Category Archives: Life

Developmental robustness and species diversity: A special issue of Annals of Botany open for submissions

Magnolia flowers

Flowers from the same Magnolia tree have different numbers of perianth organs, indicative of a low degree of robustness in perianth organ number determination.
Photos by Susanne Schilling.

J.B.S. Haldane is often quoted to have said that ‘God has an inordinate fondness for beetles’. Arguably, Haldane himself would not have accepted this as an explanation for the enormous number of beetle species – they make up some 25 – 30 % of all described animals. However, Haldane’s statement demonstrates that we still lack a satisfying explanation for an oddity in the tree of life: it is only a few taxa that contribute disproportionately strongly to species diversity, whereas other taxa contain relatively few species. This observation is by no means restricted to the animal kingdom; if Haldane would have been a botanist, he may have said that god (like most of us humans) has an inordinate fondness for flowering plants – these make up some 85 – 90 % of all described plant species. The question is obvious: Why are there so many flowering plant species but so few gymnosperm species? Likewise, one may ask: Why are there so many orchid, daisy and grass but so few early diverging angiosperm species? A number of explanations have been suggested over the years: the age of clades, evolutionary innovations and co-evolution may all well have contributed to the success (in terms of species number) of some taxa over others. But as obvious as some of these explanations might be for certain groups – for example, co-evolution with pollinators may well have accelerated the radiation of orchids – they fail to explain other cases of species diversity: co-evolution with pollinators can hardly explain why there are more than 10,000 species of mainly wind-pollinated grasses, for example.

However, one striking observation is that successful taxa appear to be morphologically rather uniform: all orchid flowers share a basic floral bauplan, the same applies to grasses or daisies (and also beetles have a highly standardized body plan). Highly standardized or uniform structures may be an indication for a high degree of developmental robustness. Thus, in contrast to what one may intuitively assume, robust developmental processes might facilitate rather than prevent the evolution of species diversity.

We started exploring the relationship between species diversity and developmental robustness on a symposium at the Euro Evo Devo 2014 conference in Vienna that was supported by the Annals of Botany. However, we are still far from understanding the relevance of robustness for species diversity. On account of this, a Special Issue on that topic will appear in the Annals of Botany. Authors already committed to contribute to this Special Issue are Peter Endress (Zürich), Angela Hay (Cologne), Matthew Wills (Bath), Koichi Fujimoto (Osaka), and Veronica Grieneisen (Norwich).

This is an open call for submission of manuscripts on developmental robustness, biodiversity and the relationship between the two for consideration for the Special Issue. We intend to have a mixture of papers treating the topic from the perspective of developmental genetics, evolutionary biology, plant morphology, paleobiology and systems biology. If you have a manuscript that you would like us to consider, please send an outline (Title, Authors and 250 to 500 words) until the end of 2014 to annalsbotany@le.ac.uk. If agreed, the full paper would need to be submitted by 31 March 2015, in order to enter the full review process.

Picture Perfect

Young Woman Taking Photos Of Sunflowers.

Are you a keen photographer? You are reading a botany blog, so we can speculate that you have at least a passing interest in plants! Over at photocrowd.com you can combine these two passions and throw in a little healthy creative competition, as they are currently running a photo contest to showcase your best images on the theme of ‘Seeds and fruit’ (entry closes Sept 19th 2014, midnight UK time, winners announced 25th September 2014).

Simply join photocrowd, and upload one or two images. By submitting your images into a contest you gain the right to see what other members have submitted on the same topic, and you can vote for your favourite images as part of the ‘Crowd vote’. You can choose to ‘love’, ‘like’ or ‘pass’ an image. The crowd votes are updated in real time, be warned – checking your current score and seeing what new images have been submitted can become a bit of an addiction! There is also an expert judge who choses their favourite image. In this contest the top voted pictures, as chosen by the crowd and expert, each win £50 of professional photo retouching.

Good luck!

This photo © Belahoche/BigStockPhoto.

Domestication – rabbits now catching up with plants

Wild rabbits: how do their genomes differ from domesticated rabbits?

Wild rabbits: how do their genomes differ from domesticated rabbits?

