at risk.  Parasites are the most diverse and species-rich metazoan group on earth, and form a highly important part of host ecosystems, so they deserve our conservation efforts just as much as their hosts.

Further reading:   Miller HC, Conrad AM, Barker SC, and Daugherty CH (2007) Distribution and phylogenetic analyses of an endangered tick, Amblyomma sphenodonti. New Zealand Journal of Zoology, 34: 97-105.

Tuatara tuesday — Spring fever Hilary Miller Oct 12

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I haven’t had much time for writing this week, so instead I thought I’d share this photo as a reminder to my New Zealand readers that it is actually spring, even though it doesn’t feel like it!

 

Tuatara basking in the daisies on Stephens Island

 

Tuatara tuesday — how cold is too cold for a tuatara? Hilary Miller Oct 05

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ResearchBlogging.org Tuatara like it cold.  Unusually so, for a reptile.  While reptiles in most other countries are happiest with temperatures over 25 degrees celcius, here in New Zealand our reptiles prefer much lower temperatures.  Alison Cree’s group at the University of Otago has been investigating exactly which temperatures tuatara prefer, with a view to determining whether new populations of tuatara could be established in the southern South Island.

Research just published in Animal Conservation by PhD student Anne Besson examined the effects of cool temperature on juvenile tuatara sourced from Stephens Island, the southern-most natural population.  Sub-fossil remains tell us that tuatara were once present in Otago and Southland, but they have been extinct in this region for possibly hundreds of years.  Temperatures on Stephens Island are on average 3-4 degrees warmer than those at proposed translocation sites in Otago, and it is possible that tuatara originally living in the deep south had special adaptations to enable them to withstand the cold that are absent in animals from more northerly present-day populations.  To test whether Stephens Island tuatara are likely to be able to survive in the deep south, Besson compared tuatara behaviour at low temperatures with that of three lizard species found in the wild in Otago (common geckos, jewelled geckos and McCann’s skinks), hypothesizing that if tuatara have the same responses as these lizard species, then its likely they will be able to survive similar temperatures.

Besson investigated feeding behaviour at 20, 12 and 5 degrees, measuring the time it took an animal to catch, handle and digest prey at the three different temperatures.  She found few differences between tuatara and the lizards.  For all species, feeding performance dropped off significantly at 5 degrees as animals became very sluggish at catching and handling their food, and neither skinks or tuatara could digest food at this temperature.  However, one important difference between tuatara and lizards was seen at 12 degrees.  At this temperature lizards were able to digest food, albiet more slowly than at warmer temperatures, but tuatara were not.  Besson also measured preferred body temperature and critical thermal minimum (i.e. the temperature at which animals can effectively no longer function) across the four species and again found little difference between tuatara and the lizard species.

Besson’s results suggest that Stephens Island tuatara would survive a move south, but their inability to digest food at temperatures of 12 degrees or lower has important implications for choosing translocation sites in Otago, given that ambient temperatures rarely rise above 12 degrees in winter in this region.  As tuatara do not hibernate and still feed throughout the winter, Besson and Cree recommend that proposed translocation sites for tuatara should provide plenty of opportunities for animals to bask in the sun in order to digest their food.

Testing physiological and behavioural responses to investigate whether animals are likely to be survive in new environments is something that is rarely done in conservation studies, but is likely to become increasingly important in the face of climate change.  Tuatara are particularly vulnerable to warming temperatures, as sex determination in tuatara is temperature-dependent and warming temperatures are likely to produce an excess of males.  Establishing new populations further south may be one way of countering future temperature rises.  Besson’s research shows that this is likely to be a viable strategy for conservation management of tuatara, but whether they can produce self-sustaining populations at cooler temperatures still needs to be tested.

