Phenotypic Plasticity

2 05 2013

daphniaSome organisms can change their appearance, physiology, and development in response to changes in the environment. This is called phenotypic plasticity, and some examples of phenotypically plastic organisms include the Junonia octavia butterflies described in my natural selection lecture, or water fleas that develop a spiny helmet in the presence of predators, as shown in the picture above (left: exposed to predators; right: same species and sex, not exposed to predators; source: Agrawal (2001)). More mundane examples include the changes experienced by bodybuilding humans, or even the effect of learning on the brain – it’s a ubiquitous phenomenon, but here I’ll only be concentrating on the sort of phenotypic plasticity that leads to set phenotypes: bodybuilders have complete control over their muscle sizes and a genius can atrophy their brain at will, but Junonia octavia can only be blue or orange, nothing else.

The most phenotypically plastic organisms are plants. Unlike animals, plants are forced to stay put and must weather any and all conditions thrown at them by the environment with no option of an immediate migration or a run for shelter. Hence, they’ve evolved to be plastic in their physiology and development, with the best example of this being heterophylly, the ability of many wetland plants to change leaf structure and physiology in drought and in flood conditions (hetero = different; phylly = related to leaf).

How do such things work? A genotype is not a blueprint and what results as a final form is the product of both hardwired developmental processes combined with the effect of external factors such as temperature, interactions, or nutrition. Look at the examples I named above: the butterflies develop their colours in response to temperature; the water fleas in response to predators; the plants in response to abiotic changes. These do not somehow trigger sudden reversible mutations, but the culmination of their physiological effects enable the crossing of a threshold, called the reaction norm, which leads to different genes getting turned on and off, leading eventually to the modified phenotypes.

Intuitively, we can guess at how such mechanisms can evolve: they allow the organism to adapt to varying conditions in real-time, potentially allowing for an optimal phenotype for every condition rather than have to settle for one phenotype for that may just be average in most conditions. But such intuitions are not scientifically sound, merely thoughts. A look through the history of phenotypic plasticity research shows two divergent lines of thought:

  • Phenotypic plasticity evolves as stated above, by selecting for complete phenotypes and hardwired reaction norms. This view can be seen fully-formulated as early as Via & Lande (1985).
  • There are gene regulation mechanisms that respond to changing environmental conditions, and these regulatory mechanisms and they genes they affect are what are selected for in the evolution of phenotypic plasticity. In other words, the capacity to be plastic, not the end product of the plasticity, is selected for. Arguments for this view and evidence for such genes can be found as early as Pigliucci (1996).

The reality is that both of these views are valid. The second point describes genotype by environment interactions (GxE interactions), and treats phenotypic plasticity as a trait in and of itself. Since all traits evolve, the second point is valid almost by definition, and this is reflected in the ubiquity of phenotypic plasticity as noted at the end of the first paragraph in this post.

However, it’s also true that some plasticities are set, for example the Junonia octavia butterflies with the blue and orange morphs for the different seasons. Such cases are evidence for the first point, and are collected as a special type of phenotypic plasticity called adaptive phenotypic plasticity: the product of the plasticity provides a distinct advantage, and so it’s set that whenever specific conditions arise, the track towards the alternative phenotype is embarked upon.

The practical significance of phenotypic plasticity shouldn’t be underestimated. As an example, plants, the most phenotypically plastic of all, will probably be relying on that capacity to get through global warming (Valladares et al., 2007). Thankfully, phenotypic plasticity is one of the larger areas of current research from developmental biology, ecology, and evolution.

pigliucci_book

For more on phenotypic plasticity, the eponymous 2001 book by Pigliucci, Phenotypic Plasticity: Beyond Nature and Nurture, may be old and somewhat outdated, but still a useful reference. I also forgot while writing this that I’ve already written a post on phenotypic plasticity, but at least it does take on a different tack…

References:

Agrawal AA. 2001. Phenotypic Plasticity in the Interactions and Evolution of Species. Science 294, 321-326.

Pigliucci M. 1996. How organisms respond to environmental changes: from phenotypes to molecules (and vice versa). TrEE 11, 168-173.

Valladares F, Gianoli E & Gómez JM. 2007. Ecological limits to plant phenotypic plasticity. New Phytologist 176, 749-763.

Via S & Landa R. 1985. Genotype-Environment Interaction and the Evolution of Phenotypic Plasticity. Evolution 39, 505-522.





Phenotypic Plasticity

23 03 2013
Aschania levana, spring morph. © Manuel Valdueza

Araschnia levana, spring morph. © Manuel Valdueza

The nymphalid above, the map butterfly Araschnia levana, produces multiple generations each year. Its pupae come in two forms, dark and light, the difference arising from varying melanin concentrations. These differences persist in the adult. Above you see the adult that emerged from a light pupa; below is the adult from a dark pupa.

Aschania levana, summer morph. © David Short

Araschnia levana, summer morph. © David Short

This butterfly exhibits seasonal polyphenism: the orange morph emerges in spring, while the drab brown morph emerges in summer.

The eulophid wasp Melittoba chalybii is a parasitoid on bees and other wasps, laying eggs in the host for the larvae to feed on. Two forms of larva can be found in a parasitised victim. The first develops during the first 30 days after hatching, while the second takes 60-75 days to develop. This allows the larvae to best exploit their food source, allowing them to extract a very high nutrition:larva ratio, ultimately leading to more pupation and thus more adult parasitoids (see Mathews et al., 2009).

Both of these are examples of phenotypic plasticity. The appearance of the butterfly changes according to the seasons in order to better match the environment. In spring, the orange allows it to blend in well with flowers, giving it more camouflage and thus less predation risk. The environments that species find themselves in fluctuate between states of regularity. Winter is a time of short photoperiod, low temperatures, and less nutrition available; summer is the exact opposite. Spring and fall have their own intermediate properties. A species that has the ability to adapt to each of these special conditions by developing specific phenotypes obviously gains a distinct advantage, allowing it to exploit the conditions for its optimal survival.