Domestication of species is critical for our farming and own nutrition, as well as being important for retrospective studies of evolutionary genetics and future applications in animal and plant breeding. The genes involved in the first stages of domestication in plants are relatively clear: a single, tasty, energy-rich, product over-produced with a high proportion easily harvested, quick and easy establishment when planted, and disease resistance (free: Special Issue Preface and full issue of Annals of Botany). It has been less clear what is needed from a newly domesticated animal: many are multi-purpose (wool, leather, milk, meat, draught/traction, as well as companions and guarding), but why haven’t more animals been domesticated? What traits are being selected? (In particular, not one of the nearly 1000 sub-Saharan vegetarian mammal species has been domesticated.) Remarkably, most of our current crop plants and animals were domesticated in a relatively short period about 10,000 years ago, so, particularly for animals, finding near-relatives for genetic studies has been difficult.

A new paper from Miguel Carneiro Porto, Portugal, and colleagues from Sweden and the US in Science this week (Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication – Carneiro et al. p. 1074; 29 August, on the Science website) uses genomic analysis of DNA in domestic and wild rabbit with whole-genome DNA sequencing information. They address some of the key questions about animal domestication. Another summary of the paper is given by Penny Sarchet in New Scientist today. Rabbit domestication is recent – only in the last 1400 years; wild populations exist for comparison, and there are multiple selected breeds, so it is a good system to work with compared to other animals. I met first Miguel Carneiro when he talked about a related paper at a meeting in Portugal in 2010 (2011 Mol Biol Evol, The Genetic Structure of Domestic Rabbits Carneiro et al.), but have not had other contact with him, although we have continuing collaboration with a nearby lab Prof Raquel Chaves at Vila Real, Portugal, on bovid genome structure and evolution.

Domesticated rabbits - friendly and little fear

Domesticated rabbits – friendly and little fear

Key points for me from the rabbit paper are that they found about 100 regions that were selected to be different and showed evidence for selective sweeps (genomic regions of reduced variation and segregation distortion or linkage disequilibrium) in the domesticated compared to wild rabbits. This means that many genes were selected simultaneously (new result) so domestication was difficult and involved only a dozen to a thousand individuals (those latter data are in the 2011 Mol Biol Evol paper) with the appropriate combination of genes. This high number also explains why domestication loci have been hard to find in animals – it is too many to study with crosses and genetic analysis, only with genome sequencing (a new result). The second really interesting new point is which genes are in these regions: they find genes affecting brain development and sensory organs are strongly over-represented in these regions. In other words, selection during domestication might have focused on tameness and lack of fear: as a farmer, you neither want the animal to hurt you, nor for the animal to die from stress. Secondarily, an animal uses a lot of energy and time to keep a look-out and flee – energy that humans would rather went into meat and milk! It is notable that gene loss is not significant during evolution: most of the changes are due to gene allele polymorphisms.

A wild rabbit on guard, using lots of energy and sensory perception. These genes are selected in domesticated rabbits.

A wild rabbit on guard, using lots of energy and sensory perception. Carneiro et al. 2014 show these genes are selected in domesticated rabbits.

I do mention sensory perception, ‘friendliness’ and fear in my lectures on animal domestication – zebras kill more people in zoos than any other animal because they bite and hold on to their keeper, while deer panic and have heart attacks or break a leg. But until now there have been minimal real data about the changes in this group of genes – I think this paper is a first. (I once heard a talk about reduced brain size in farmed trout fish, but forgot the author and never found a reference.) Given the large number of loci, possible introgression and crosses to wild rabbits every few dozen generations (although this was not noted in the study and should have been evident), and large regions around genes affected by the genomic sweep that include non-coding polymorphisms, the results make a lot of sense. They also explain why previous studies have had difficulty in showing genetic signatures of domestication in farmed animals – lots of loci, too long periods to study, more difficult population structures without wild relatives.

I did contact Miguel Carneiro about the introgression question: he replied “there is good solid data that domestic rabbits when released in the wild and in the native range (Iberia and France) are very unlikely to survive the first couple of days due to predation pressure, indicating that introgression in this direction is difficult.” So indeed, the reduced sensory perception and reduced fear response has an immediate and large consequence. He comments that the reverse of wild introgression into domestics is likely to have happened, but the genetic bottleneck signature in domestic rabbits perhaps suggests that this is not so frequent.