Besson, A., & Cree, A. (2010). Integrating physiology into conservation: an approach to help guide translocations of a rare reptile in a warming environment Animal Conservation DOI: 10.1111/j.1469-1795.2010.00386.x

Tuatara Tuesday — Stephens Island Hilary Miller Sep 21

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This little guy lives on Stephens Island in the Marlborough Sounds, and is affectionately known as “tree tut” to the Victoria University researchers who frequent the island.  Because he lives in a tree, of course.  His tree is along the pathway between the house occupied by the DoC rangers and the house where the researchers stay, so he has plenty of passing foot traffic to keep an eye on.

Stephens Island is tuatara central, home to a staggering 30,000 – 50,000 individuals.  Given that the island is only about 150 ha in size, this means that tuatara are EVERYWHERE on the island and it is sometimes difficult to avoid treading on them.  Stephens Island has an interesting history, which may have partly contributed to the high densities of tuatara found there.  A lighthouse was constructed on the island in 1893, and three houses were also built to accommodate lighthouse keepers and their families.  During World War II a radar station was set up there, and an accommodation building known as the “Palace” was constructed.  The Palace is still there and these days serves as a lab and storage shed.

The clearing of land for the construction of the lighthouse and houses, and the introduction of cattle and sheep decimated the Stephens Island forest, and photos of the island from 50 years ago or so show barren hillsides with only a few remnant patches of bush.   However, for the last 20 years a revegetation program has been in full swing and the forest is returning.  The lighthouse was automated in 1988, and the last lighthouse keeper left the island in January 1989.  The last sheep left the island in 2005, and today the only permanent human presence on the island are the DOC rangers, who live in one of the old lighthouse keeper’s houses.

Despite the human settlement and rampant habitat destruction, the only introduced predators that made it to the island were the lighthouse keeper’s cats.  These cats decimated some of the local wildlife, including the Stephens Island wren, an unusual flightless passerine which famously went extinct virtually as soon as it was discovered.  However, the tuatara population escaped virtually unscathed and cats were eradicated in 1925 after only about 30 years on the island.  Ironically, the clearing of forest on the island may have actually increased tuatara numbers, by increasing the availability of suitable nesting sites in open areas.  The island currently appears to be above its carrying capacity, and once the forest regeneration is complete tuatara numbers may decrease somewhat.

Stephens Island, with patches of regenerating forest clearly visible

Tuatara tuesday — its not a dinosaur, OK? Hilary Miller Sep 14

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From today I’ll be starting a semi-regular series of posts about my favourite reptile and #1 study organism, the tuatara.  I want to start by clearing up a misconception that I see repeated time and time again, that tuatara are “New Zealand’s living dinosaur”.

Tuatara are an entirely different lineage of reptiles from the dinosaurs.  Here’s a simplified phylogenetic tree of reptiles to illustrate:

Phylogeny of reptiles, based on that of Hugall et al. 2007 with additional information from the Tree of life (http://tolweb.org/Dinosauria/14883). Dinosaurs, including the lineage that evolved into birds, are in blue.

The closest living relatives of the dinosaurs are the crocodilians (alligators and crocodiles), and birds.  In fact, it is birds that are the “living dinosaurs”, as they evolved from the Theropod dinosaurs, the lineage that includes tyrannosaurs, Velociraptors and Archaeopteryx.  Crocodilians, dinosaurs and birds are collectively known as Archosaurs.

Tuatara are in their own Order, Rhynchocephalia, which is entirely separate from the Archosaurs.  The closest relatives of the Rhynchocephalids are the squamates (lizards and snakes), but they are not particularly close relatives at all, having diverged early in reptilian evolution, around 250 million years ago.  The tuatara is the only remaining species of Rhynchocephalid living today, but back in the time of the dinosaurs (around 65-230 million years ago), Rhynchocephalids were everywhere.  Numerous different species of fossil Rynchocephalid have been found across Europe, Africa and the Americas.   However, Rhynchocephalids appear to have died out everywhere except New Zealand around the same time the dinosaurs went extinct 65 million years ago.  Why they hung on in New Zealand is a mystery, but may have something to do with the apparent lack of competition from mammals.