More generally, phenotypic plasticity implies that a species has the ability to expand and conquer diverse environments, since its genotype is geared to adapting to different conditions. An insect’s ability to use a variety of host plants is one example of such plasticity, since it means an insect is not dependent on one specific plant that only grows in one environment – hency why phenotypic plasticity is important to consider, as invasive pests tend to be plastic.

Phenotypic plasticity can be expressed at any level. Morphological plasticity includes the Aschania above, or pond snails that develop spiny shells in the presence of predators. Life history plasticity is possible, as with deciduous trees who shed their leaves once specific environmental triggers are encountered – the trees experience a change in temperature or photoperiod, causing a cascade of biochemical changes, causing changing gene expression, which then leads to senescence in the leaves.

Phenotypic plasticity may just be incidental, as with the ability to use various host plants, or it can be selected for and hardwired as a beneficial trait, as with all the other examples I’ve used in this post. This is why phenotypic plasticity is an important factor to study in evolutionary ecology specifically, and evolutionary biology in general. Phenotypic plasticity in that sense merges into the debate on canalisation and the relationship between micro- and macroevolution that I’m interested in: is phenotypic plasticity the result of canalisation, or is it a component needed for increased evolvability? (That’s an excellent essay question for an evolution exam.)

Further Reading:

Gotthard K & Nylin S. 1995. Adaptive Plasticity and Plasticity as an Adaptation: A Selective Review of Plasticity in Animal Morphology and Life History. Oikos 74, 3-17.

Matthews RW, González JM, Matthews JR & Deyrup LD. 2009. Biology of the Parasitoid Melittobia (Hymenoptera: Eulophidae). Annual Review of Entomology 54, 251-266.

Nijhout HF. 2003. Development and evolution of adaptive polyphenisms. Evolution & Development 5, 9-18.

Van Asch M & Visser ME. 2007. Phenology of Forest Caterpillars and Their Host Trees: The Importance of Synchrony. Annual Review of Entomology 52, 37-55.





My Research: Carabid networks in a variable landscape

19 01 2013

In this study, I will be setting up sets of pitfall traps (preservative-filled cups in the ground that ground insects fall into) in ecosystems with very different habitat types, e.g. a forest with clustered tree species and shrub types, clearings, human structures, ponds.

This will not only give me a good estimate of the ground insect diversity, it will also allow me to analyse landscape patterns and networks. In other words, I will be studying how insects move around the landscape. Do some species become isolated in certain habitats? What habitats serve as corridors through which species can move? Are there any habitat combinations that foster a particularly active or biodiverse community?

Such a study provides important data for environmental management. It’s fallacious and oversimplistic to view a forest as a single habitat, because it’s an ecosystem comprising of many habitats that vary at a small spatial scale. An environmental manager absolutely needs to take this into account before approving any changes. Data accumulated from such studies allow a limited, but crucial, amount of prediction to be made for the effects of human modification, from logging to reforestation to construction of artificial lakes. The same is true for agricultural managers and farmlands: do hedgerows serve as habitats and corridors in otherwise inhospitable arable land? How does intercropping affect insect movements? What is the best solution to keep pollinator biodiversity up while reducing pest numbers?

My analysis will be focused on carabid beetles, most probably in a forest landscape (because I don’t want to get shot by a farmer while doing fieldwork), but other groups and ecosystems can be examined in due time, or by interested parties or universities/schools.





Top Research of 2012: Environmental

1 01 2013

Jump to: Arthropods; Botany; Developmental Biology; Ecology; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

This is a listing of my top 10 environmental research of the year. I don’t follow energy or sustainability research, so don’t expect anything on those; only climate change and its effects, and whatever else humans are doing to screw around with the planet and other species. The master list contains 19 paper. [OA] indicates open access papers.


10. Impacts of Biodiversity Loss Escalate Through Time as Redundancy Fades.

The single greatest danger to biodiversity isn’t climate change, it’s habitat loss and the resulting reduction in ecosystem complexity. This paper underlines this by finding that in the long term, species richness in an ecosystem compounds its productivity, meaning that losing even a couple of species that may appear redundant will be damaging.


9. Ecosystem responses in the southern Caribbean Sea to global climate change.

itcz

As the graphs above show, this paper finds that phytoplankton abundances have experienced a sudden statistically significant decrease since ~2005 in the Carribean, as measured by the CARIACO coastal station off the coast of Venezuela. This is linked to changes in hydrological and circulation cycles (specifically the ITCZ and the Azores High) caused by global warming: they lead to less upwelling, warmer water at the surface, and more stratification, which overall leads to less nutrients, and thus less productivity.


8. The 27–year decline of coral cover on the Great Barrier Reef and its causes. [OA]

greatcoralreef

The result of this study is summed up in B above: a halving of the living coral cover in the Great Barrier Reef from 28% to 13.8% from 1985 to today. If that’s not cause enough for concern, realise that the GBR is one of the most protected marine localities, and it’s a World Heritage Site. Despite that, it’s getting devastated (no need to mince words). The reason for the coral deaths here are increased bleaching (driven by higher temperatures), lower water quality (global warming leading to increased precipitation, leading to more run-off into the ocean), and lower growth rates (warming leads to thermal stress). Corals are some of the most sensitive organisms living today, and this paper just gives us a glimpse of what the marine future will be like.


7. Blue Whales Respond to Anthropogenic Noise. [OA]

dcalls

In the diagram above, the orange Ds indicate when blue whales did D calls, characteristic low-frequency calls they make when foraging. In the presence of ship sonar, the calls stop. When ships are around, D calling increases, most likely to overome the sounds made by the ship (similar to how urban birds sing more loudly than their rural counterparts). What the functional effects of these influences are still need to be researched, and probably will be soon given that blue whales are endangered.