Lack of segregation of characters in crosses to look at rabbit (or indeed other animals,where wild x domestic crosses are possible) domestication characters suggests many genes are involved (unlike the small number of genes controlling, say, coat colour in rabbits, or growth-related genes like broiler vs egg-laying chickens). I would speculate that many different monasteries in France in the middle ages tried to keep wild rabbits, eventually with a few finding rare rabbits with a suitable combination of characters which were then progenitors to the current domestic breeds.

A cow tooth found in a milking parlour: cows loose their own milk teeth in their second lactation. Humans selected early breeding but not loss of other juvenile characters.

A cow tooth found in a milking parlour: cows loose their own milk teeth in their second lactation. Humans selected early breeding but not loss of other juvenile characters. Wild relatives would have their first calf years later.

The genomic loci give many suggestions where we should look to improve rabbits. I have blogged about the possible importance of aquaculture and fish or crustaceans as a part of improving agricultural sustainability already, but introduction of rabbits as a more exploited source of animal protein also has potential: they (or at least their bacterial gut microbiome) means they digest grasses and fibres. Thus, like cows but unlike pigs or chickens, they can use agricultural products that do not compete with human food uses. Since rabbit domestication is so recent, we can also anticipate what ‘second stage’ domestication traits we should be looking for – rather as we suggested earlier this year should be done in proso millet, Panicum miliaceum, which was domesticated in the first wave but has since declined in relative importance despite having extremely high water efficiency.

What wasn’t found in the the genes associated with rabbit domestication was remarkable. There is no mention of disease-resistance loci and nor of reproduction or breeding-related genes – I would expect these to be over-represented in selected regions (both of which are important traits for domestication of both plants and animals). Disease and reproduction are very important in other domestic animals: high population densities mean diseases spread quickly, while we need fast and easy breeding with no photoperiodic breeding response (not least so we can have eggs and milk all through the year and don’t need to keep cattle until they are 4 or 5 years old before breeding). It is possible these are single-gene loci which would be found but not necessarily stand-out in a genome-wide analysis. Or maybe these are characters where wild rabbits already have the domestication-required genes: they live in large inter-connected colonies (not unlike a farm already) and of course are a byword for reproductive success!

The ultimate friendly, domesticated rabbit

The ultimate friendly, domesticated rabbit.

Another summary of the rabbit genomics of domestication paper is given by Penny Sarchet in New Scientist.

Science 29 August 2014:
Vol. 345 no. 6200 pp. 1074-1079
DOI: 10.1126/science.1253714

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro, Carl-Johan Rubin, Federica Di Palma, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. Chang, Veronique Duranthon, Luca Fontanesi, Hervé Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel-Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand, Kerstin Lindblad-Toh, Leif Andersson

ABSTRACT
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

Stevia hits the mainstream with ‘Life’

Last year Aurélien Azam blogged about Stevia in his post, Can we find all the tastes we like in the Wild? He mentions Stevia in it and if you don’t remember it, then Coca Cola will try to change that. Stevia is the plant behind the new Coke variety, Life.

Coca Cola Life and Death

The marketing department at Coca Cola are about to discover that if the green bottle is called ‘Life’ there’s an obvious name for the red bottle.

Stevia rebaudiana leaves are complicated sugar factories. Initially they import carbohydrates, but as leaf area increases photosynthesis means they start producing more sugars to supply the rest of the plant. The key chemicals are Steviol glycosides. These are, for the same concentration, around 300 times more sweet than sugar. The exciting feature is that human body cannot produce any calories from these sugars. For marketing, it’s the fact that it’s a plant that’s the chemical factory that’s news. If it’s made in a plant then you can label it: From Natural Sources.

But this is one of those situations where natural is probably not a synonym for good.

Stevia growing naturally in Paraguay. #156515950 / gettyimages.com

Abdel-Rahman et al. (2011) report on Stevia, among other natural products in Toxological Sciences, and note that in aqueous, crude or partially purified form Stevia can be bad news for rats. One side-effect can be reduced fertility in female rats. It’s always best to be wary from directly applying animal tests to humans, but they also note that the Guarani Indians of Paraguay would make something a bit like a tea from the Stevia leaves. They used it as an oral contraceptive.

For this reason it’s a relief that the sweetener isn’t natural, but a highly processed form of Stevia. But how does it taste?

I set up a comparison taste test with Coca Cola Life (green bottle) and the Cola Cola from the red bottle – which for ease of labelling we’ll call Death. I also added Coke Zero as a third option. All bottles were chilled and the opened with ice added. I then ignored protests from the tasters that they weren’t that thirsty.