Modern-day tuatara share a lot of morphological features with some of the earliest Rhynchocephalid fossils.  That, combined with the fact that they are the only living species from this lineage, has earned them the title of “living fossil”.  However, it is premature to say that tuatara are “unevolved” or “unchanged since the dinosaur era”.  For one thing, we don’t actually have any ancestral tuatara fossils  from New Zealand dating back to the dinosaur era for comparison (the earliest tuatara fossil dates to a measly 16 mya), and recent studies have shown that many aspects of their morphology and biology are derived, making them just as “evolved” as any other species (but that’s the subject for another post).

So, although tuatara are the last member of an ancient reptile lineage, and still retain some morphological characteristics of these early reptiles, they are a completely different type of reptile from dinosaurs.  Their ancestors lived alongside the dinosaurs, but so did the ancestors of modern-day turtles, crocodiles, lizards, and snakes.

References:

Hugall AF, Foster R, Lee MSY (2007) Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Systematic Biology 54: 543-563
Jones MEH, Tennyson AJD, Worthy JP, Evans SE, Worthy TH (2009) A sphenodontine (Rhynchocephalia) from the Miocene of New Zealand and palaeobiogeography of the tuatara (Sphenodon). Proc. R. Soc. London B 276: 1385-1390.

Tuatara: one species or two? (re-post) Hilary Miller Aug 21

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The chicken or egg blog family is on holiday in Germany during August, so I probably won’t have a chance to write any new posts.  To keep you all entertained, I’ll be re-posting some of my earlier (pre-Sciblogs) articles. This post was written in July 2009.

New Zealand’s most iconic reptile, the tuatara, is currently regarded as two separate species — Sphenodon guntheri, which is found naturally only on North Brother Island in Cook Strait, and Sphenodon punctatus, which are found on other islands in Cook Strait and off the north-east coast of the North Island.  However research just published online in Conservation Genetics shows that Sphenodon guntheri is not as genetically distinctive as first thought, and suggests tuatara should be regarded as one species. 

Deciding where to draw the line between species is a common dilemma in biology.  There are many different ways of defining what a species is (John Wilkins on Evolving Thoughts lists 26 different ’species concepts’).  One of the most common definitions is the evolutionary species concept, which classifies a species as ’a single lineage of ancestor-descendant populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate” (Wiley 1981).  Under this definition it doesn’t matter whether species are reproductively isolated (as in the Biological Species Concept), what is important is whether they remain genetically or morphologically distinct from one another over time.  A major problem with this definition however, is deciding just how genetically or morphologically distinct two populations need to be before they are regarded as separate species.  (See here for more on these and other species concepts).

In small, geographically isolated populations founder effects can be an additional complicating factor.  A founder effect happens when populations are founded by only a few individuals, or when a large population suddenly becomes very small (a bottleneck).  In these situations genetic variation can be rapidly and randomly lost, and result in the new population looking quite different from the old even if they have only been separated for a short period of time.  This is particularly relevant to the North Brother tuatara population, which was almost exterminated in the 1800s and is now restricted to a 1.7ha patch of scrub on the island.

Natural populations of tuatara are now found only on off-shore islands (32 individual island populations in total), ranging from the Poor Knights Islands in the north-east, to Stephens Island in western Cook Strait (see the map below).  Tuatara were first described by John Edward Gray of the British Museum, who received a tuatara skull in 1831.  In 1877 Walter Buller described the population on North Brother Island as a new species, S. guntheri, because of differences ’in appearance’, especially ’colour’, and in ’habits and disposition’.  However, this distinction appears to have been largely ignored until the early 1990s — taxonomic reviews in the 1950s and 1970s describe tuatara as a single species, with the North Brother Island population listed as a sub-species.  In 1990 Charles Daugherty published the first genetic results on tuatara, and showed a striking divergence between the North Brother Island population and other tuatara populations.  This work was published in Nature with the great headline ’Bad Taxonomy Can Kill’ and resulted in their reinstatement as a full species.