6. Fukushima-derived radionuclides in the ocean and biota off Japan. [OA]

Oh dear, oh dear, caesium levels in the ocean rose 1000 times in the aftermath of Fukushima! That sounds like a big number, until you realise that they’re still less than naturally occurring radionuclides, like polonium. Think about this next time you want to use Fukushima as an example of a nuclear disaster.


5. Sea anemones may thrive in a high CO2 world.

I may sound like a bitter alarmist when speaking about climate change, but I also like to remind people that climate changes happen all the time, and while this one is drastic, there will alwways be some organisms who will profit (it just so happens that humans will not be one of them, for better or for worse). This paper finds that sea anemones might be one of those who profit: ocean acidification appears to enhance their productivity and growth. They don’t have a calcified shell to worry about maintaining, hence their getting a leg up over calcifying corals and molluscs.


4. Adaptive evolution of a key phytoplankton species to ocean acidification.

This is an example of experimental evolution done well. Lohbeck et al. took Emiliania huxleyi, one of the most dominant coccolithophores, and let it evolve for 500 generations through serial transfers to increasingly more CO2-enriched water. They show that instead of dying out, they gradually adapted, increasing their growth in the higher acidic conditions by the end of the experiment. It’s only a lab experiment though, so it just shows that the possibility to adapt is there; whether this will occur in the rough-and-tumble of the wild cannot be guaranteed.


3. Extensive dissolution of live pteropods in the Southern Ocean.

pteropod

In #5, I made a distinction for calcified organisms being more affected by ocean acidification because of their shells. This paper gives the starkest example of this using pteropods: in the pictures above, a and b are regular shells; c and d are under slight acidification; e and f are at high acidification, and the shell is extremely deteriorated because of its dissolution – and these are from the wild (the paper also has experimental analyses to determine at what level they dissolve). There is no need to stress how damaging this is to pteropods, and similar effects are observed in all calcium carbonate-shelled organisms.

Ocean acidification induces budding in larval sea urchins is a relevant paper that shows a negative response by sea urchins to ocean acidification: larval budding, leading to unviable clones.


2. Genetic consequences of climate change for northern plants. [OA]

gendiv

Climate change will affect plants by reducing their range and by reducing their genetic diversity. This paper estimates just how much genetic diversity will be lost in 27 alpine and arctic species by 2080, under a range of climate models. It’s a lot, although it does vary by species and model, and most of these plant species will fall into the endangered category if the IUCN starts taking genetic diversity into account (which they probably will at some point). So, bad news.


1. A synthesis of carbon dioxide emissions from fossil-fuel combustion. [OA]

ffco2

I am making an exception and adding a review paper, because this one really is excellent and thorough, and a great placeholder until the new IPCC report comes out. If you need up-to-date data on CO2 emissions from fossil fuels, and details on how those numbers are compiled and calculated, this is exactly the paper you want.


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Top Research of 2012: Ecology

31 12 2012

Jump to: Arthropods; Botany; Developmental Biology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

My subjective picks for the top 10 ecology papers of the year. Ecology as a science is rather esoteric, and the ecology I follow for my own work is too specific to be of broad interest, so I tried to diversify the list with more general-interest stuff. The matser list had 29 paper. [OA] indicates open access.


10. Relationships between arthropod richness, evenness, and diversity are altered by complementarity among plant genotypes.

This paper contributes to our knowledge of how arthropod biodiversity is maintained. If you have plant polycultures, species richness will increase. However, that increase may not be proportional or even: in the experiment done in the paper, while there was an increase in overall richness, one species of generalist plant bug, Plagiognathus politus, became dominant in terms of numbers. In other words, ecosystems are not as simple as “increase plant diversity → more insects”, because those more insects will not be proportionally distributed. You might get thee more species visiting your fields, but have one pest species outcompeting everything else.


9. Flying shells: historical dispersal of marine snails across Central America.

flyingsnails

The Central American Isthmus – the narrow ridge connecting North and South America – is an obvious geographic barrier for marine organisms. No fish or octopus can jump across it in any case. When it first arose 3 million years ago, it cirectly separated the Pacific and Atlantic biota on each side of the Americas (going around the Poles isn’t a trek most organisms will take or survive). But look at the above diagram, a phylogeny of two closely-related intertidal Cerithideopsis snails. You have 2 ancestral species. Both split a couple of times after the rise of the Isthmus… and the terminal populations investigated in the paper are found on both sides of the Isthmus. The only explanation for this pattern is that they must have dispersed from one side to the other, as the arrows point out. Miura et al. suggest that it was done by shorebirds, the explanation that I also find most reasonable (more plausbile than crawling), since I’ve also observed snails and other invertebrates get dispersed by waterbirds between salt lakes here in Cyprus – migratory birds are prolific dispersal agents.


8. The Discovery of New Deep-Sea Hydrothermal Vent Communities in the Southern Ocean and Implications for Biogeography. [OA]

esr

This paper reports the very first Antarctic hydrothermal vent community, from the Eastern Pacific Rise of the Southern Ocean. If you’ve seen pictures of vent communities elsewhere in the world, you’ll notice that the animals here are different. There are no Riftia worms. There are no bathymodiolid mussels. There are no alvinocaridid shrimp. Instead, what you have are endemic species, consistent with the general levels of endemism in the Southern Ocean, where animals have become endemic because of the Polar Front (which also doesn’t allow new animals to come in). This makes this hydrothermal vent a brand new oceanic biogeographic province, as well as a rich source of new species to be described.


