Revisiting spatial scale in the productivity-species richness relationship: fundamental issues and global change implications

14078S1R1The relationship between climate and biodiversity has been long debated. In a changing environment, there is new emphasis to resolve this debate for practical reasons: to manage conservation efforts we need to understand how diversity will change from both our own actions and natural global cycles. In a new study published in AoB PLANTS, McBride et al. show that the roles played by different ecological and evolutionary factors in shaping plant diversity change across the world’s ecoregions, and—critically—that these differences scale with ecoregion size. Ecoregions that are both large and productive are globally important biodiversity sources that shape the biota of the smaller regions around them.

Plants, grafty little critters…

Image: Richard Reames/Wikimedia Commons, www.arborsmith.com.

Image: Richard Reames/Wikimedia Commons, www.arborsmith.com.

When it comes to making new combinations of genes – which may help to generate new species  in the evolutionary process known as speciation – the most usual route in eukaryotes  is via sexual reproduction.  In this ancient process, and speaking rather generally, gametes, made via meiosis (in which the complement of genetic material is reduced), fuse with each other and thereby create a new individual with the full genetic complement of the adult. Generally, this mode of reproduction, whether leading to development of new species or not, is viewed as ‘good’. And sex is favoured during adaptation to new environments. But sex is also ‘expensive’,  and one might expect some organisms to have found a cheaper – better? – way. Although alternatives to sexual reproduction exist – so-called asexual reproduction –  they don’t generate the genetic variety that could give rise to creation [oops, controversial term… – Ed.] of new species.

But, guess what? Plants seem to have hit upon an asexual method that can give rise to new species, as work by Ignacia Fuentes et al., straightforwardly entitled ‘Horizontal genome transfer as an asexual path to the formation of new species’, suggests. Using grafting (a time-honoured, horticultural technique used to join parts from two or more plants so that they appear to grow as a single plant), the team demonstrated that entire nuclear genomes  could be transferred between plant cells of unlike species (and which you wouldn’t expect to be able to be able to reproduce sexually in nature…). Or, in the technical language of a scientific paper, the authors ‘provide direct evidence for this process resulting in speciation by creating a new allopolyploid  plant species from a herbaceous species (Nicotiana tabacum, ‘cigarette tobacco’) and a woody species (N. glauca, ‘tree tobacco’) in the nightshade family (Solanaceae).  The new species is fertile and produces fertile progeny’ (and has even been christened N. tabauca).

All intriguing stuff. And which just goes to demonstrate – again, and if ’twere needed – how much more interesting (better?) plants are than animals! Finally, the authors suggest that this phenomenon could be exploited for the generation of novel allopolyploid crop species. But where will this all end? And isn’t this genetic engineering? Albeit of a kind that occurs naturally? And what should one make of the tree that’s been so multiply and repeatedly grafted that it’s a composite of dozens of different species? Or is it now just one species…? Discuss!

Collaboration between grass seedlings and rhizobacteria to scavenge organic nitrogen in soils

Photo of annual bluegrass seedlings on agarose with 0.01% protein, showing dark brown H2O2 zones around roots of seedlings.

Photo of annual bluegrass seedlings on agarose with 0.01% protein, showing dark brown H2O2 zones around roots of seedlings.

Plants require nitrogen to make proteins, nucleic acids and other biological molecules. It is widely accepted that plants absorb inorganic forms of nitrogen to fill their needs. However, recently it has become clear that plants also have the capacity to absorb organic nitrogen from soils. In a new study published in AoB PLANTS, White et al. describe a new kind of symbiosis involving seed-vectored rhizobacteria and grasses that is targeted at enhancing acquisition of organic nitrogen from soils. The authors propose a diurnal process where during the day roots produce and release hydrogen peroxide that oxidizes microbial exoenzymes around roots; at night hydrogen peroxide production ceases, then roots and symbiotic rhizobacteria secrete proteases that degrade the oxidized proteins to form peptides that are absorbed by roots. The existence of a mechanism for organic nitrogen scavenging in grasses emphasizes the nutritional importance of non-pathogenic microbes that associate with roots. Future applications of this process could result in new methods for the cultivation of crop plants.

