Apparently New Zealand was confused with New Caledonia, and is actually ranked number 22 on the list, with 22% of its original forest cover remaining.  Easy mistake to make, I guess (although the folks over at Kiwiblog of course think its all a big conspiracy of the part of the Greens).

So its not quite as alarming as we thought, but this is no reason to be complacent about the state of our forests.  A timely bit of research published online in the journal Science last week shows how even small changes in the makeup of our forests, like extinction of one or two key species, can have a cascading effect on biodiversity.  I’m not sure that it matters whether we are number 2 or 22 on Conservation International’s list, when we still have one of the worst records of biodiversity loss in the world.

Back in 1985, Stephen O’Brien and colleagues at the National Cancer Institute in Maryland reported extremely low levels of genetic variation in cheetahs - so low in fact, that skin grafts from one animal were not rejected by another, a sign that their immune systems are genetically identical.  This lack of genetic variation was attributed to a decline in population numbers at end of last ice age, plus more recent declines that have led to inbreeding.  The species appeared to be highly susceptible to feline infectious peritonitis (FIP), a disease which had decimated some captive populations, and attempts to breed cheetahs in captivity were hampered by poor reproductive success and apparently high levels of sperm defects.  O’Brien and colleagues attributed these problems to their extremely low levels of genetic variation, and the species quickly became a classic example of the perils of inbreeding. 

The cheetah (Acinonyx jubatus) is found mainly in southern and eastern Africa

However, in the early 1990′s, field studies questioned whether the cheetah’s survival in the wild was being compromised by their lack of genetic variation.  In a commentary in Science in 1994, Caro and Laurenson pointed out that disease susceptibility and breeding problems only appeared to be an issue for captive cheetahs, and that predation of cubs, habitat destruction and persecution by humans were greater threats to the species.

Still, a lack of variation at immune genes is still an important potential threat to any species, as shown by the case of the Tasmanian devil, where low variation at Major Histocompatibility Complex, or MHC genes, has allowed Devil Facial Tumour Disease to spread unchecked throughout the population.  MHC genes are key part of the immune system in vertebrates as they code for the molecules that distinguish self from non-self, and instruct the immune system to respond when foreign proteins (i.e. from a pathogen) are detected.  High diversity at MHC genes plays an important role in protecting populations from disease epidemics as it allows wide array of foreign pathogens to be resisted, and means that some individuals are likely to be more resistant to new diseases than others (instead of all individuals being equally susceptible).  

The skin graft experiments of the mid-1980s indicated that cheetahs have virtually no MHC variation, because of the absence of an immune response when skin from one cheetah was grafted onto another.  However the disease susceptibility seen in captive cheetahs doesn’t seem to extend to cheetahs in the wild – a recent study on wild cheetahs in Namibia  found that the population was generally in good health, and that many individuals carried antibodies to a range of diseases (suggesting they had been exposed to those diseases) but no clinical symptoms of acute disease.  These results suggest that wild cheetahs may have more MHC diversity than the captive population, and that their immune systems work just fine. 

Somewhat surprisingly, only a couple of studies in the 26 years since the skin-graft study was published have actually attempted to quantify cheetah MHC diversity.  These studies found low diversity and seemed to corroborate the skin-graft results, but either used low resolution methods to measure MHC diversity or had small sample sizes, so weren’t particularly conclusive.

This latest study, by Aines Castro-Prieto, Simone Sommer and colleagues at the Leibniz Institute for Zoo and Wildlife Research in Berlin, takes a much more comprehensive approach to measuring genetic variation.  Castro-Prieto and colleagues determined how many different alleles are present at two types of MHC genes in 149 Namibian cheetahs.  They found more variation than was previously described for the first type (Class I MHC), but not for the second type of gene (Class II MHC).  The number of different MHC alleles counted in the Namibian cheetahs is still quite low compared with what is seen in other big cat populations, so it appears that cheetahs have lost a fair amount of variation as their numbers have declined.  However, the amount of DNA sequence variation among the alleles is fairly high - that is the different alleles code for proteins that are quite different from one another in their sequence, so overall they can probably recognise a wide array of foreign proteins. 

Castro-Prieto and colleagues also found hallmarks of selection on the MHC sequences, and speculate that selection, driven by exposure to a range of pathogens over thousands of generations, has led to highly divergent alleles being retained.  However, they point out that although wild cheetahs appear to have enough MHC variation to respond to common infectious diseases, they may still be at risk from new emerging diseases, as the few remaining alleles might not be sufficient to be able to recognise and ward off an entirely new pathogen.   

This study provides some much-needed data on immune variation in cheetahs, and it seems that the idea of the cheetah being a classic case of disease vulnerability associated with low genetic diversity is looking a little shaky.  As Castro-Prieto et al point out, “the long term survival of free-ranging cheetahs in Namibia seems more likely to depend on human-induced rather than genetic factors”.