7. Life in the hydrated suboceanic mantle.

This paper belongs more in the geology listing, but I put it here because I consider its implications more important for ecology. What this paper studies are serpentinised peridotites from the Mid-Atlantic Ridge. These are rocks from the mantle that have been modified by superheated water flowing through them, a process called serpentinisation that happens at all hydrothermal vents and seafloor spreading centers, or basically anywhere where there’s a deep crack in the ocean floor. Ménez et al. found a lot of organic matter, including aromatic compounds and other organics that could very plausibly be of biological origin. In other words, it could be that there are bacteria living down in these very deep and very hot cracks, feeding off the results of the serpentinisation process (notably hydrogen and methane). And the next step is obvious: send some high-tech sterilised probe to see if there really is something there. I hope someone is working on that.


6. The island–mainland species turnover relationship. [OA]

islandturnover

Islands are my personal favourite evolutionary arena, hence why I’m doing my own research on one. This paper is significant because it shows that islands really do have their own unique biodiversity-generating processes, rather than just being “miniature continents”; the diagram above summarises the differences, with black being island data and grey being mainland data. For all the details, head over to Anole Annals where the main author wrote up a description of the paper, saving me the bother.


5. The latitudinal position of peak marine diversity in living and fossil biotas.

In the terrestrial realm, biodiversity follows a more or less linear decline as you move away from the equator. This paper is a comprehensive study of marine biodiversity records, and finds that modern peak diversity isn’t at the equator, but rather between 10-20° latitude. As we know from the fossil record, marine biota are sensitive to environmental changes, and this may be just a temporary condition, a consequence of today’s continental distributions and sea levels.


4. A serpentinite-hosted ecosystem in the Southern Mariana Forearc. [OA]

mariana

This paper described the discovery of a hydrothermal vent ecosystem at a depth of 5500+ m, on the outskirts of Challenger Deep, the deepest point of the Earth’s sea floor. This isn’t a type of vent with chimneys, but rather an ecosystem with energy sources coming from the products of serpentinisation. This is the surface, relatively low-temperature version of what I envision for #7. While it’s not the first to have been discovered, this one supports a surprising amount of biomass.


3. Hydrothermal vent fields and chemosynthetic biota on the world’s deepest seafloor spreading centre. [OA]

cayman

#4 is not a spreading centre (it’s a convergent plate margin, the opposite), so do not be confused by the title. The vent fields described here are between Cuba and Central America, with vents at depths of ~2300m (Von Damm, pictured above in c and d) and ~4960m (Beebe; pictured above in a and b). I mentioned biogeographic provinces in my comment for #9. This serves as a great example: the animals and communities pictured above from the vents here are very similar to the ones found on Mid-Atlantic Ridge vents. They belong to the same province, instead fo being affiliated with the faunas of Mexican cold seeps that are much closer. It demonstrates that the deep ocean, unlike some popular conceptions, is not a static place where everything goes. Environmental conditions are as variable as in the terrestrial realm, leading to these consistent differences and similarities between faunas.


2. Spider silk reduces insect herbivory.

Technically a paper in a 2013 issue, but it’s all already online, so I put it here because of the elegance of the experiment and potential research. And it really is a simple experiment that I will be doing with my schoolkids. Rypstra & Buddle coated the leaves of a commonly-predated plant with spider silk, with silkworm silk, and left other leaves untouched. They then measured predation on them from two common pest species, and in a repeat of the experiment, in the wild from all herbivores. The results are consistent and visible in the diagram above: The presence of silk drastically reduces herbivory, especially spider silk. The potential future research that I would like to see done with this is to see if maybe plants can attract spiders as an extended defence mechanism, similar to how some tropical plants attract ants to defend them from caterpillars. Or it could be another example of insect intelligence, spotting the silk and avoiding it. Either hypothesis is cool, although the former excites me more. I can’t wait for this research to be done (I’d do it, but I have no chemical lab at my disposal to detect and characterise plant volatiles, or a neuro lab to do electrophysiology on spiders).


1. Global distribution of microbial abundance and biomass in subseafloor sediment. [OA]

cells

C above shows the results of this landmark paper: calculated estimates of the numbers of microbes found in subseafloor sediment, with the dots being sites where cells were counted. The numbers are a whopping 92% lower than the first such estimate, meaning that the previous estimates for the numbers of prokaryotes in the world are slashed by half to 3/4, with the number now standing at 9.2 to 31.7 x 10²⁹ cells. The study can be improved with more sampling to provide more resolution, but this is a sound base. The notable trend is that cell number decreases with ocean depth, and that there is a correlation with sediment depth.

Subseafloor basalts as fungal habitats [OA] is a related paper that looks at thin sections of basalts (petrified magma) and finds fossilised fungal colonies in them. The basalts range in age from 81 to 48 Ma, but there’s no reason that fungi couldn’t live on modern subseafloor basalts too. Any readers with deep-sea submersibles should get on this at once.


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Top Research of 2012: Botany

29 12 2012

Jump to: Arthropods; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

My top 10 picks for botanical research this year. I’m not a botanist, and although I am fascinated by plant physiology, I’m not intellectually able to keep up with that research. So I only really follow plant evolution, palaeobotany, and plant-arthropod interactions; I have tried to make the list more varied though. Picks and rankings are subjective, based on a master list of 17 papers. [OA] indicates an open-access paper.


10. Broad Phylogenomic Sampling and the Sister Lineage of Land Plants. [OA]

charophyta

Land plants (Embryophyta) are highly-specialised streptophyte green algae. Of the other streptophyte groups, three are variably recovered as the sister group to the land plants, the results depending on the genes and methods used, and none ending up with truly rigorous support: the Charales, the Coleochaetales, and the Zygnematales (pond scum). The Charales (stoneworts) are the ones commonly depicted in textbooks and have always gained the most support. This paper may change our view on things: it uses a large dataset of 160 phylogenetically-significant genes, and gets perfect support values for a Zygnematales+Embryophyta clade. This has numerous implications, chief of which is that multicellularity is a convergent land plant innovation rather than a condition inherited from an ancestor (as would be the scenario if Charales are the sister).


9. Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges.