Distribution of tuatara populations – each dot represents an island or island group where tuatara naturally occur. North Brother Island is represented by the yellow dot.

So why has this result now been overturned? The key lies in the type of genetic marker and analysis methods used.  Daugherty and colleagues used protein markers called allozymes, which were the most commonly used genetic markers at the time.  The levels of divergence they measured between North Brother Island and the other populations were equivalent to levels seen between species in many other vertebrates, and correlated with the morphological differences between the groups.  Therefore their recommendation to reinstate the North Brother Island population to full species status was entirely justified based on the evidence available at the time.  However, these days allozymes are regarded as a rather insensitive genetic marker and have fallen out of favour.  In some cases they can be influenced by selection, in which case patterns of divergence will reflect environmental differences acting on a particular protein rather than reflecting overall differences between populations.  The DNA-based genetic markers used nowadays evolve more quickly and are regarded as ’neutral’ (i.e. not likely to be skewed by selection), so are more likely to accurately reflect population history.

Hay and colleagues have now analysed genetic differentiation between tuatara populations with two additional types of DNA markers - mitochondrial DNA(mtDNA) and microsatellite markers, and have also re-analysed the original allozyme data using more powerful methods.  The mtDNA data shows a strikingly different pattern to the allozymes (see figure below).  The phylogenetic tree of mtDNA suggests that the North Brother population is closely related to the other populations in Cook Strait, but that the northern populations are distinct from all the Cook Strait populations.  This reason for this discrepancy is not clear, but probably reflects the different type of marker.  Unlike allozymes, mtDNA is maternally inherited (passed only from mother to offspring).  The two markers also provide information on different timescales and differ in their susceptibility to selection and founder effects.

The allozyme results in the original paper by Daugherty et al were presented as a phylogenetic tree based on genetic distances between populations.  The same type of analysis done on the microsatellite data shows North Brother tuatara as distinct, but the difference is not as great as for the allozyme data.  Hay and colleagues have reanalysed the original allozyme data using principal components analysis, which is a more robust and sensitive method than genetic distance measures for revealing patterns in this type of data.  The PCA tells a somewhat different story from the phylogenetic tree — this shows that the primary division is between all the Cook Strait populations and all the northern populations, and that the split within Cook Strait which separates North Brother is not as large.

So taken together, the results from all three markers suggest that the major genetic divisions between tuatara populations occur between the northern and Cook Strait islands.  The North Brother Island population is genetically distinct from others in Cook Strait, but whether the population is different enough to be regarded as a separate species is debatable.  Hay and colleagues suggest that if the North Brother population is to be retained as a separate species, then the northern populations should be regarded as a third distinct species.  However, they recommend that tuatara is best regarded as a single species, with three distinct genetic groups: northern, western Cook Strait, and North Brother.

The phylogenetic tree of mtDNA data (on the right) groups North Brother with the rest of Cook Strait, but the original allozyme analysis had North Brother completely separate. Reanalysis of allozyme data gives a pattern similar to the mtDNA, with the major division between Cook Strait and northern populations

This study adds another chapter to the tuatara’s already complex taxonomic history. However it is unlikely to impact on tuatara management in the short term, as the Department of Conservation already manages the northern, western Cook Strait, and North Brother Islands separately.  Of more concern is that the North Brother Island population has extremely low levels of genetic diversity, high levels of inbreeding, and a male-biased sex ratio.  Animals from North Brother have been translocated to new islands to boost their numbers, but their lack of genetic diversity has the potential to handicap future growth of these new populations.  So, if tuatara are all one species, and the distinctiveness of North Brother from the rest of Cook Strait is largely the result of human-mediated founder effects — an artefact of small population size, rather than reflecting a deeper difference in evolutionary history — why not mix in a few animals from other Cook Strait islands to boost their diversity? (I’m not necessarily advocating this, but it is an interesting question).

