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Archive for the ‘Genetics’ Category

A leucistic green sea turtle (spotted on r/pics).

On first appearances I’m sure the majority of us would proclaim with interest and enthusiasm, “WOW! An albino green sea turtle.” However, that isn’t the case interestingly enough! It’s actually a turtle with what’s known as leucism. According to wikipedia:

Unlike albinism, it is caused by a reduction in all types of skin pigment, not just melanin.

From my understanding, the best way to tell the difference is by looking at other parts of the body like the eyes (leucism can also be patchy in appearance where only some parts of the animals skin is affected). Melanin is the only pigment that contributes to eye colour (in the iris specifically), and hence why it’s possible to detect the difference between these two genetic disorders. (However, this method isn’t necessarily fool proof as I’m sure pigmentation attributed to melanin may vary a great deal across many different species, so genetic tests would probably be the only thing that is truly fool proof when it comes down to it).

A leucistic pigeon (not the normal coloured eyes and legs, and patches of normally coloured feathers).

In the below example using the alligator, when the eyes appear as they normally do, with grey/blue pigmentation, the animal is most likely leucistic, and if it has pink eyes lacking melanin pigmentation then it’s an albino.

A leucistic alligator

An albino alligator

People may ask why traits like albinism or leucism still exist in the wild when surely it has little if any benefits for animals? Evolution via natural selection unfortunately finds it relatively impossible to weed out traits like albinism and leucism which are recessive. That is that they aren’t exhibited by the animal (in what’s called its phenotype) unless the animal has two copies of the recessive alleles (one from its mother and one from its father). If it only has one, it will exhibit the same phenotype (it will appear the same) as would an individual without any copy of that allele.

Because of this fact, individuals who carry two alleles and appear white are likely to have a lower fitness level than other normally appearing individuals, and is thus more likely to be killed/predated prior to passing on its genes. However, because individuals can carry a single recessive allele for albinism or leucism without any changes to its appearance, if it ever mates with another individual who is carrying a single (or two) recessive alleles then offspring may be produced carrying this phenotype. Similar to genetic disorders in humans such as cystic fibrosis or sickle-cell anemia.

On a side note, during my volunteer work in Queensland at Mon Repos with sea turtles, I would often find white hatchlings. Unfortunately, the majority of them normally didn’t make it out of their shells and died in the burrows as a result of other genetic defects they also carried (they often had contorted bodies, and one I found had no eyes at all). In once case I even found twin albinos sharing a single egg shell. Sometimes you’d find abnormally large eggs an these would have two yolks or embryos in them. It was rare enough that they would actually develop at all, let alone develop and both be albino or leucistic.

Looking back I wish I’d had a closer look and could’ve worked out whether they were carrying albinism or leucism! I might have to rummage through my turtle photos and see if I can find some images of them.

Green sea turtle hatchlings, clearly some can survive, but also note the distortion of the vertebral scales along the spine of the white hatchling (though this is often seen on average hatchlings too).

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This is a photo of an African tribal woman with an albino child. Albinism is a recessive trait that is passed on from both parents to their child. This woman will have one recessive albino gene, and the father will either be the same, ie. heterozygotic, or he will himself be an albino with two copies of the recessive gene, ie. homozygotic, as the baby does.

When two heterozygotic people have children the chances of having an albino child is 1 in 4, if one of the parents is heterozygotic and the other is homozygotic the chances are 1 in 2, and if both parents are homozygotic every child will be albino.

Below is apparently a picture of the same child but many years later with her tribe.

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The fruit was found in the banks of the Kolmya River in Siberia, a top site for people looking for mammoth bones.

The Institute of Cell Biophysics team raised plants of Silene stenophylla – of the campion family – from the fruit.

Writing in Proceedings of the National Academy of Sciences (PNAS), they note this is the oldest plant material by far to have been brought to life.

Prior to this, the record lay with date palm seeds stored for 2,000 years at Masada in Israel.

Species: Silene stenophylla, the fruits of which grew into healthy plants, but were subtly different from modern individuals of the species

Here’s the full article from BBC News. What would be, and hopefully will, be cool is to examine the genetic differences between the historic specimens of this plant species and modern species today. I’m unsure if any species frozen or fossilised from >30 000 years ago would be able to have its genome fully sequenced and examined today, this may be the first example once it’s done.

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A man who had both grapefruit and orange trees in his backyard apparently discovered this recently when chowing down on one of his homegrown oranges. He had discovered that his grapefruit tree had pollinated his orange tree, giving this as the result.