This paper studies the molecular basis for UV light detection (280-320 nm) in plants, by looking at the reactions of UVR8, a photoreceptor known to react to UV light. Christie et al. went classical in this paper: they used crystallographic methods to elucidate UVR8′s structure, best summarised as a doughnut; then they used targeted mutations to find out how the protein works. When inert, it’s found as a dimer: two doughnuts connected by bridges. When UV light shines on the plant, these bridges break due to electrons getting excited. The single doughnut then binds to another protein, COP1, to complete the reaction.


8. Phylogenetic niche conservatism in C4 grasses.

c4

I’ve written an overview of C4 photosynthesis, so refer to that post for necessary background. This paper analyses various traits in grasses of the Chloridoideae and Panicoideae, grasses in which C4 photosynthesis is dominant (in the phylogeny above, yellow indicates C3, all other colours are types of C4). It finds that the evolution of these traits, as well as ecological preferences, are determined not by the evolution of C4 photosynthesis, but by phylogeny. In other words, it’s the ancestry that counts. This in turn has implications about how we should treat C4 photosynthesis: there is a tendency to lump C4 plants together as one functional group, regardless of phylogeny. This finding says we are better off sticking to phylogenetic lumping, since there is clear niche conservatism: C4 photosynthesis doesn’t determine the ecology of these plants. Ancestry does, and C4 photosynthesis just tags along.


7. A critical transition in leaf evolution facilitated the Cretaceous angiosperm revolution. [OA]

veins

This paper presents a cool hypothesis for a contributing factor to the great angiosperm radiation of the Cretaceous: leaf vein density (Dv in the above diagram) as a key feature. This is an observation in the fossil record, that the density of the veins increases in two bursts, once in the initial angiosperm radiation (100 Ma) and another time at 65 Ma to reach today’s levels. The greater vein density leads to vastly improved gas exchange rates, which would have provided them with a distinct advantage as the CO2 levels decreased in the Cretaceous, allowing them to more easily outcompete the conifers and other land plants.


6. Widespread impact of horizontal gene transfer on plant colonization of land. [OA]

hgt

This genomic analysis of a moss, Physcomitrella patens, finds that it has 57 nuclear gene families by horizontal gene transfer from bacteria, fungi, or viruses. 18 of them are inherited ancestrally; 18 of them are recent acquisitions; and 15 of them are also found in more derived land plants, passed on from the last common ancestor with mosses. To put these numbers into perspective, the functions of the acquired genes are essential, involved in defence and stress tolerance, hormone biosynthesis, and even DNA repair. The picture painted by these facts is one of a harsh environment that early land plants had to colonise, in which UV radiation was rampant and the ground was inhospitable; these genes enabled the early mosses to survive by helping DNA stability in early mosses (later plants got yellow pollen, the yellow pigment serving as a UV shield), and numerous stress tolerance mechanisms and development helpers to keep them surviving in the harsh environment.


5. Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior.

This is some pretty cool research from an ecological and from a plant-insect interaction perspective. The study finds that plant defence systems can be synchronised with insect feeding times; at least it is so in the case of the caterpillar of Trichoplusia ni and the Arabidopsis weed this experiment was done on. The synchronisation is achieved not by detecting the caterpillar, but by circadian rhythms – when raised on the same day/night cycle, the plant’s defence system will adjust to be active at the same time as the caterpillar is active. When circadian mechanisms are interrupted or the hormone jasmonate’s production is deficient, then the synchronisation gets thrown off and the plant experiences much higher herbivory levels and are thus at a physiological disadvantage. I’m interested in seeing how this plays out in nature with day-active vs. night-active insects.


4. Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants.

This paper reports the draft nuclear genome of the basal glaucophyte alga Cyanophora paradoxa. The most significant result is evidence for the monophyly of the Plantae, as even the untypical plastid of the glaucophytes appears to be homologous with that of the rhodophytes and green algae (together, these three groups make up the Plantae). The data gathered from the genome says that 274 of the alga’s proteins were transferred from endosymbiotic cyanobacteria, and that 444 gene families were transferred by horizontal gene transfer from other bacteria. Many of these proteins and genes are involved in photosynthesis and associated processes, as well as plastid integration, meaning that we now have more light shone on how built-in photosynthesis in plants first evolved.


3. Oldest known mosses discovered in Mississippian (late Visean) strata of Germany.

Mosses are expected to be one of the earliest plants to have evolved on land, but their early fossil record has been severely lacking because of their very low preservation potential. This paper describes the oldest mosses to date, which grew in the tropical forests of the German Carboniferous. Older ones are still to be expected, but their lack is merely an example of an expected inadequacy in the fossil record.


2. Underground leaves of Philcoxia trap and digest nematodes.

I admittedly include this so high up because of the coolness factor, but it does bring up deeper issues. But first, the cool stuff: the plant has sticky leaves that grow underground. Nematodes stick to them, and the plant digests them. In other words, this is a carnivorous plant, and it uses a completely novel way to capture its food. The deeper ecological and evolutionary issue to be brought up is about how such a unique strategy can evolve.The plant grows in a region with one of the poorest soils of the world, the Brazilian Cerrado. So it could be that the evolution of carnivory is instigated by soil nutrient deficiencies, and so they eat animals in order to get those critical nutrients.


1. Rise to dominance of angiosperm pioneers in European Cretaceous environments.

This paper reviews the early record of angiosperm fossils from Europe to propose a temporal framework for their megadiversification in the Cretaceous in which they outcompeted the conifers and other land plants. The scenario Coiffard et al. synchs up with the view from the North American record, so it can be viewed as reliable. The scenario has three bursts of diversification into new habitats. From the abstract: “(i) Barremian (ca. 130–125 Ma) freshwater lake-related wetlands; (ii) Aptian–Albian (ca. 125–100 Ma) understory floodplains (excluding levees and back swamps); and (iii) Cenomanian–Campanian (ca. 100–84 Ma) natural levees, back swamps, and coastal swamps.”