In many cases, species definitions are kind of semantic issues, based on our human need to put things in categories.  The tuatara demonstrates that when populations are geographically isolated and founded by only a few individuals, deciding where to draw the species line can be difficult.  However, understanding the differences between populations is important for managing them successfully.  Whether tuatara are ultimately regarded as one, two or three species, the work of Hay and colleagues gives conservation managers a much clearer picture.

Hay, J., Sarre, S., Lambert, D., Allendorf, F., & Daugherty, C. (2009). Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia) Conservation Genetics DOI: 10.1007/s10592-009-9952-7

Chemical attraction? (re-post) Hilary Miller Aug 12

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The chicken or egg blog family is on holiday in Germany during August, so I probably won’t have a chance to write any new posts.  To keep you all entertained, I’ll be re-posting some of my earlier (pre-Sciblogs) articles.  This one is the very first post I wrote for this blog, from March 2009.

Research published in last month’s Chemistry and Biodiversity journal heralded the discovery of a new compound ’tuataric acid’. Yes, isolated from our very own tuatara.

Stefan Schulz and his colleagues at University of Braunschweig, and collaborator Paul Weldon at the Smithsonian Institution, have analysed the constituents of the cloacal secretions in tuatara and found an unexpectedly diverse array of compounds. As tuatara have no external sexual organs, the cloaca is the ’one stop shop’ opening at their posterior end, with prominent skin glands on either side of the opening that secrete a greasy white substance. When the tuatara secretions were analysed, Schulz and colleagues found over 150 different types of glyceride-based molecules, including one never-before seen compound, which they dubbed ’tuataric acid’.

Perhaps even more excitingly though (for me at least), was the finding that individual tuatara secrete specific mixtures of these glycerides and that the makeup of these individual profiles remains stable over years. This could provide a mechanism for chemical recognition of individual tuatara, a finding which ties in nicely with some behavioural work we have recently been doing on tuatara.

Our research group at Victoria University has been investigating mating behaviour and territoriality in tuatara, and we have found evidence to suggest that tuatara do indeed use some form of olfactory recognition in their social lives.  We analysed the genetic makeup of mated pairs at immune genes (called MHC genes). These genes are linked to odour recognition in many species, and several studies (mostly in mammals and fish) have found that individuals preferentially choose mates with a differing MHC genotype to their own. This theoretically produces offspring that have high genetic diversity at these immune genes, and are thus more resistant to disease. When we compared mated pairs of tuatara with randomly chosen pairs, we found that the mated pairs were more different from each other at their MHC genes than would be expected by chance, suggesting that odour recognition plays a role in how they choose their mates.

However, this MHC-related effect in tuatara is relatively weak, and is largely overshadowed by the fact that large males tend to be more successful in mating, regardless of their MHC genotype. In fact at the time of mating there appears to be little mate choice at all — it’s all about male machismo, with males fighting among themselves for access to the females that live nearby. Tuatara maintain relatively stable territories, and don’t move far to mate, so it’s possible that the apparent influence of MHC genotype on mate choice actually reflects choice of territory. Perhaps tuatara use their sense of smell, mediated by their MHC genes, when deciding who to shack up next to, and in doing so avoid mating with their close relatives.

The finding of individual differences in the makeup of cloacal secretions provides us with a mechanism for how tuatara may recognise each other. However, more field studies will be required to confirm the link between these two streams of research and nail down both the biological roles of the glycerides, and the extent to which tuatara use chemical communication in their social lives. Watch this space…

References: Flachsbarth, B., Fritzsche, M., Weldon, P. J. & Schulz, S. (2009) Composition of the Cloacal Gland Secretion of Tuatara, Sphenodon punctatus. Chemistry & Biodiversity 6, 1-37.