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I finished my Masters of Science (MSc) at the University of Melbourne at the end of last year, and thankfully scored first class as did many of my good masters maties! I was looking at the goanna species Varanus varius and more specifically at the species phylogeography (wide-scale, historic gene flow), and its population / landscape genetics (small-scale, contemporary gene flow).

Brief findings:

  • Historic gene flow – mtDNA analysis of ND4 showed the presence of 3 clades within the species, separated by montane biogeographic barriers (Great Dividing Range (GDR) and Mcpherson Range), and possibly the Burdekin Gap in northern Qld (dry habitat barrier). Although I’m just finishing up some final lab work and analysis to reveal whether its the Burdekin Gap or a pattern of isolation by distance that has split the clades in this area.
  • Contemporary gene flow – Microsatellite analysis indicated male sex-biased dispersal was present within the species (males move further than females), no significant genetic structure over the 600kms^2 that I sampled indicating the species is incredibly dispersive (can move large distances), and that there was a more recent area of contact between two clades at the Hunter Valley, NSW.
  • Evidence from both these markers and their analyses also indicated that the species was more historically restricted to the north coast of Australia in QLD, and when the climate become more favourable (warmer/wetter) in the south they expanded southwards.
  • I also found evidence that the species had used the Murray-Darling river system and its surrounding forest as dispersive corridors to spread west inland and south from QLD. (Amazingly, some individuals from the GDR in Qld were more closely related to individuals from near Adelaide and northern Victoria (2000kms west/southwest) than they were to individuals 50kms to their east in Qld. It’s thought that flooding events will have also facilitated the spread of individuals down these river systems.

Anyway, I thought I’d share some of the photos taken during my 2 year MSc project. So bring on the photos! I’ll chuck my 2 cents in on top of each photo. By the way sorry for the poor quality of the photos, a lot were taken on my iPhone.

So this is the beasty I was studying and chasing around in the field on several field trips throughout 2009, ’10 and ’11, Varanus varius aka Tree Goanna or Lace Monitor. They were often found running along the sides of roads as it is easy terrain for them to walk on, or running around camping and picnic grounds.

I went on 3 field trips out to East Gippsland and Wilson’s Promontory, Victoria, Australia, where my supervisor had already been trapping for 2 or 3 years and had other MSc students doing their research on other creatures. I also went on a 2 week long field trip starting in Brisbane, Qld and drove down the east coast of Australia through NSW and into Victoria to try and fill sample gaps where museums had not collected genetic samples previously. I did pretty well, but often saw many more than I caught each day… Damn goannas were incredibly fast and quick to run up tries and evade us weirdos running around with dog noose polls.

Here are a few photos of the places and habitat I was trapping/catching these guys in.

The first 3 photos are from Wilson’s Promontory

The rest of the photos are from various locations along the coast in NSW.

At the time of the field trip down the east coast many areas of Qld and NSW were suffering those severe floods. The below are photos taken at Nymboida Pub, NSW.

This was the scene behind the pub, usually a small creek.

These were the 2m long aluminium traps I used to capture the goannas. They were a simple trap that just had a trap door held up by a pin that was attached to a wire running to the other end of the trap and inside it was tied to some chicken. When the goanna pulled on it the door shut and it was trapped. I also hung future baits from a tree nearby to fester up and send the smell off into the surrounding bush to attract them. Unfortunately they’d also attract things like wasps, one time in Wilson’s Prom a bag had 100s of European wasps all over it and in it eating the chicken… bastards!

Sand pads were also left outside the traps to see if goannas had come to check the location out but hadn’t triggered the trap. I also set up camera traps outside the aluminium traps at Wilson’s Prom (left side of the below photo tied to the tree).

This was a boy I caught near Newcastle, NSW. Once caught I duct taped their mouths and legs together to prevent the goannas hurting us or themselves while I measured them, weighed them and took blood samples from them for the genetic work.

Another big boy being measured out in East Gippsland.

I’d also take measurements of the head size, this one below has just had its snout taped and is about to be measured.

I’d use a syringe to take a blood sample from each individuals caudal vein/artery in their tail situated just below their spine. It took a while to get used to it but eventually I could do it within a few seconds.

Lizards would also be weighed. Although they are a sexually dimorphic species you couldn’t tell the females from the males if they were below 4kgs. Males were the only sex that grew past 4kgs, sometimes reaching up to 12kgs if they lived near a tip or camp site where food was abundant. This one below is on the smaller side so could have been either a male or a female.

Occasionally they’d be kind enough to hock up their last meal in the aluminium traps. The photo below is from the individual caught at Newcastle (pictured above). That camping spot had literally millions of cicadas pretty much screaming their calls constantly, so it was no surprise when this guy’s stomach turned out to be full of them, and a bit of fur from a possum.