Reference: Castro-Prieto A, Wachter B, & Sommer S (2010). Cheetah paradigm revisited: MHC diversity in the world’s largest free-ranging population. Molecular biology and evolution PMID: 21183613

Further reading:

For an excellent write-up on why genetic diversity is important (and more stuff about cheetahs), see this (fairly old) post on Mauka to Makai .

O’Brien SJ, Roelke ME, Marker L, Newman A, Winkler CA, Meltzer D, Colly L, Evermann JF, Bush M, Wildt DE (1985) Genetic basis for species vulnerability in the cheetah. Science 227: 1428-1434

Caro TM, Laurenson MK (1994) Ecological and genetic factors in conservation: a cautionary tale. Science 263: 485-486.

Thalwitzer S, Wachter B, Robert N, Wibbelt G, Muller T, Lonzer J, Meli ML, Bay G, Hofer H, Lutz H (2010) Seroprevalences to Viral Pathogens in Free-Ranging and Captive Cheetahs (Acinonyx jubatus) on Namibian Farmland. Clin. Vaccine Immunol. 17: 232-238.

This DNA fingerprint of kakapo clearly shows how distinct Richard Henry was. His fingerprint is marked with an asterisk - all the others are from Stewart Is. birds

More from Stuff.co.nz:

One of the key players in the Kakapo Recovery Programme was found dead on Codfish Island yesterday, marking the end of an era.

Kakapo Richard Henry was discovered by one of the recovery team members after what was believed to be an 80-year life.

Richard Henry, who was named after a Victorian conservationist who pioneered kakapo recovery, was originally found as an adult in Fiordland in 1975 when his species was believed to be extinct.

Since that time he has contributed to the genetic diversity of kakapo in the recovery programme and is well known for his efforts.

Department of Conservation programme scientist Ron Moorhouse said Richard Henry would be sorely missed by everyone who knew him.

“Richard Henry was a living link to the early days of kakapo recovery and perhaps even to a time before stoats when kakapo could boom unmolested in Fiordland,” he said.

Richard Henry was showing signs of ageing for some time before he was found, including blindness in one eye, slow movement and wrinkles, he said.

Meanwhile, the kakapo breeding season is under way on Codfish and Anchor islands and the first eggs are expected to appear next month.

*Disclaimer: I was part of that study, and the fingerprint gel is one of my more arty pieces of molecular biology, so I thought I’d post it in tribute.

The reference is: Miller HC, Lambert DM, Millar CD, Robertson BC, Minot EO (2003) Minisatellite DNA profiling detects lineages and parentage in the endangered kakapo (Strigops habroptilus) despite low microsatellite DNA variation. Conservation Genetics, 4: 265-274.

The researchers carried out their study at Ohau stream waterfall, Kaikoura, near the location of the recent attacks that saw 23 animals bludgeoned to death.  Over a period of 9 months they recorded the behaviour of tourists in the presence or absence of a volunteer observer who was wearing a neon vest and made to look “official”.  Tourists were deemed to be harassing the seals when they approached the animals to within a few metres or threw an object at them.  They found that harassment dropped by two-thirds when the observer was present – from 38.4% down to 13% of groups with at least one person who harassed the seals  - even if the observer said nothing to the tourists. 

Viewing of fur seals is regulated by the Marine Mammals Protection Act 1992, but the researchers had previously found that simply having a sign up stating these regulations does nothing to ensure that tourists actually comply.  Having an actual person wearing a neon vest is far more effective at preventing harassment, even if this person is a volunteer with no authority to actually enforce compliance with the regulations. 

The researchers point out that using volunteers in this way is a cheap and effective way of managing tourist-wildlife interactions at popular wildlife viewing areas, and has the added bonus of observers being able to educate tourists about the animals. They found that approximately half the tourist groups approached the observer and asked questions about the behaviour of the seals, and all of them had misconceptions about how to behave around young seals.

Other posts on sciblogs about the fur seal attacks are here and here

Reference:

Acedevo-Gutierrez et al.  Effects of the Presence of Official-Looking Volunteers on Harassment of New Zealand Fur Seals.  Conservation Biology. Article first published online: 3 DEC 2010 | DOI: 10.1111/j.1523-1739.2010.01611.x

http://www.guardian.co.uk/environment/gallery/2010/nov/17/gdt-wildlife-photography#/?picture=368699851&index=0

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

Firstly, the report of a boa constrictor giving birth to two litters of offspring without the need for a father.  This sort of “virgin birth” is called parthenogenesis, and is not that uncommon in itself, having been previously observed in a few other reptile and fish species, and numerous invertebrates.  What separates this latest report from the others is the unusual complement of sex chromosomes observed in the offspring.