Miller, H.C., Moore, J.A., Nelson, N.J. & Daugherty, C.H. (2009) Influence of MHC genotype on mating success in a free-ranging reptile population. Proc. R. Soc. Lond. B, 276:1695-1704.

Tuatara holds clues to human evolution Hilary Miller Jun 16

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ResearchBlogging.orgA while ago I wrote about the value of genome sequences, not just for helping us understand the biology of a particular organism, but also for enabling large-scale comparisons across species that can help spot patterns in genome evolution which wouldn’t otherwise be apparent.  A recent paper in Journal of Heredity by Craig Lowe, David Haussler and colleagues at the University of California provides an excellent example of this in action, using sequences from the tuatara genome to identify the evolutionary origin of parts of the human genome.

Lowe and colleagues were looking for functional elements (like parts of genes and their regulatory regions) in the human genome that originated from retrotransposon insertions.  Retrotransposons are mobile bits of DNA that have a tendency to make copies of themselves and insert themselves in various different places in the genome.  They contain everything needed for this copying, plus often include functional modules like exons of genes, or transcription factor binding sites.  These functional modules may be co-opted for a new function in the new site, a process known as exaptation.  Once a retrotransposon is inserted in a new location it is often inactivated, and then begins to accumulate mutations which render it unrecognisable as a retrotransposon. This makes it difficult to identify exaptation events in any given genome and hence trace the origin of many of the functional elements of that genome.  However, by comparing the genomes of many different species in different lineages it may be possible to identify ancestral versions of these elements, and so trace their evolutionary history.

Lowe and colleagues found a previously unknown retrotransposon in the small part of the tuatara genome that has been sequenced.  This retrotransposon is of a type known as a LINE – Long Interpersed Nucleotide Element - and was named EDGR-LINE  (endangered-LINE).  A search of human genome against this sequence found 18 elements that are likely to be the result of insertion of this retrotransposon into the genome at some point in evolutionary time.  Seventeen of these elements are gene regulatory regions and one is an exon of a gene called ASXL3.  ASXL3 is important for regulation of other genes during development and the additional exon co-opted from EDGR-LINE appears to help control its expression.

These 18 exaptation events likely occurred early in mammalian evolution, but the retrotransposon itself has long since been inactivated in humans so all traces of it have been lost.  The functional elements it contained are able to be identified because they are under strong purifying selection (i.e. have not accumulated many mutations), so can still be aligned with the tuatara sequence.  Its only through this comparison that it is possible to know that these 18 elements originated from the same retrotransposon.

EDGR-LINE was also found in the lizard, frog, and coelecanth, but no traces of it remain in mammals, crocodylia and birds.  EDGR-LINE appears to be more slowly evolving in tuatara than in lizards, so is closest to the mammalian ancestral version of EDGR-LINE and hence more informative for identifying elements in the human genome. In fact, 10 of the 18 elements could only be identified by comparison with tuatara and not with these other species.

Evolution of the EDGR-LINE in vertebrates. The EDGR-LINE appears to have been introduced in the common ancestor of tetrapods and lobe-finned fish, and lineages where the LINE was active are shown with green. The LINE is not noticeable in mammals, crocodylia, aves, or testudines, so it has already been inactivated at least twice in evolution.

