The Genetics of White and Gold, Blue and Black: A Holler to 23andMe

The internet is currently losing its collective composure over the perception of colour in the following unremarkable photograph:

Blue and black, or white and gold?

Buzzfeed’s explanation invokes the illusion of compensation; that a single shade can be perceived in multiple ways depending on the lighting context (see image below). There is an excellent write up of the illusion on Jerry Coyne’s blog so I won’t go into any more detail on it here. But you should click through to see a vivid example of the illusion in action.

Compensation illusion: A and B are the same shade.

What I am more interested in is the ratio of “Black and Blue”, to “White and Gold” in that Buzzfeed survey. The sample size is large (>200000 people have voted), and those numbers look suspiciously Mendelian, which got me thinking that perhaps there might be an opportunity to look for a genetic link to colour perception.

Source: Buzzfeed

For those who remember high school genetics, Mendel was the Monk who discovered genetic inheritance by crossing pea flowers of varying colours. When we refer to simple inheritance of traits they are often described as “Mendelian”. At a single locus, perhaps there is a dominant ‘White and Gold’ gene, and a recessive ‘Blue and Black’ gene. At equal frequency in the population, one would expect the phenotypes (white/gold versus blue/black) exactly as shown in the survey. That’s a lot of “ifs”, and highly unlikely, but it is possible that there may be some genetic control underlying this variation in perception.

Mendelian inheritance

Is it possible that compensating in colour perception could be partly influenced by just one locus? It sounds absurd, but if this is not some elaborate trolling then it might actually be a real possibility.

This is where you come in 23andme! As holder of one of the greatest collections of human genetic variation data, I implore you to carry out the white and gold, blue and black survey yourselves. Linked to 600,000 single nucleotide polymorphisms for over 1 million people, we could get a pretty powerful association study done really quickly. The result could tell us something fascinating about the genetics of perception.

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Pollination, evolution and an orchid’s seductive ruse.

In a PR coup for dumpy little green orchids everywhere, research from my PhD recently landed on the cover of the journal Evolution. But what is it about?

Spring. The Blue Mountains, west of Sydney. Altitude 1000m. Frosty winds whip a swaying eucalypt canopy infiltrated by billowing cloud. Down below, amongst snowgrass tufts, rotting logs and bracken dwell the diminutive bird orchids. Genus: Chiloglottis. They huddle in tight colonies, sporadically sprayed by the high country squall.

Each plant holds two leaves pressed flat to the damp ground. Between the leaves a stem rises, holding aloft a single intricate flower in dusky shades of green and burgundy. When banks of cloud give way to azure sky and the shrike-thrushes resume their piping, these small blooms become irresistible lures.

Their target are the gracile flower wasps. Slim glossy black insects, zooming silently on shimmering wings. They are helplessly drawn to the flower. The bird orchid is emitting a scent, detectable only to wasps, which signals the promise of a mate. Known as ‘sexual deception’, the elaborate ruse uses a precise mimicry of female wasp pheromones to fool male wasps into pollinating the orchid.

However, here on the forest floor there is not only one species of orchid outwitting wasps for its own reproductive ends. Look closer and slight differences in the characteristics of flowers and visiting wasps betray something more complex and interesting. There are actually two species here, looking largely the same, growing in the same places, both deceiving their wasp pollinators through the false promise of sex.

By emitting subtle variations of their chemical trickery, these orchids have “tuned in” to two different pollinator species. This research paper explores this phenomenon as a way of separating the gene pools of closely related organisms. At the heart of it, the story here is about the forces that keep species apart once they split, or reproductive isolation.

First, we show that the different pheromones emitted by the two orchids are responsible for attracting different pollinators. Through arcane powers of chemical synthesis that I do not understand, chemists created synthetic orchid pheromones for us. We took these into the landscape and showed that the two chemicals attract two different wasps. The only perceivable difference between the wasps involved is yellow spangles on the carapace of one of the varieties. What’s more, this specific attraction is exclusive. Chemical A only attracts wasp A, and chemical B only appeals to wasp B.

Next, we take real flowers of both kinds and place them in a row and watch the hapless wasps roll in. We see that wasp A is only attracted to flower A, even when flower B is present just centimetres away. The results are identical to the results of the synthetic pheromone experiment.

