Tag Archives: Evolution

Plant evolution: The inevitability of C4 photosynthesis

Photosynthesis Although atmospheric carbon dioxide (CO2) levels are currently rising, the last 30 million years witnessed great declines in CO2, which has limited the efficiency of photosynthesis. Rubisco, the critical photosynthetic enzyme that catalyses the fixation of CO2 into carbohydrate, also reacts with oxygen when CO2 levels are low and temperatures are high. When this occurs, plants activate a process known as photorespiration, an energetically expensive set of reactions that release one molecule of CO2.

C4 photosynthesis is a clever solution to the problem of low atmospheric CO2. It is an internal plant carbon-concentrating mechanism that largely eliminates photorespiration: a ‘fuel-injection’ system for the photosynthetic engine. C4 plants differ from plants with the more typical ‘C3′ photosynthesis because they restrict Rubisco activity to an inner compartment, typically the bundle sheath, with atmospheric CO2 being fixed into a 4-carbon acid in the outer mesophyll. This molecule then travels to the bundle sheath, where it is broken down again, bathing Rubisco in CO2 and limiting the costly process of photorespiration.

The evolution of the C4 pathway requires many changes. These include the recruitment of multiple enzymes into new biochemical functions, massive shifts in the spatial distribution of proteins and organelles, and a set of anatomical modifications to cell size and structure. It is complex, and it is also highly effective: C4 plants include many of our most important and productive crops (maize, sorghum, sugarcane, millet) and are responsible for around 25% of global terrestrial photosynthesis. A new paper in eLife examines how this process may have evolved, first to correct an intercellular nitrogen imbalance, and only later evolved a central role in carbon fixation.

Cause for optimism (maybe not…)

Image: Wikimedia Commons.

Image: Wikimedia Commons.

As an ‘old-fashioned’ botanist my heart was gladdened to see that Number 1 in the ‘Top 10 most viewed Plant Science research articles in 2013’ from Frontiers in Plant Science was one that dealt with fundamental botany of the taxonomic kind. The paper in question was entitled ‘Angiosperm-like pollen and Afropollis from the Middle Triassic (Anisian) of the Germanic Basin (Northern Switzerland)’ and was written by Peter Hochuli and Susanne Feist-Burkhardt. Whilst that recognition may engender a feel-good view that plant taxonomy is doing rather well, Quentin Wheeler’s timely New Phytologist Commentary, ‘Are reports of the death of taxonomy an exaggeration?’, offers a more cautious interpretation. Commenting upon an article by Daniel Bebber et al., he concludes that plant taxonomy (though one suspects taxonomy of all biota fares as badly) is still in desperate need of greater attention – in terms of people to undertake the work and appropriate funding – as befits its importance to a true appreciation of the planet’s biodiversity and the inter-relationships between living things. Sadly, this state of affairs is unlikely to be helped by news that the Royal Botanic Gardens at Kew (London, UK) – one of the world’s premier centres of plant taxonomic endeavour – is in the midst of a funding crisis. Indeed, the situation is apparently so bad that ‘about 125 jobs could be cut as… Kew… faces a £5m shortfall in revenue in the coming financial year’. This must be particularly concerning since it comes shortly after news that visitor numbers to Kew increased by 29% last year compared to 2012. And this bad news on the plant taxonomy front is echoed in the USA where ‘too few scientists are being trained in agriculture areas of science’. So, there’s an insufficiency of people to grow the new crops that aren’t being identified because of the dearth of plant taxonomists. Where will it all end..?

[If you’re not put off by the precarious state of life as a taxonomist and want a little bit more of a career insight, then you could do much worse that read Elisabeth Pain’s ‘Science Careers’ article.  And for a welcome boost to publicising the plight of the endangered species known as Taxonomus non-vulgaris var. biologicus, see Tim Entwisle’s news article in The Guardian – Ed.]

One of a kind…

Image: Scott Zona/Wikimedia Commons.

Image: Scott Zona/Wikimedia Commons.

These articles have been going long enough(!) to be able now to report a successful outcome to a research project whose initiation was announced in a former news item entitled ‘Old meets new’. The project is the elucidation of the genome of Amborella trichopoda. “Amborella is a monotypic genus of rare understory [sic! What ever happened to understorEy??? - Ed.] shrubs or small trees endemic to… New Caledonia”.

Not only is this plant rare and monotypic – truly ‘one of a kind’! – but it is also probably the living – extant – flowering plant [angiosperm] that is closest evolutionarily to the earliest true first member of the angiosperm plant group, and may therefore be “the last survivor of a lineage that branched off during the dynasty’s earliest days, before the rest of the 350,000 or so angiosperm species diversified”. Given Amborella’s exalted status (which “represents the equivalent of the duck-billed platypus in mammals”), it is hoped that understanding its genetics will shed light on the evolution of the angiosperms as a whole. Indeed, the University of Bonn’s Dietmar Quandt is reported as describing Amborella as a more worthy model organism than Arabidopsis(!!!).