This is not the only example of genomic information from a rare species shedding light on the evolutionary history of human genome.  The genome of the threatened desert tortoise Gopherus agassizii also harbours an ancient LINE that has enabled functional elements of the human genome to be identified.  Lowe and colleagues speculate that this may be due to the very nature of endangered species, and ran simulations to show that theoretically, mobile elements like LINEs are active for longer and evolve more slowly in small populations.   This effect comes about because of the relationship between population size and selection – selection is more efficient in large populations so is more likely to remove genetic variants which are mildly harmful (or deleterious) to the organism, and to fix mutations which are beneficial.  The smaller the population, the more likely it is that deleterious genetic variants will become fixed in that population and beneficial mutations will be removed.  Insertion of mobile elements into new places in the genome is almost always deleterious, as it messes with existing genes and their regulatory regions.  Thus small populations will be more likely to accumulate additional copies of the mobile elements, and less likely to accumulate mutations which would remove or inactivate them.  I should point out here that tuatara are not actually classified as endangered (as the paper claims), but they have had a historically low population size, with probably a severe population bottleneck during the oligocene inundation of the New Zealand land mass.  In addition, we now know that even large tuatara populations can have a small effective population size, as few individuals actually contribute to mating at any one time.

Lowe and colleagues point out that without the tuatara, we would not have been able to identify these particular functional elements in the human genome, and that we never know what additional information about human evolution we might glean from threatened species in the future.  This underscores the importance of projects like the Genome10K initiative to sequence 10,000 vertebrate genomes.  Of course I would add that we should preserve these species for their intrinsic worth not just because of what they can tell us about human evolution, but this paper does highlight the unexpected ways that genomic data from diverse species can help us understand evolution.

Lowe, C., Bejerano, G., Salama, S., & Haussler, D. (2010). Endangered Species Hold Clues to Human Evolution Journal of Heredity DOI: 10.1093/jhered/esq016

How hard can a tuatara bite? Hilary Miller Jan 06

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ResearchBlogging.orgAs a geneticist, I’m only rarely let out of the lab to chase after my study animal, the tuatara.  I count these occasions as a gift, where I get to feel like a “real” biologist and learn to talk knowledgably about the ecology and habits of tuatara (which, lets face it, are generally of more interest to the lay person than their genes).  I also count myself lucky that I’ve never been bitten by a tuatara – although I have helped extract other people’s fingers from the mouths of tuatara and can confirm that it is an eye-watering experience.

We now know exactly how hard a tuatara can bite, thanks to a recent study published in the Journal of the Royal Society of New ZealandMarc Jones (University College London) and Kristopher Lappin (California State Polytechnic University) have measured bite force in adult tuatara and found that a male tuatara could produce a bite force of up to 238 Newtons.  Jones and Lappin measured bite force using a custom-designed isometric force transducer.  They report that the tuatara needed little encouragement to bite onto the leather-covered bite plates, and that “once biting commenced the tuatara would maintain its grip with considerable reluctance to release”.  Something that will come as no surprise to those who have been on the receiving end of a tuatara bite!

When comparing their results with previously published data from juvenile tuatara, Jones and Lappin discovered that adult tuatara bite proportionately harder than juveniles, even when the difference in skull size between adults and juveniles is accounted for.   This phenomenon has been observed in many other reptiles, but the reason for it is unclear. 

Knowing how hard a tuatara can bite is of more than just academic interest to researchers interested in knowing how much it will hurt when they get bitten.  Bite force is linked to many aspects of behaviour, influencing, for instance, the range of potential food items that an animal can consume, and the outcome of competitive interactions.  In some lizard species, bite force is a better predictor of territory size and reproductive success than body size.   Although yet to be confirmed in field studies, this may also be the case for tuatara, as males in particular aggressively compete for territories and access to females.

It appears that tuatara cannot bite as hard as agamid lizards of the same size, and Jones and Lappin speculate that agamid lizards could have out-competed rhynchocephalians in the late Mesozoic, contributing to their demise everywhere except New Zealand.  However, they point out that “it is unknown how the bite force of the modern day tuatara compares to that of Mesozoic rhynchocephalians, which were very diverse in terms of their tooth shapes and skull structure. Therefore it is unlikely that all but one rhynchocephalian lineage went extinct because of prey competition with a single group of lizards”.  

Marc E. H. Jones, & A. Kristopher Lappin (2009). Bite-force performance of the last rhynchocephalian Journal of the Royal Society of New Zealand, 39 (3), 71-83

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