AmJBot explains Auxin to the perplexed

I’m delighted that there’s a review of Auxin in this month’s American Journal of Botany, Auxin activity: Past, present, and future by Enders and Strader. This might surprise a few of my friends as I’m not a fan of Auxin, Auxin is a difficult topic, and that’s why this review is so welcome.

Pink Perfection Camellia

Pink Perfection Camellia. Photo by Trish Hartmann. Construction by Auxin.

Auxins are hormones that are impossible to avoid if you’re studying botany. Sooner or later you’ll run into them. Recently in Annals of Botany they’ve been involved in inflorescence and floral organ development, adventitious rooting and xylogenesis, the growth of maize coleoptile segments and working with Arabinogalactan proteins in a paper with the best title I’ve seen in a while: Back to the future with the AGP–Ca2+ flux capacitor. AoB PLANTS is averaging a paper a month with an auxin influence this year to date (February).

What I find so confusing about Auxin is that it is everywhere, and it’s so well-known to botanists that it’s a necessary shorthand when writing a paper. This is great, but it makes papers featuring Auxin very difficult to read if you don’t already know about it. Enders and Strader cover a century of Auxin research for AmJBot and by placing Auxin research in a historical context, they help highlight how we know what we know about this very important hormone.

They start early with the quest to identify Auxin, but they highlight two key points in Auxin research in their review. One is the 1939 paper by Thimann and Schneider, The relative activities of different auxins. This pulled together what was known about Auxin, and helped clear some controversy. The other pivotal moment was adopting Arabidopsis as a model organism in the 1980s, and the associated advances of molecular biology that allowed experimentation with much greater resolution than before.

Like any good review there are plenty of links to other papers to read more, with major sections on metabolism, transport and signal transduction, but there’s also a helpful section at the end. Enders and Strader point to questions that are still open in Auxin research, like have all Auxins been discovered or are there still more to be found? There’s also an interview with Barbara Pickard on Kenneth Thimann which adds a human dimension to the research.

The impression I’ve had of Auxin research is that a lot of people have been finding out some really exciting stuff about the building blocks of plants. Reading one paper hasn’t turned me into an expert, but is has helped give me some idea about why people get so excited about Auxin.

You can pick up the paper free from AmJBot.

Find Article PDFs easily with Lazy Scholar

Looking to speed up your research? The Lazy Scholar extension for Google Chrome is now even more helpful.

Lazy Scholar Extension Page

I’ve mentioned Lazy Scholar before, but it’s worth mentioning again as it’s had an update. It’s an extension for Google Chrome that looks for PDFs of articles when you’re browsing abstracts. It also has some other nifty features.

You can search for papers by typing scholar.google.com into your address bar, then your search. With Lazy Scholar you can shorten this by typing ls search term which works as a direct search on Google Scholar for whatever you’re searching for.

The recent updates are easy paper sharing links and something else that looks useful: Lazy Scholar now checks Beall’s list of Predatory Journals. These are open access journals that will accept more or less anything, so long as you hand over the money. I have seen one or two good authors publish papers in predatory journals, but Lazy Scholar now adds a warning to let you know that what you’re looking at is a questionable journal.

If you use Chrome during your research then it’s well worth downloading Lazy Scholar from the Chrome Web Store (for free).

Genetic diversity of high-elevation populations of an endangered medicinal plant

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A map representing 24 populations of Podophyllum hexandrum of Indian Himalayan range along with its pictorial representation from nature and bar plots represent STRUCTURE inferences of individual assignments two types of genetic populations.

Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Despite its wide distribution across the entire Himalayan range, the current status of Podophyllum hexandrum, a highly important anti-cancerous herb, remains endangered. In a new study published in AoB PLANTS, Nag et al. characterized the genetic diversity of 24 populations comprising 209 individuals representing the whole of the Indian Himalayas, and found that regardless of geographic location, all of the populations were intermixed and composed broadly of two types of genetic populations. Their findings suggest that these populations have evolved well in response to the environment. This study will help in the formulation of conservation programs for P. hexandrum populations in this region.