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Zoology





Top Books of 2012: Evolution

20 12 2012

Jump to another list: Environmental and Climate Change; Historical Geology; History of Science; Human Evolution and Anthropology; Palaeontology; Zoology

The subjects covered here are varied and not limited to pure evolutionary theory. There is a bias towards academic books; the popular and layman level ones are numbers 5 (creationism), 6 (simulated evolution), 8 (epigenetics), and 9 (molecular biology). The others are on the expensive side and are meant for undergrads and up.

  1. Pfennig & Pfennig. Evolution’s Wedge: Competition and the Origins of Diversity. (University of California Press)
evolutions-wedge-competition-and-the-origins-of-diversity This book is all about an evolutionary phenomenon first formalised in the 1950s called character displacement, where the differences between two closely-related species become more pronounced when the species coexist, most often due to the action of natural selection minimising sexual confusion and maximising competition. The Pfennigs, two leading evolutionary ecologists, argue that character displacement is an engine for speciation. Get this book if you want to get your biological thinking honed and challenged, because it isn’t a book stating facts to memorise, it’s a book stating hypotheses – in other words, it’s one of those essential reads that any biologist interested in the subject should try to get to grips with and critique. For that, it gets the number 1 spot.

  1. Royle, Smiseth & Kolliker (eds.). The Evolution of Parental Care. (Oxford University Press)

the-evolution-of-parental-care

While parental care (parents altruistically investing into the survival of their offspring) is common in mammals and birds, overall it’s fairly rare and so worthy of study wherever it occurs. This book explains the evolutionary conditions needed for parental care to arise, using phylogenetically diverse case studies and evolutionary theory to puzzle out all sorts of related questions, such as the varying roles of males and females and subsequent sexual selective effects, the role of life history and life history evolution, familial cooperation and conflict, and many other subject. Recommended if you’re interested in animal sociality and related evolutionary theory.


  1. Dieckmann, Doebeli, Metz & Tautz. Adaptive Speciation. (Cambridge University Press)
lg Adaptive speciation is biologically-driven speciation that occurs due to disruptive selection, i.e. when the extreme traits in a population are selected for. The book gets third place because adaptive speciation has been a focus in speciation research for the past decade and a half, with a lot of theoretical studies and modelling having been done by now, and this book provides a timely summary and outlook.

  1. Kunz. Do Species Exist? Principles of Taxonomic Classification. (Wiley-Blackwell)
do-species-exist-principles-of-taxonomic-classification No evolution book list would be complete without one book on the age-old species problem. This year’s version is an interesting hybrid that lays out the various concepts, but deals with them with the practicing biologist in mind, not the philosopher. For that, I applaud it.

  1. Fitch. The Three Failures of Creationism: Logic, Rhetoric, and Science. (University of California Press)
the-three-failures-of-creationism-logic-rhetoric-and-science This year’s token creationism-destroying book, written by one of the founding fathers of the study of molecular evolution. It’s a very thorough takedown of creationism from every aspect, as the subtitle suggests. I do have to warn that it isn’t an easy read that you can quickly flip through to find an easy answer to a creationist argument. It’s meant to be read and the essence of its arguments taken in, rather than be a quick rebuttal source (there are a lot of other books if that’s what you want). I, for one, enjoy this approach, but I can see others not liking it. The book is aimed at undergraduate level.

  1. Long. Darwin’s Devices: What Evolving Robots Can Teach Us About the History of Life and the Future of Technology. (Basic Books)
darwins-devices-what-evolving-robots-can-teach-us-about-the-history-of-life-and-the-future-of-technology If I had to choose my top pop. evolution book of the year, it would be this one, and I heartily recommend it for everyone to read. Its topics include simulated evolution and the origin of intelligence. The latter is interesting for those who like the idea of AI or want to see just how easy it is for intelligence to evolve. The former is something I’ve often thought about – I have written evolution-simulating programs before, and I’m a big fan of SimLife and SimEarth, but the things that Long describe here go way beyond such simplicities. I don’t want to spoil it, so I will just say that you are missing out by not getting this book.

  1. Wheeler. Systematics: A Course of Lectures. (Wiley-Blackwell)
253698 If you want to teach yourself systematics, this book is for you.It’s just a series of lectures and exercises compiled by Wheeler, one of the top systematic biologists. It’s not an advanced text on the bells and whistles of systematics, it’s just aimed at making sure you understand what you’re doing and why, and getting results from the very beginning of the process.

  1. Francis. Epigenetics: How Environment Shapes Our Genes. (W. W. Norton & Company)
epigenetics-how-environment-shapes-our-genes If I had to choose the one field that gets warped and misunderstood popularly, it’s epigenetics. I recommend this book as the most basic level introduction to the subject – it’s not an advanced book at all, meant purely for the lay reader. It’s a quick read and will help you clarify the bullshit from the real science next time the science journalists screw things up.

  1. Hoffmann. Life’s Ratchet: How Molecular Machines Extract Order from Chaos. (Basic Books)
lifes-ratchet-how-molecular-machines-extract-order-from-chaos One of my pet peeves is watching those cell biology videos showing reactions happening purposely and all in order. I understand the need to educate, but this is extremely deceptive – the cell is a fundamentally chaotic place where reactions occur stochastically. This book is a breath of fresh air because it emphasises this point, and then uses biophysics to explain how order arises. It’s a brilliant exploration of emergence, and it’s all written with the layman in mind. Get it if you’re at all interested in how cells work, in the origin of life, or even if you just want an indirect debunk of intelligent design lunacy.

  1. Grime & Pierce. The Evolutionary Strategies that Shape Ecosystems. (Wiley-Blackwell)
0470674814 The last book is a return to academic fare. This book showcases reductive ecology at its best, distilling the wild variety of ecological interactions and life histories into their evolutionary advantages and tradeoffs, thereby showing that there is common ground among the ecological disparity. The case studies range from microbes to animals, and even palaeontology is included in the mix, making the book a very comprehensive resource for those interested in eco-evolutionary dynamics.