When vertebrates reproduce by parthenogenesis, the offspring are usually “half clones” of the mother.  Chromosomes come in pairs, and normally you get one half of the pair from your father and the other half from your mother.  But in parthenogenesis, both halves come from the mother – that is, two copies of one half of the mother’s chromosomes are inherited.   This means that when it comes to the sex chromosomes, the offspring end up with two of the copies of the same chromosome.  In all other recorded instances of pathenogenesis in vertebrates, species like snakes with the ZW sex chromosome system (where males have ZZ and females have ZW chromosomes) produce only male offspring, and species with XY chromosomes (males XY and females XX)  produce only female  offspring.   In other words, only the sex where the two sex chromosomes are the same is produced and the opposite scenario (WW females or YY males) was thought to result in non-viable offspring.  Until this boa constrictor came along, that is -  yep, her litters are made up entirely of WW female snakes, a finding which “up-ends decades of scientific theory on reptile reproduction”.

This study was published online this week in Biology Letters, and the BBC news has more on the story here

The second study, published online in Nature this week, is an great example of just how malleable sex determining systems can be.  For many reptiles, sex is determined not by sex chromosomes, but by what temperature the egg is incubated at.  In tuatara for example, incubating eggs at high temperatures produces males, while low temperatures produce females.  You might think that chromosomal and temperature-dependent sex determination are two fundamentally different, mutually exclusive ways of determining sex.  However, in some species the line between these two systems is blurred, suggesting that switching between systems is easier than you would think.  This study found that the Tasmanian snow skink (Niveoscincus ocellatus) has both types of sex determination, and all it has taken to switch between the two is a shift in climate. 

The snow skink lives in both the warm lowlands and cool highlands of Tasmania.  The study found that in the highlands, the skink uses chromosomal sex determination, producing an equal ratio of male and female offspring regardless of the temperature.  However, in the lowlands its sex determination is temperature-dependent - cool cloudy days produce males, and warm, sunny days produce females.  The researchers speculate that the divergence in sex determination mechanisms was caused by temperature differences, enabling the lizards to maximise their reproductive output in the differing climates. 

The paper is here, and ABC news has a report on this here.

Development of male and female reproductive organs in flowers is controlled largely by a group of genes called MADS-box transcription factors. Different versions of these transcription factors (known as A, B or C function genes) are expressed in different parts of the developing flower, acting either alone or together to produce sepals, petals, stamens (male) or carpels (female)*.

Much of what we know about flower development comes from studies on two “model” plants – Arabidopsis (rockcress) and Antirrhinum (snapdragon).  In these species, and in many other flowering plants, the MADs-box C-function gene that controls the production of carpels vs stamens has duplicated. In Arabidopsis, one of the copies (called AG) makes both male and female organs, but the other copy has taken on the completely new function of making seed pods shatter (and is appropriately called SHATTERPROOF).  However, in Antirrhinum both copies still play a role in sex organ development: one copy (called FAR) makes only male parts, while the other copy (PLE) makes mainly female parts but also has a small role in making male parts.

Thus in Antirrhinum, the function of the original gene (making both male and female parts) has almost been split between the two duplicate copies.  In a study published online in PNAS last week, researchers at the University of Leeds, led by Professor Brendan Davies,  found a surprisingly simple difference in the two copies has led to their profoundly different roles.

Davies and colleagues created chimeric versions of PLE and FAR, swapping domains between the proteins to determine exactly what parts of the different proteins are responsible for their differing function.  They narrowed down the difference between the two genes to a single amino acid that is present in FAR but not in PLE. When this amino acid was removed from FAR, the gene switched to making both female and male parts.  FAR and PLE are estimated to have duplicated around 120 million years ago, and the researchers estimate that the mutation responsible for inserting the extra amino acid into FAR happened around 20 million years after the duplication.

Duplicated genes often take on new functions because changes in their regulatory regions change how and where they are expressed.  Thus, finding an example such as this one, where a simple change in the protein coding sequence causes a profound change in function is somewhat unusual.  However, these proteins don’t act in isolation – they are just one part of a network of genes that must work together to control sex organ development.  Davies and colleagues found that the single amino acid change alters the ability of the protein to interact with other proteins in this network.

The additional amino acid in FAR is found in the part of the protein that interacts with other types of MADs-box proteins called SEP proteins.  C-function genes without the additional amino acid (like PLE) can interact with 3 different SEP proteins (SEP1, SEP2 and SEP3), but proteins with the additional amino acid (like FAR) can only interact with SEP3.  The SEP3 gene is not expressed in the first whorl of the flower, where female parts are produced, so FAR doesn’t have anything to interact with in this whorl and therefore doesn’t produce female parts.

Davies describes this as “an excellent example of how a chance imperfection sparks evolutionary change”.  It is also a nice example of subfunctionalization in action, where a simple amino acid change provides a means of separating the functions of the duplicate copies by causing a change in how the protein operates in a larger regulatory network.

Reference: Airoldi CA, Bergonzi S, & Davies B (2010). Single amino acid change alters the ability to specify male or female organ identity. Proceedings of the National Academy of Sciences of the United States of America PMID: 20956314

*For more on the ABC model of plant development, see here or 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.