On the basis of scent, we therefore expect that orchid A may never mate with orchid B. Exclusive attraction ensures that despite living amongst one another, some orchids may never exchange genes. Despite looking almost the same to us, they may as well exist on separate islands. They distinct separate species.

In order to back this up we then looked at the genetics of the species. By using the same kind of genes used in human DNA fingerprinting we were able to show that the two kinds of orchid exhibit differences in their gene pools of a degree expected if they were different species. Furthermore, analysis showed not a single individual displaying the genetics of a hybrid. Our last tests were to make hand-pollinated hybrids to check that hybrids could indeed form. These crosses showed hybrid offspring germinated and grew faster than pure crosses.

The potential for animals to drive the formation of plant species has long been recognized. This study gives us a strong case study of how that process might look. Our orchids are spectacular examples of the power of pollinators to create and maintain plant species. Through selective pollinator attraction, the orchids have been set upon unique and separate evolutionary journeys.

Further reading:

Whitehead, M. R. and Peakall, R. (2014) Pollinator specificity drives strong prepollination reproductive isolation in sympatric sexually deceptive orchids. Evolution 68: 1561–1575. doi: 10.1111/evo.12382

Rod Peakall and Michael R. Whitehead (2014) Floral odour chemistry defines species boundaries and underpins strong reproductive isolation in sexually deceptive orchids Annals of Botany 113 (2): 341-355 first published online September 19, 2013 doi:10.1093/aob/mct199

Plant pollinator interactions in the South African flora

The slides from my recent departmental seminar at the ANU are below.

The first half of the talk concentrates on plant-pollinator interactions, floral guilds and floral evolution. The second half is a slideshow of vistas, creatures and plants I encountered in my work.

Roses reflect greatest above 620 nm, Violets reflect at 420 – 480 nm…

Roses are red,  Violets are blue,  Botany is sexy, But less so than you.

Roses are red,
Violets are blue,
Botany is sexy,
But less so than you.

Along with odour, flower colour is perhaps the most important cue plants use to advertise to pollinators. Change the colour of a flower and that change can have large consequences on which pollinating animals are likely to visit[1]. Bees, for example, are attracted to purple flowers with UV highlights. If that plant were to mutate to white, it could very well find itself being visited by nocturnal moths[2].

In studying plant-pollinator evolution and ecology, it is very important then that we have some objective quantification of the colour of a flower. Human eyes are famously fallible and many insects and birds can see outside the range of our colour vision (400 – 700 nm).

The instrument we use is a spectrometer[3]. It uses optic fibres to bounce an initially white-light beam off the surface you want to measure. The wavelengths of light that are reflected (as opposed to absorbed) determine the colour of the surface you are looking at. The spectrometer collects the reflected light, separates the wavelengths through diffraction and digitises the signal. The result is a graph such as the one above.

In the graph, the wavelength is given on the horizontal axis, while the proportion of reflectance is on the vertical. The rainbow bar above provides an approximation of how the human eye perceives a given wavelength of light. The rose therefore will reflect greatest at wavelengths above 620 nm, the red part of the spectrum. A violet most strongly reflects around 420 – 480 nm. A pure white surface would show high reflectance across the range of the visible light spectrum.

Dedicated to my sweetheart, who for the second year in a row has been alone on Valentine’s.

Kniphofia are red, Agapanthus are blue.

Fieldwork is fun, But I do miss you. 

My bruised human ego

IMG_1344-1

This is the best photo I got of a group of baboons who gave me quite an experience the other day.

On a sandy fynbos trail, I rounded a corner obscured by vegetation and came abruptly face to face with a troupe of seven of these creatures. The closest member was only 3 metres from me. All of them were stopped, standing or sitting,  looking at me as I did the same. My first reaction was one of awe, these creatures are impressively muscular and intimidating up close. One of them, a very large male, was wearing a radio collar. My second instinct was to take advantage of the photo opportunity, but my camera was in my backpack.

My only close experience with monkeys comes from Indonesian macaques, and extrapolating from the damage these ones wreak on tourists’ belongings I was not keen to get the baboons interested in anything I owned. I was also aware that some baboon troupes in the Cape have a reputation for raiding. Bins, bags, picnics, cars, houses are all fair game. They have overcome their fear of humans and are now a famous nuisance requiring full time management.