What should the science fiction of tomorrow look like?

I’ve been reading with interest about Hieroglyph, the first anthology of science fiction stories from Project Hieroglyph based at ASU. The idea is that inspirational science-fiction can aid science:

The name of Project Hieroglyph comes from the notion that certain iconic inventions in science fiction stories serve as modern “hieroglyphs” – Arthur Clarke’s communications satellite, Robert Heinlein’s rocket ship that lands on its fins, Issac Asimov’s robot, and so on. Jim Karkanias of Microsoft Research described hieroglyphs as simple, recognizable symbols on whose significance everyone agrees.

Project Hieroglyph

It’s a description of hieroglyphs that will cause a few Egyptologists to choke, but the idea behind it is definitely interesting. If science fiction inspires future scientists, what modern icons could point in a direction toward the future in science fiction?

In Hieroglyph most of the alternative futures seem grounded in physics, computing or engineering making the collection seem more retro-futuristic. Perhaps the problem of coming up with a 21st century equivalent of a ‘moon-shot’ is that the target is couched in 20th century terms.

Another problem might be the fact be that the Hieroglyph approach might be in reverse to good story-telling. Robert McGrath calls some of the stories preachy, which would suggest that the fiction is there to push the idea. First of all fiction has to work as fiction before it does anything else.

Brian Stableford has argued that good science fiction explores what he calls a novum, a new thing like an invention or discovery. It’s not simply how its use changes the world but also how its unintended use can change human action. He’s pointed out that Asimov’s simple Laws of Robotics remain a fertile source for stories. Bob Shaw was able to pull plenty of ideas from slow glass, which is glass that slows down light so it takes years to pass through it.

Is there is simple iconic biological idea that could inspire science, but is also interesting enough in itself to produce stories?

CRISPR will be a major phenomenon over the next few decades, but by itself it’s not easy to explain, though Carl Zimmer gives it a good effort. Instead, thinking of a use, could pharming become one of Stephenson’s hieroglyphs?

Pulp sci-fi cover

Created with the Pulp-O-Mizer.

Pharming, creating pharmaceuticals with plants, could become a major source of medicines over the next century, along with engineered microbes. The idea itself is simple enough to understand but there are plenty of consequences to explore.

One example is where do you grow the pharm crops? We already know there will be pressure on agricultural land, so will new crops be engineered to grow on marginal land or will the conditions they treat, for people in rich nations, mean they get prime land and drive up the cost of food elsewhere?

Another consequence: Imagine you could engineer a brassica with a variety of benefits to make it a superfood. Like a lot of people, I loathe cabbage and turnip. To nudge people into eating this healthy food, the makers add a mild non-addictive additive to give people a sense of well-being after they eat it. What effect on society could a food like Lotus have? What effect would depriving a society of it have, like if you introduced a pest into a rival country?

I notice that even trying to produce a positive innovation there’s still room for a negative aspect, but even in golden age sci-fi there were dark sides to progress.

I’m sure that pharming isn’t the only possible hieroglyph that botany could offer. I’m sure that there’ something could be done with phytomining, though I’m not sure what and plenty of other things that I’ve missed. Can anyone else think of positive botanical hooks for science fiction and traditional physical sciences based authors overlook?

Host specificity in vascular epiphytes: a review of methodology, empirical evidence and potential mechanisms

A considerable number of plants depend on structural support by other plants. To understand their diversity and ecology, it is essential to know how strongly potential host species differ in their suitability as hosts. A new review in AoB PLANTS by Wagner et al. focuses on vascular epiphytes, i.e. structurally dependent plants that do not parasitize their hosts. Despite a longstanding interest in the topic, knowledge on the strength of their host specificity is still scanty. This is arguably due to conceptual confusion, but also because of the large complexity of the study system, which makes quantifying host specificity in the field rather challenging. The authors conclude that future research should use a more comprehensive approach by (i) determining the relative importance of various potential mechanisms acting locally and (ii) testing several proposed hypotheses regarding the relative strength of host specificity in different habitats and among different groups of structurally dependent flora.

Why would a plant make its pollination less efficient?