Jump to another list: Environmental and Climate Change; Historical Geology; History of Science; Human Evolution and Anthropology; Palaeontology; Zoology





C4 Photosynthesis

2 11 2012

C4 plants are plants that undergo a specialised extrametabolic pathway, the C4 cycle, in which CO2 is transferred from mesophyll cells to a special ring of bundle sheath cells by a pump. CO2 gets dissolved by carbonic anhydrase, forming bicarbonate, which is then fixed with phosphoenolpyruvate carboxylase into C4 oxaloacetic acid (hence the name), which is then converted to malate. This diffuses to the bundle sheath ring through plasmodesmata, where the CO2 is set free by decarboxylases, including the all-important RuBisCo (Hatch, 1987). Regular C3 photosynthesis occurs, but under the locally very high CO2 concentrations 3-8x higher than other area of the leaf.

The net result is a minimisation of CO2 loss through photorespiration, a reduction in use of stomata leading to less water loss through transpiration, and a much higher rate of photosynthesis, at the cost of substantial energy needed to drive the CO2 pump, energy acquired from sunlight. C4 plants are also more efficient in using nitrogen, since they need to use less enzymes to maintain their higher photosynthetic rates (Pearcy & Ehleringer, 1984).

In practical ecological terms, what those advantages bring is either an ability to grow faster than C3 plants, or an ability to grow in more challenging environments than C3 plants (Hatch, 1987).

The reason why C4 photosynthesis works is the evolutionary history of C3 enzymes, especially the main one, RuBisCo. RuBisCo evolved back in the times when the atmosphere contained very little oxygen and 100x more CO2 than today (Rye et al., 1995). Therefore, all that C4 photosynthesis does is recreate that atmosphere very locally around the enzyme so that it acts in the environment it evolved to be optimal in, namely an atmosphere with very high CO2 and low O2, so that the competitive inhibition of RuBisCo by O2 is eliminated. For those with engineering experience, C4 photosynthesis works just like a supercharged combustion engine.

Although only 3% of vascular plant species undergo C4 photosynthesis, those plants are responsible for almost a quarter of the photosynthesis that happens on land (Lloyd & Farquhar, 1994). Its evolution is therefore quite an important development not only from a physiological perspective, but also from an ecological one.

C4 metabolism evolved convergently from regular C3 photosynthesis in over 45 land plant families, both monocot and dicot (Sage, 2004), as a result of the steady depletion atmospheric CO2 levels between 40-15 Ma (Edwards & Smith, 2010). This reduction in CO2 levels led to inefficiency in carbon uptake in land plants, especially those in warm and arid landscapes (most C4 plants are grasses), providing a strong selective pressure to reduce photorespiration, and by the Pliocene, C4 grasslands had displaced C3 grasslands in lower latitudes. Tropical grasslands and savannahs are dominated by C4 plants, as are many breakfast tables (Sorghum, maize, and sugarcane are all C4). At higher latitudes, the cost of driving the CO2 pump outweighs the gains: the C4 vs. C3 biogeographical dominance has a threshold defined by temperature (Ehleringer et al., 1997), with C4 plants dominating in warm temperatures and C3s in cold temperatures (the distinction also applies with altitudinal gradients). Other important factors influencing distribution are moisture/precipitation and light intensity.

There are no novel enzymes involved in C4 photosynthesis, it is all achieved using cooption of pre-existing enzymes and changes in their expression patterns causing the enzymes to accumulate to various levels in the mesophyll and bundle sheath cells. These changes are pretty complicated considering that they involve 20-30 unlinked genes (Wyrich et al., 1998) – it’s remarkable that this all evolved convergently so many times. We know of some intermediate species exhibiting some “proto-C4″ characteristics, e.g. several species in the Neurachne, Flaveria, Parthenium, Mollugo, and Alternanthera genera (list just random examples I dug up, there are definitely more!). Xu et al. (2012) show that both C3 and C4 pathways work at the same time in the alga Ulva prolifera.

It’s also worth noting that some unique lineages have managed to make a C4 mechanism that takes place within individual cells rather than in different tissues, see Keeley (1998) for examples.

References:

Edwards EJ & Smith SA. 2010. Phylogenetic analyses reveal the shady history of C4 grasses. PNAS 107, 2532-2537.

Ehleringer JR, Cerling TE & Helliker BR. 1997. C4 photosynthesis, atmospheric CO2, and climate. Oecologia 112, 285-299.

Hatch MD. 1987. C4 photosynthesis: a unique blend of modified biochemistry, anatomy and ultrastructure. Biochimica et Biophysica Acta 895, 81-106.

Keeley JE. 1998. C4 photosynthetic modifications in the evolutionary transition from land to water in aquatic grasses. Oecologia 116, 85-97.

Lloyd J & Farquhar GD. 1994. 13C discrimination during CO2 assimilation by the terrestrial biosphere. Oecologia 99, 201-215.

Pearcy RW & Ehleringer J. 1984. Comparative ecophysiology of C3 and C4 plants. Plant, Cell & Environment 7, 1-13.

Rye R, Kuo PH & Holland HD. 1995. Atmospheric carbon dioxide concentrations before 2.2 billion years ago. Nature 378, 603-605.

Sage RF. 2004. The evolution of C4 photosynthesis. New Phytologist 161, 341-370.

Wyrich R, Dressen U, Brockmann S, Streubel M, Chang C, Qiang D, Paterson AH & Westhoff P. 1998. The molecular basis of C4 photosynthesis in sorghum: isolation, characterization and RFLP mapping of mesophyll- and bundle-sheath-specific cDNAs obtained by differential screening. Plant Molecular Biology 37, 319-335.