These two photos below are of an individual from East Gippsland that had somehow managed to eat a juvenile echidna, spikes and all, and then been able to vomit them up?! That cannot have been pleasant at all…

While in Newcastle on the field trip we also hooked up with some of my supervisors scientist friends who were working on the biomechanics of varanids’ skulls and their bite force. They’d set up about 5-6 digital cameras in a semicircle around the individual to get a 3D image of its head, and then test its bite force using a pressure sensor. However, the one below wasn’t too interested in biting down as I suspect it was tired and had had enough.

See those bloody claws?! They use them for climbing trees, and most probably to tear at and hold carcasses they find while pulling flesh off them with their jaws. Here’re some closeups of the claws… epic talons! I was scratched quite a few times.

I often had to go to some extreme lengths, or heights rather, to capture some of these sneakily evasive goannas. They’d often climb straight up the tree at the first sight of a human and into the very thin branches at the top of it.

You probably can’t see it but there were actually 2 big males in the tree in the below photo. My mate and field assistant, who also was a freak rock climber, would happily tear up their trees bare hand with the noose pole to get the samples and data I needed! To attract these guys below we had by chance come across a dead wallaby and pulled it away from the road and under this tree where we tied it so it couldn’t be moved. When we showed up though there were 3 of them, one bailed before we were out of the care and the other two went straight up the tree. We got them both though muahahaha!

When letting them go I’d place them on a nearby tree so their claws were otherwise occupied with a grip and wouldn’t scratch me once I cut the tape. Then while holding the body against the tree with its freed limbs grabbing the tree trunk I’d take the tape on their snouts off. Often they wouldn’t move an inch and would just sit there pretending to be dead while you walked off.

Here are some more photos of the goannas we saw, and sometimes caught, on the road trip down the coast.

My supervisor and his son with one of the largest goannas caught in East Gippsland.

Some other herps I got to see on my trips. Feel free to tell me what the species are if you know them as I haven’t bothered to look these guys up yet.

A friendly little venomous surprise was waiting for me under a leaf in a pit fall trap bucket one morning, wasn’t keen to get him out by hand…

However, this guy below I was brave enough to pick up and have a better look at.

And non-herps. These are what I’ve always known as ‘spit-fires’ because if you touch them they spray some nasty chemical on you that burns like hell. Happened to me once as a child in the playground at school, since then I’ve never been done!

Eastern Grey Kangaroos at Wilson’s Prom.

THE END!

If for some reason you’d be interested in reading my thesis I’m more than willing to email it out just send me your email 🙂

Pete

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After doing a recent podcast episode with Jake Farr-Wharton on The Imaginary Friends Show I thought I’d repost this article from Evolution 101 written by Dr. Zachary Moore on the evolution of homosexuality. I’ve added a few pictures and links to the text. Enjoy!

Why did homosexuality evolve? I realize that, just as with evolution, homosexuality is still somewhat of a controversial issue in pop culture (well, at least in American culture, for my international listeners). But nothing’s more interesting then sex, and what could be better than sex and evolution?

The common argument goes like this: if evolution is true, then only those individuals who are able to reproduce will contribute offspring to the next generation. Thus, individuals who are homosexuals will not be able to reproduce, their genes will not be passed on to the next generation, and so if there is some genetic or biological reason for homosexuality, evolution should have removed it a long time ago.

First of all, is homosexuality a specifically human behavior? If it is a fundamentally biological behavior, there should be some other species which share it. And, in fact, there are close to 500 known species which are known to engage in homosexual behavior, including elephants, dolphins, sheep, bears, deer, rats, cats, dogs, cows, rabbits, kangaroos, squirrels, whales, bats, pigs, mice, goats, as well as just about every other primate. And that’s just the mammals! There are many more birds, fish, reptiles, and even insects which have also engaged in homosexual behavior.

So it really doesn’t seem as if homosexuality is really all that uncommon. But so what? Why should homosexuality be a trait found in so many organisms if it’s so fatal to the evolution of the species.

Well, the answer is, as with most things I discuss here, that sex really isn’t black and white. And homosexuality isn’t fatal to the evolution of species. Remember the definition I gave for evolution way back in the first podcast- “change in allele frequency in a given population over time.” There’s a reason why I specified “population,” and not “individual.” Individual organisms don’t “evolve” any more than a single pixel makes up a picture on your computer screen. What is necessary for evolution to take place is for there to be a group of individuals, a population, within which genes can change and flow.

Now, it certainly is the case that, for most organisms which utilize sex, heterosexual sex is required for propagation. But consider- not all species employ strictly monogamous sexual strategies. For many species, males compete for control of several females, meaning that there are many males who are left out in the cold, so to speak, with nothing but each other and raging libidos. One hypothesis fits this scenario- homosexuality occurs in these organisms to placate the male aggression that is left over after competition for females.