Since the angiosperms are probably the most ‘successful’ of all the groups in the Plant Kingdom (‘the land plants’, the Plantae), hopes are understandably high that unravelling the genome of Amborella – reported by the aptly named Amborella Genome Project – will lead to the identification of “the molecular basis of biological innovations that contributed to their geologically near-instantaneous rise to ecological dominance”. And accompanying the main nuclear genome article, Danny Rice et al. report on Amborella’s mitochondrial genome (mitochondria have some of their own DNA additional to that located in the nucleus) and find that numerous genes were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. So, as ancient as it is, Amborella was still prepared to ‘learn’ from the experiences of even older land plants – mosses – and plant-like algae (which are in a different kingdom entirely to the land plants, the Protista). Adopt and adapt: a life lesson for all living things, I suggest.

[For more on this fascinating story, visit the home of the Amborella genome database. And if you still need some ‘proper’ botany (after all this genomery), you need look no further than Paula Rudall and Emma Knowles’ paper examining ultrastructure of stomatal development in early-divergent angiosperms (including Amborella…).  Notwithstanding all of this understandable present-day excitement, I can’t help but think that the importance of Amborella was foretold many decades ago, as "popular-in-the-mid-1970s" British-based pop band Fox seemingly declared: "things can get much better, under your Amborella…". Indeed! So, arabidopsis had better watch out! – Ed.]

Where do gingers some from?

Plastid genomes and relationships in Zingiberales

Plastid genomes and relationships in Zingiberales

The tropical angiosperm order Zingiberales comprises a clade of eight tropical monocot families including approximately 2500 species believed to have undergone an ancient, rapid radiation during the Cretaceous era. Zingiberales show substantial variation in floral morphology, and several members are ecologically and economically important – such as ginger, cardamom, turmeric, galangal, bananas and plantains. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. The Zingiberales comprises a diverse clade of eight families, but deep phylogenetic relationships within them are poorly understood.

A recent paper in Annals of Botany uses next-generation sequencing to generate complete plastid gene sets and finds that plastid genomes provide strong support for many relationships, but only weak support for inclusion of the Heliconiaceae order. Manipulation of various data matrix properties affects tree topology in an unpredictable fashion, suggesting that complete coding regions of the plastome do not provide sufficient character information to resolve this rapid, ancient radiation.

 

Barrett, C.F., Specht, C.D., Leebens-Mack, J., Stevenson, D.W., Zomlefer, W. B., & Davis, J.I. (2014) Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?. Annals of Botany, 113(1), 119-133.

How important is gene flow?

There’s a handy article available from the American Journal of Botany that’s caught my eye: Is gene flow the most important evolutionary force in plants? by Norman C. Ellestrand. It opens with a strong statement.

Some scientists consider the word “evolution” to be more or less equivalent with “natural selection” or adaptation. They would, of course, be wrong.

DNA sequence on awall

DNA. Photo by John Goode / Flickr.

Ellestrand states that biological evolution is the change in allele frequencies in a population over time, and that this is due to four evolutionary forces: mutation, selection, drift, and gene flow. Gene flow is important because even low levels of gene flow can have a large impact, counteracting the other evolutionary forces.

So what is gene flow?
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Nectary evolution in Disa orchids

Nectary evolution in Disa orchids

Nectary evolution in Disa orchids

The Orchidaceae have a history of recurring convergent evolution in floral function as nectar production has evolved repeatedly from an ancestral nectarless state. Hobbhahn et al. study the South African orchid genus Disa and find that independent nectary evolution has involved both repeated recapitulation of secretory epidermis, which is present in the sister genus Brownleea, and innovation of stomatal nectaries. These contrasting nectary types and positional diversity within types imply weak genetic, developmental or physiological constraints in ancestral, nectarless Disa. With its morphologically diverse solutions to the problem of nectar production, Disa is a good example illustrating the contribution of functional convergence to phenotypic diversification, which probably also underlies the extensive diversity of nectary types and positions in the orchid family.

Can the Grant-Stebbins model explain where all the flowers come from?

Rainbow rose

Rainbow rose by Pamela Carls/Flickr

Valentine’s Day is coming, and many people are looking for the right flower to express their feelings, though it’s hard to beat a multi-coloured rose. But where do all the different sorts of flowers come from?

The Grant-Stebbins model suggests that pollinators drive speciation. Shifts in pollinators cause angiosperms (flowering plants) to adapt and form ‘ecotypes’ which then become new species. To someone like me, who is not a botanist, this is an appealing explanation. In reality it’s more complicated than that.