My bag therefore remained zipped and in place on my back. I raised my arms and hissed, to try and persuade them off the trail. One of the leaders began to advance on me, and the others stood up to follow suit.

Finally, I was forced to concede the path to the baboons. I back-stepped into the bush beside the track, allowing them a 2 metre thoroughfare which they calmly took in an orderly and nonchalant fashion. Only after passing me, when their backs were exposed, did they pick up speed into a quick trot for a dozen metres to put some distance between us.

 

Red Hill fynbos track

Kleinplaas Dam fynbos track

 

Die Selfish Gene, Die.

I was recently asked by a friend for my opinion on David Dobbs’ piece “Die Selfish Gene, Die.” The article spins a yarn on why Richard Dawkins’ “Selfish Gene” thesis is sunk and the battle for updating it with a new theory of “genetic accommodation”.

It has attracted much attention as a great piece of science writing popularising the battle for a paradigm shift in genetics and evolution. Unfortunately its inaccurate and a bit too puffed up on its own bravado. My brief statement is below, however Jerry Coyne, Richard Dawkins and PZ Myers provide a more thorough commentary.

***

Dobbs’ article describes a battle of two straw men. 

The term “genetic accommodation” is a new one to me, but the description of it sounds like phenotypic plasticity together with pleiotropy and epigenetics in a fancy jacket, but maybe we needed a word for that. Nonetheless, contrasting it with the selfish gene hypothesis is a false dichotomy. The messy truth for many traits lies somewhere in between, where the convoluted cascade of genetic-epigenetic-genetic interactions involved in “expression” will face selection as soon as its resultant phenotype hits the environment. 

The complexity of gene expression via interactions between genes and epigenetics (non-DNA inheritance) is blowing a lot of our heads off right now. It’s chaotically complex in there. I think the article therefore makes a mistake in referring to “gene expression” as a singular process.

Work I saw presented by John Mattick from the Garvan Institute provides a good example. Gene expression in human neurons can be governed by the interaction of RNAs, binding to “non-coding” DNA and interacting in 3 dimensions with complex protein molecules. In other words, it starts with a gene, which makes an RNA. That RNA’s action depends on the interaction between its sequence and where it binds on the genome. The sequence of DNA to which it binds, governs how it binds; simple like a zip, or more complex and looped up. Along comes a protein molecule (encoded earlier, elsewhere, by another gene) and the molecular properties of that gargantuan tangle of amino acids determine how it interacts with that looped up bit of RNA stuck to the DNA. This binding provides but a step in some long chain of protein interactions in a biological pathway. 

This kind of combinatorial complexity of interactions provides huge plasticity of action for a single set of tools (the genome).

One could argue that the first step of environmental interaction of any gene is the “environment” of the genome and epigenome it inhabits. This could still be squared with the selfish gene thesis.

As you were, Australian researchers.

Waking up to look at this before a coffee and a shower was enough to put me into fight or flight mode this morning.

With hackles raised I read on and found a sciency corner of Australian Twitter users in a flap about Abbott’s 20% ARC cuts. #AbbottsRazor #ARCcuts etc etc

While the wording of these Tweets is strictly true, they are also completely misrepresenting the politics of these ARC funding estimates.

The numbers are below. The top row is the current budget handed down by Labour in 2013. The middle row is the Abbott Government amendment. The bottom row is the difference. Numbers represented in thousands (000’s).

2013-14

2014-15

2015-16

2016-17

TOTAL

May budget

$883,959

$879,983

$834,587

$788,710

$3,387,239

Amendment

$883,959

$853,110

$783,253

$716,205

$3,236,527

Difference

$0

$26,873

$51,334

$72,505

$150,712

YES. ARC funding will dive by 19% in the next 4 years. But this is a dive courtesy of the Labour Government’s May 2013 budget.

YES. Abbott is cutting funding further, but this amounts to 4% cut in total ARC spending over the next 4 years. The majority of the sliding investment trend came from the initial budget trajectory set out in May.

The time to make a flap about budget cuts was in May. And some of us had a good whinge then. The truth of this latest news is that it is a continuation of the prevailing “death by a thousand cuts” trend, as another shaving is whittled off our future investment in research and innovation.