The taste test followed a predictable pattern.

After glass 1 Zero: “Hmm.”
After glass 2 Death: “That’s definitely the full-fat Coke and the first is Stevia.”
After glass 3 Life: “Euww! No, that’s Stevia isn’t it?”

Stevia has a distinctive taste, and one that’s unexpected in Coke. Success will depend on how much the public develop a taste for it.

If it does succeed, the payoff could be big. As well as the battle against obesity, Stevia-derived sweeteners promise other benefits including fighting diabetes, high-blood pressure and tooth decay. However for now if it’s a choice between liberty from health issues or Death, a good chunk of the public will opt for Death.

The hidden cost of frankincense

A while back we covered a paper in Annals of Botany on tapping frankincense for resin. The mapping of the canals in the tree promised to improve the efficieny of tapping. Now in Tree Physiology Mengistu et al. have a paper Frankincense tapping reduces the carbohydrate storage of Boswellia trees, that’s recently become free access.

Boswellia Trees

Boswellia Trees in Ethiopia. Photo by Motuma Tolera.

Mengistu et al. show that tapping for resin reduces the trees’ stores of starches and sugars. They also show that stores deplete anyway, as the tree uses them itself. The resin is part of a store that tides the tree over the dry period, and get replenished during the wet period.

The paper ties in well with the Annals paper. In that Tolera et al. argued resin tapping could be done just as effectively with fewer cuts. Fewer cuts means less chance for disease to enter the tree. In the TreePhys paper Mengistu et al. argue that fewer cuts also means that trees have more of a chance to hold on to necessary stores of carbon, if they need them.

The evidence is that intensive tapping of Boswellia papyrifera is a problem and that the trees need some respite. However, there is also a religious imperative to tap them. Balancing supply and demand looks likely to remain a contentious problem.

Does Plant Science need a Sagan or Sheldon?

Here’s a slow reaction to a post at ASPB Plant Science Blog by Ian Street, Communicating Plant Science in the Digital Age. It’s taking me a while to respond, because I think it’s a good post – but I don’t quite agree with it. However, every time I think I’ve worked out why I don’t agree with it, I find I don’t agree with myself either.

In the original post, Ian Street holds up Neil deGrasse Tyson as an example of someone who is an excellent communicator and points out there’s no plant science equivalent. Here I start to feel a bit of a weasel. In terms of audience and fame he’s right. However, if you’re looking for people who can communicate plant science in an exciting way, there are plenty of researchers who could do a similar job to Tyson, given the opportunity. I think there are plenty of good communicators in botany, but they don’t have the audience.

I can see why not having a Plant Tyson is a problem, but I’ve not been sure that broadcasting is the answer. I don’t think astronomy is popular because Tyson is a good communicator. I think it’s the opposite way round. Tyson is such a good communicator because Astronomy is so popular. That might sound odd, but imagine if Tyson decided he’d had enough and was retiring to Tahiti, would Astronomy cease to be popular?

No. There’s a demand for astronomical talking heads. There’s someone almost as good who could do the job. The demand for popular astronomy means there’s almost certainly a pool of talented communicators that the media could draw upon. Tyson is at the top of a competitive field. There are plenty of talented plant science communicators, but lack of demand means we con’t see them so much.

I think a top plant science broadcaster lies at the end of the road to making botany more popular, it’s not part of the journey itself.

Sheldon Cooper

Is CBS’s Sheldon Cooper the face of Science in the 2010s?

That works as far as it goes, but elsewhere I think Ian Street proves me wrong and gives an example where broadcasting does work. He mentions The Big Bang Theory that, love it or hate it, humanises physicists.

In the UK it’s been credited with an increase in the number of physics students. For a similar effect see archaeology and Indiana Jones. You can’t learn physics from The Big Bang Theory any more than you can pass a course in archaeology with Indiana Jones – but the lack of facts hasn’t prevented them from changing how people value their respective sciences.

Street also points out the importance of using comedy to take the edge of hard science. I think he’s hit on a key point there. It’s not simply a matter of making plant sciences prestigious, you also need to make them likeable. Yesterday we had a post on a genetically engineered plant that might help fight Ebola. It’s a huge tragedy where plant science could make a major contribution to saving lives. But I’m also willing to bet that anti-vaxxers will decide it’s a secret Monsanto project.