Pollinator-Driven Speciation is the subject of a recent special issue for Annals of Botany. I’ll be blogging about papers from the issue during the week. In their introductory paper for the issue, Van der Niet, Peakall and Johnson point out there’s plenty of evidence of floral adaptation to pollinators, and evidence at the large-scale of angiosperms diversifying with pollinators, but there’s a gap in the middle. How do you get from floral adaptation to speciation?

Van der Niet et al. identify four key factors in their paper. First you need to show that pollinators are selecting which plants get fertilised and which don’t. Next you need to show that this selection has consequences for floral traits. After this you’d need to look at the geographical context. What is it that causes you to find a certain plant here but not there? Finally, you’ll want to show that the pollinators are helping isolate populations so the differences between plant populations don’t spread back through the parent population.

Breaking down the problem really helps, because it means we can move from a general idea to some testable hypotheses. This is what the viewpoint paper does and each step is peppered with citations showing how each one of them can be tested with evidence. In the case of pollinator selection it’s possible to do direct experiments.

One of the most important factors in experimenting is that you also have to accept you may be wrong about something. In the conclusions Van der Niet et al. say the Grant-Stebbins model does a good job of explaining speciation, but there are some non-pollinator factors involved too. Strangely I think this is actually an excellent result for the model.

A model that explains everything risks being a just-so story. The fact it breaks down in places shows that scientists aren’t simply recording what they expect to see. However, the model breaking down doesn’t make it useless. The fact that it usually works means that when it does fail, it is pointing out that something really interesting and unexpected is going on. This is one of the most useful things a scientific model can do, take a lot of different observations and help you sort out what results are excitingly weird.

You can pick up the viewpoint paper that introduces the pollinator-driven speciation issue from the Annals of Botany.

Image

Rainbow rose by Pamela carls/Flickr. This image licensed under a Creative Commons by licence.

Novel structure of placenta in a lycophyte

Novel structure of placenta in a lycophyte

Novel structure of placenta in a lycophyte

Lycopodium obscurum has a subterranean, mycoheterotrophic gametophyte that nourishes the embryo for several years. An examination of an embryo in an underground gametophyte by Renzaglia and Whittier reveals a massive foot with ultrastructural variability comparable to that across major clades. The intergenerational zone in unlobed regions shows unidirectional transport of materials toward the foot. Lobed, more mature areas contain degenerated gametophyte cells that lack wall ingrowths and sporophytic transfer cells. They conclude that placental features in Lycopodium reflect a dynamic, invasive and long-lived foot, and the unique reorientation of all embryonic regions during development. Homoplasy in transfer cell appearance and location is explained by diverse patterns of embryology across archegoniates.

Hybridization and long-distance colonization at different time scales

Evolution and biogeography of Anthoxanthum

Evolution and biogeography of Anthoxanthum

Repeated hybridizations and/or polyploidizations confound taxonomic classification and phylogenetic inference, and multiple colonizations at different time scales complicate biogeographic reconstructions. Pimentel et al. sequence three plastid and two nuclear DNA regions in 17 Anthoxanthum taxa in order to unravel the role of these processes in shaping the current structure and diversity of the genus. Variation of floral morphology in Anthoxanthum (sections Anthoxanthum and Ataxia) can be explained by a Miocenic hybridization event between lineages with one and three fertile florets. All diversification events in the genus except one are dated back to between the Late Pliocene and the Late Pleistocene. Africa was apparently colonized twice from two different sources, namely Europe and East Asia.

Stomatal development of early angiosperms

Stomatal development of early angiosperms

Stomatal development of early angiosperms

Stomatal structure is highly conserved across land plants – a symmetric pair of specialized guard cells delimits a central pore. However, when viewed from a developmental perspective, the patterning of the stomatal complex (the stoma and neighbouring cells) differs among taxa. Most hypotheses of stomatal evolution in angiosperms are based on comparative studies of mature stomata of both extant and fossil taxa, with a primary focus on three widely recognized stomatal types – anomocytic, paracytic and stephanocytic – which differ in the patterning of their neighbour cells.

Understanding evolutionary pathways requires a more explicit phylogenetic context than over-simplistic comparisons between dicotyledons (a non-monophyletic group) and monocotyledons. Such comparisons are most commonly exemplified by the model organisms Arabidopsis and rice, respectively. A recent paper in Annals of Botany presents a novel ultrastructural study of developing stomata in leaves of Amborella (Amborellales), Nymphaea and Cabomba (Nymphaeales), and Austrobaileya and Schisandra (Austrobaileyales), which represent the three earliest-divergent lineages of extant angiosperms. The authors show that similar mature stomatal phenotypes can result from contrasting morphogenetic factors. Loss of asymmetric divisions in stomatal development could be a significant factor in land plant evolution, with implications for the diversity of key structural and physiological pathways.