But that doesn’t mean that homosexuality is always a consolation prize. Among the American Bison, male-male intercourse accounts for almost half of all mating, and not just among the losers. Both parties seem to enjoy themselves, with the subordinate male even accommodating the advances of the dominant male. The same phenomenon can be seen in bighorn sheep, where the male being mounted even adopts the arched-back posture called “lordosis,” which is typically associated with the female sexual response. Clearly, these animals seem to be enjoying what they’re doing.

But the males don’t get to have all the fun. Female homosexuality is also common, with female antelope mounting each other in simulation of heterosexual courtship behavior when males are not present. In bonobo chimpanzees, the female-dominated social network is composed of close bonds which are shown by frequent homosexual interactions between female members of the group. In fact, more than half of an adult female bonobo’s sexual interactions will be homosexual in nature. (An in depth paper on homosexuality in primates)

So how, you’re probably wondering, do these populations ever manage to reproduce with so much homosexuality? Well, the reason is because, as I said before, it’s not that black and white. Sure, individuals engage in homosexuality some of the time, or even a lot of the time, depending on the species. But not all of the time- they still find time to mate heterosexually. Sex seems to be a very fluid trait in many animals- pretty much any sexual configuration that can be performed within anatomical limits is done by some kind of animal. Sorry to say, but although humans can be kinky, we’re just not that original.

Now, you remember that I said that evolution takes place in populations, not individuals? Well, consider the social benefits of a population in which all members can share the close bonds of a sexual relationship, not just males and females. Clearly, in the case of bonobo chimpanzees, the bonds formed between females by homosexual relations are socially stabilizing. A stable society is much more likely to promote successful reproduction of young. Thus, homosexuality would be an evolutionarily beneficial behavior.

But what about some molecular evidence? Well, if you’re hoping that a “gay gene” has been found you’re not in luck. One hasn’t been found, although more and more scientists are starting to look at the genetics of homosexuality. Most likely, homosexuality as a behavior is a more complex phenomenon than just blue or brown eyes- a number of factors are considered- including the number of older male siblings a person has. Scientific research out of Toronto has shown that the more older male siblings a man has, the more likely he is to be a homosexual. The hypothesis is that the mothers becomes immunologically sensitized to the successive male fetuses within her, since they contain male proteins that she is not used to. According to this hypothesis, by the time the youngest male child is being carried in utero, she has developed anti-male antibodies which effectively diminish the normal masculinization process, resulting in a tendency towards homosexuality. But there may be some other benefits to the mother- a recent study from Italy showed that the maternal relatives of homosexual men have more children than the maternal relatives of heterosexual men. If this is repeated, it would suggest that there is a reproductive benefit to women whose DNA tends to result in homosexual male children- they have more children overall, meaning that their evolutionary fitness is actually increased because of the fact that they have homosexual sons. This is a fascinating possibility, especially because a better understanding of the genes involved in this phenomenon could have a major influence on our understanding of reproduction in general, and could point towards some better therapeutic targets for women who have problems with fertility.

All right- well, that was a lot to chew on for this week. To review- homosexuality is not a strictly human trait- it is practiced commonly throughout the animal kingdom. It has a clear evolutionary benefit in that it fosters better socialization among members of both genders. In humans, the evidence strongly suggests some kind of genetic component in the development of homosexuality, although the specific genes have not yet been discovered.

Before I sign off, I do want to make it crystal clear that the discussion here is in no way establishing a moral position in favor of, or against homosexuality. To do either would be to commit a clear naturalistic fallacy- to say that because something is natural, it is either right or wrong is clearly illogical. The moral discussion of homosexuality is reserved for other, non-scientific settings. Thanks for listening, and have a great week. I’ll see you next time.

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I bet you won’t guess what it is?

Australian scientists from the University of Western Australia have recently done genetic work on this organism and found it to have an estimated age of up to 200 000 years!? It’s a patch of giant sea grass in the Mediterranean.

Patches of sea grass were sampled across a 2000km area spanning from Spain to Cyprus, and after analysis it was found that patches had were between 12 000 and 200 000 years old, and expected to be at least 100 000 years old.

Damn Australian scientists, until now Australia held the record for oldest living organism, a Tasmanian plant species (Lomatia tasmanica) with an age of 43 000 years old.

This kind of makes our kingdom, the animals, look like chumps in comparison. The oldest living animals belong to the black coral genus Leiopathes, continuously living organisms with an age of around 4,265 years old.

Full article here

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