The special issue on pollinator-driven speciation is available with free access now. We covered a few of the papers last year, but now they’re all free. One of the more puzzling papers is Novel adaptation to hawkmoth pollinators in Clarkia reduces efficiency, not attraction of diurnal visitors by Miller, Raguso and Kay. Why would a plant make its pollination less efficient?

Miller et al. look at the effect of novel pollinators. If new pollinators arrive, or plants move into an area with pollinators they’ve not encountered before, there’s a resource to exploit. They looked at Clarkia concinna and C. breweri which have parapatric distributions. Parapatric wasn’t a word that I knew so I had to look it up. They’re species that live next door to each other without overlap.

Clarkia flowers

Different functional groups show different efficiencies on C. concinna (left column of photos) and C. breweri (right column). (A, B) Small bees either collect pollen or nectar at the opening of the hypanthium tube. With both foraging behaviours, they frequently contact the stigma of C. concinna but rarely contact the highly exserted stigma of C. breweri. (C, D) . Photo by Miller et al.

C. concinna and C. breweri get different visitors. Miller et al. wanted to find out what it was that caused this difference. Was it the different ranges the plants live in, or was it floral differences? So they examined visits to arrays of the plants and also created arrays that had the two species of plant at a shared location. They could then see if the flowers from one species were more attractive to certain pollinators than another.

What they found was that diurnal visitors were happy to visit both plants. Even hawkmoths were happy to visit C. concinna even though it looked like C. breweri had evolved traits to attract them. The difference was due to pollinators in different ranges. Puzzle solved.

However, this opens another problem. If C. concinna and C. breweri share the same visitors, how could the differentiate? They could swap pollen so there should have been gene flow between the populations and so no divergence. Miller et al. cut through this by reducing the effectiveness of flowers down to two attributes. Attraction is one, the flower has to get the pollinators to visit. The other is efficiency, once there the flower has to get the pollinator to carry the pollinator away.

C. breweri might pull in many visitors, but the ones that really work are the hawkmoths, thanks to the adaptations it has made. The hawkmoths could visit C. concinna but they weren’t so successful in depositing pollen. It’s no surprise then, given the issue the paper is in, that it seems that it’s the effectiveness of the pollinators that seems to be driving differentiation.

Graph showing how hawkmoths are more efficient for C Breweri.

Two measures of hawkmoth pollinator effectiveness. (A) Total visits to Clarkia breweri and C. concinna in choice trials. Hawkmoths visited both species equally (P = 0·41), but successfully probed C. breweri more (P = 0·052), and approached C. concinna without probing more (P = 0·012). (B) Number of pollen grains deposited on the stigmas of both species per probe in single species pollen deposition trials. Hawkmoths deposited more pollen per visit on the stigmas of Clarkia breweri than Clarkia concinna (P < 0·001). Error bars, ±1s.e. From Miller et al.

It also shows some of the complexity of evolution, including that the premise of question is wrong. Often simple explanations of evolutionary changes are that a plant changed something in order to…. This is an simplification because teleology doesn’t work in evolution, plants don’t do something in order to get a future pay-off. Likewise Miller et al. show that Clarkia didn’t change to attract new pollinators, more that once new pollinators are available there’s an advantage to work better with those. In the case of Clarkia natural selection worked in favour of plants that could use hawkmoths, and once that happened the descendants became less able to swap pollen with the older population. Instead they tended to swap with each other, until the differences were so great they were a new species.

The key here is the difference ranges of the Clarkia species. It’s not simply that they’ve attracted a new pollinator, they’re not in a position to attract the pollinators of their ancestors. Miller et al. point out that the situation for species that share the same patch will be different. When examining pollinator-driven speciation, it’s not simply a matter of attraction, they argue but also a matter of availability of novel-pollinators and the quality of those visits.

Miller T.J., Raguso R.A. & Kay K.M. (2013). Novel adaptation to hawkmoth pollinators in Clarkia reduces efficiency, not attraction of diurnal visitors, Annals of Botany, 113 (2) 317-329. DOI: http://dx.doi.org/10.1093/aob/mct237