In a perfect world Hollywood would solve the image problem for us, but that’s not a practical solution. So instead of aiming for mass audiences, it might be more reasonable to look to the small things people can do. Ian Street says that popularising science is a core part of scientists’ mission. This may be a culture difference, but in the UK it is emphatically not. The only things that matter are scientific publications. Departments make positive noises about outreach, but when it comes to assessments time spent doing Outreach can be viewed as Time Not Working.

If outreach success is all-or-nothing, then in this situation the vast majority of results are going to be nothing. If there were support for small victories, then hopes need not rest or a Sagan nor a Sheldon. Avoiding investing in a few personalities could have benefits. Not least, because it means scientists don’t have to just look like me, they can look like you and your neighbour too.

Quite how this is going to be put in place is difficult, but I think what Ian Street and the ASPB’s Digital Futures Initiative might well be a stepping stone to support for many plant scientists. Another event to cheer is Kevin Folta, who’ll be doing a Reddit AMA this afternoon.

Plant Science around the web…

Links

The Indian Botanists have a review of ‘Green Wars- Dispatches from a Vanishing World’ by Bahar Dutt as well as an interview with her about the book.

Bibliodyssey, the art history blog, has a post on pomology and some illustrations from the 19th century.

Via Anne Osterrieder, there are the most well-referenced Frozen parodies I’ve seen, with New Under The Sun Blog’s post, Do you want to make a plastid? and For the First Time in Forever: Vernalization

I’ll assume you’ve already seen the Agricultural Biodiversity Weblog’s Nibbles.

Photo: BigStockPhoto.

How to grow plants 400km above the ground

Quora is a site for posting questions to the internet. Sometimes those questions get answer. For example Robert Frost, who has trained astronauts for the International Space Station, has answered the question: How are plants growing in the ISS?

Gravity is not the only difference between the Earth environment and the ISS environment. In the closed atmosphere of a spacecraft, volatile organic compounds (VOCs) can accumulate. VOCs need to be scrubbed from the air or seed production will suffer. There are elevated radiation levels that can cause mutations and affect growth. An experiment on Mir, that involved storing tomato seeds in space for six years found mutation rates up to 20 times higher in the space seeds than in the control seeds stored on the ground. And there are the spectral effects of using only electric lighting.

Plant in space

An autotrophic astronaut. Photo: NASA.

Because plants also respire, we have to have fans to circulate the air around the plants so that they don’t suffocate on their own exhalations. Even failed experiments can provide us with better understanding. An experiment to study plant lignin failed to produce healthy plant materials but taught us more about providing effective air movement.

You can read more at Quora.

The Art of Urban Botany

A few links have come in through the feeds today on urban botany. It could be interesting if you can’t get away for a holiday. Urban Botany, Urban Art and the Instagram Effect by Hollis Marriot at In the Company of Plants and Rocks blogs a botanical tour around Laramie. The juxtaposition of natural and urban elements like graffiti, can be striking.

She points on to Lucy Corrander who blogs at Loose and Leafy. I like her post on the wild plants of Southampton High Street which includes:

If I have a mission, it’s to persuade people that every street is a garden. Not has a garden, note; but is one.

As she finds, it can be a tough claim to defend, but given the tenacity of plants, she might well be right.

Moss Graffiti

Mossenger and Anna. Photo: Matthew Knight / Flickr.

Returning to plants and art, the tenacity can be an artistic tool in itself. I wandered on to Moss Graffiti, using moss as the ink for art. which Heavy Petal covered this back in 2007, so I’m quite slow. There’s a number of Pinterest images up, some very impressive and a how to guide at Stencil Revolution.

So what ARE the 7 most important plants?

A while back Annals Editor Pat Heslop-Harrison was asking what ten plants should botanists know about. I’ve taken it a bit further with a Buzzfeed post on the 7 Plants That Changed Your Life.

I’ve tried to pick seven plants with global consequences, but I’m not entirely happy with the list. The seven plant limit means I’ve missed out a lot of important plants. For example, there are no marine plants on the list. Nothing that really address important evolutionary steps that plants made, so no mosses or ferns,

So what plants would you add to the list and why? I’d be interested to see if our readers could compile another list of another seven plants that would be equally good, or better.

Leave your suggestions below, or at Buzzfeed or on our Facebook page.