But the big lesson here is to hold fire when it comes to social media. A forgiving person might acknowledge that this shows that scientists are only human, prone to the occasional passionate, emotional, reactionary outbursts. A harder judge might question whether researchers who don’t think critically and do a bit of their own “research”, deserve any ARC funding at all.

Thanks Alice Hutchings, for engaging your brain. And Tom Stayner for the title.

Postscript

Jeremy Shearman from the Genome Institute in Thailand has produced this graphic showing the effect of amendments on ARC funding over the last few years. The trend is one of providing more upfront dollars with increasingly steep sliding scales of less funding later.

ARC funding amendment history

Major party’s science and research policies: Update

Two weeks ago I presented a summary of policy positions for the major parties this Australian Federal Election. Since that time we have seen the release of Science and Technology Australia’s science policy questionnaire, the release of the Coalition’s costings and an official release from the ALP outlining their position on science and research policy.

Of note is Tony Abbott’s promise to redirect $104 million of Australian Research Council funds away from projects deemed wasteful and into medical and health research. This should not be a surprise if you have been reading between the lines in the Coalition’s promise to maintain health funding and nothing more. The ARC’s competitive research budget for next year is $884 million and these cuts would “reprioritise” $16 million in the first year of a Coalition Government. While this is not a great proportion of the ARC pie, the move is more worrying for the precedent it sets in letting politicians decide the national research agenda.

Science and Technology’s response to the Coalition’s policy is here.

Updated table below:

SciPolicies8

Grading the major party’s science and research policies this election

For supporters of science and research wanting to know what the major parties have on offer in this year’s election campaign, you need go no further than here.

SciencePolicyBreakdown

Slim pickings indeed, aside from The Greens recent science package proposal. The Greens policies are thoughtful and align well with the Australian Academy of Science’s election policy recommendations. Liberal and Labor’s policies are limited token reactions to the recent McKeon NHMRC review.

I hope I will get to update the table if/when the major contenders can come up with some sensible policy for the research sector.

In the mean time, please feel free to copy and distribute the table.

THE GRADES

The Greens: Solid

Labor: Chiffon

Liberal: Gossamer

For more information:

Australian Academy of Sciences election policy recommendations

Greens Science Policy

Liberal Party health and medical research funding

Labor’s McKeon Research Package

Sydney Morning Herald coverage of Green’s science policy package

A most engaging mantid

Recently, I was fortunate enough to spend eight days in Ndumo Game Reserve, where for several hours a day I remained perched above clusters of large flowers smelling rather like a long-drop toilet. Tagging along as help on a study of Stapelia gigantea promised to be a chance to see a new South African biome and the wonderful creatures that come along with it.

The carrion flower (Stapelia gigantea, bottom right) in rural Zululand aloe country.

Driving to and from the field site every day we would encounter giraffe, wildebeest, nyala, impala and warthogs going about their daily activities. At dusk we’d sit in a bird hide, count waterfowl and watch crocodiles cruise on by. Our nights were serenaded by the wailing bush baby, the guttural grunting of wildebeest, the booming-bass of hippos and occasionally the manic whinny of a hyena, while the porch light drew in a bewildering buffet of invertebrate curiosity.

Croc on dusk, silently sweeping past the bird hide.

But perhaps the most endearing animal found all trip was one of the most captivating mantids I have ever seen. She is a cryptically coloured Hymenopodidae, belonging to the same subfamily as the spectacular orchid mantis. Unlike other mantids I have encountered she is very easy to handle and shows no desire to flee the hand or captivity. She is a voracious feeder and any moth or fly introduced to her enclosure scarcely lasts 5 minutes before straying too close to her raptorial forelimbs. On her second night in our field accommodation she had already laid a small ootheca.

She also displays a charming and unusual shadow boxing routine complete with weaving, jabs and feints.

Edit: I have since learned that she belongs to genus Oxypilus, a group of mantids called “Boxer mantis”, for reasons made obvious in this video. (Thanks Mantidboy for the ID).

The above video was shot with a Canon 500D, Canon 100mm f/2.8 macro in an improvised stove-top studio. A piece of white paper provided the background, the camera was stabilized on a bag of rice. This left my hands free to experiment with the lighting, provided by a cheap head torch.