Xu J, Fan X, Zhang X, Xu D, Mou S, Cao S, Zheng Z, Miao J & Ye N. 2012. Evidence of Coexistence of C3 and C4 Photosynthetic Pathways in a Green-Tide-Forming Alga, Ulva prolifera. PLoS ONE 7, e37438.





Cyprus as an Open Evolutionary Lab

11 06 2012

This post serves as an introduction to my interest in Cyprus as an open laboratory for cool, and potentially groundbreaking, evolutionary biology research. It’s an excerpt from a talk I gave several months ago, hence the slides as pictures.

The map above shows Cyprus’s position in the Eastern Mediterranean. The nearest continental landmass, the southern coast of Turkey, is 70 km away, followed by the Middle East 100 km away. Then comes North Africa at 350+ km away, and a distant Greece, over 500 km away. These distances are reflected in the fauna of Cyprus, which has a very distinct Middle Eastern feel to it.

All islands are viewed as excellent places for evolutionary research, and Cyprus is no exception. Its relative isolation is more than enough to make endemics out of any insects that don’t routinely migrate over long distances.

If one looks at the map where endemic plants are found, this relationship between isolation and endemism is easily observable. In green are areas where endemic plants are found, in white are where they’re absent. The pattern reflects very closely the level of agricultural and other human development: the white areas are all developed or agrarian areas, where human-mediated invasives have taken over the landscape. Protected and mountainous areas, on the other hand, are rich in endemic flora.

Such a map doesn’t exist for arthropods due to the lack of research, but a similar pattern can be expected, with endemic richness being much, much higher in the “wild” areas of Cyprus.

Map Source: Tsintides TC. 1998. The Endemic Plants of Cyprus.

For me, one of the most important questions to ask is how insects first came to the island; this is especially important to consider for insects that don’t fly very well or at all. There are generally four avenues for dispersal to an island.

The first, and most opportunistic/random, is rafting. As the name says, this is nothing more than getting stuck on afloating raft (of wood) and getting carried by the currents to the island. It may seem like a stretch, but the oceanography makes this possible, and we know that insects can survive for long periods of time on a block of wood. So it’s by all means logistically and theoretically possible, and has probably happened.

Another method is by using land bridges. This is where knowing some geololgical history comes in handy. Cyprus’s case is rather unique in that it formed completely in the ocean, with the central mountain range (Troodos) being nothing more than elevated oceanic crust (as we will see later) and having collided with the northern mountain range (Kyrenia), resulting in uplift of the central and coastal areas (and uplift that is still ongoing, albeit in a different tectonic context). So at no time during its formation was Cyprus connected to the mainland. However, 6 million years ago, the entire Mediterranean did dry up during the Messinian Salinity Crisis. The area between Cyprus, the Middle East, and Turkey was definitely crossable by any insect and spider. When the Atlantic flooded back, the organisms were left stranded on Troodos or Kyrenia.

A third method applicable to Cyprus is jump-dispersal, which is when multiple small islands form stepping stones to the large island. This, again, requires some geological knowledge. With the climate changes of the Pleistocene and Ice Ages, the Mediterranean’s sea level experienced some wild fluctuations. By this time, Cyprus had pretty much emerged from the sea and looked more or less like it does today. But with the sea levels fluctuating, the land between Cyprus, Turkey, and the Middle East became exactly as in the picture above, and some scenarios even suggest that it was completely dry, resembling a sort of salt marsh. In both cases, the way is easily traversable by all but the most immobile of arthropods, and when the sea levels became normal again, they were left all over the island.

The last, and most easily-detectable, way for insects getting onto the island is through humans, either purposely introduced as pest control (as is the case with some coccinellids, for example) or accidentally. And this has a very rich history in Cyprus’s case, given that Cyprus has been conquered by just about every major seafaring civiliation from Europe, North Africa and the Middle East at some point in its history. From living on the ships, to the products in the ships (timber or food), to the clothes of the sailors, this is by far the easiest way for any small insects to make their way around the world. Luckily, it can also be very easily accounted for using genetic tests.

The point here is that merely noting the current biodiversity of the island isn’t enough. In order to fully understand how the insect communities of the island developed (and thus how endemism came to be), we need to have this historical aspect in mind.

So, now the insects are on the island. How do the new species form? I already wrote a post on speciation, useful if you need some summary background on the processes involved. On Cyprus, there are three ways in which speciation can happen: by cladogenesis, by anagenesis, or by anacladogenesis.

Cladogenesis is a case of classic sympatric speciation. Population B arrives on Cyprus from the mainland and encounters different habitats and different ecologies than what they are adapted to. One part of the population colonises one habitat, the other colonises a different habitat (either by chance of where they land, or “on purpose”). Over generations, they will adapt to the new plants and abiotic conditions, and they will be new species, distinct both from each other and from the parent population.

Anagenesis can be summed up as “speciation without branching”, occurring as change accumulates in a single lineage. For our case in Cyprus, this can happen if the migrating population lands somewhere where the identical conditions and plants are found, which is likely considering the similarities in climate and flora of the closest landmasses. Additionally, there needs to be some amount of secondary remixing by travelling back and forth or occasional waves of migration – if they get geographically isolated with their own little gene pool, they are treated as a branched-off lineage arising by cladogenesis. But even with some remixing, there will be some isolation, and by genetic drift, mutations will slowly but surely accumulate within the Cypriot population, initially resulting in some reproductive isolation (as indicated by the i in the diagram). Eventually, this will result in complete speciation.

Anacladogenesis, as the name suggests, is a mixture of the two, with part of the population undergoing anagenesis by remaining in a place with similar ecologies and abiotic conditions, while another segment of the population colonises new ground and buds off to form a new species.

There is no way of predicting, in the absence of data, which of these has played a more important role in Cyprus. I would hypothesise the obvious: insects with good dispersal ability undergo anagenesis, while more immobile insects undergo cladogenesis. This will all be tested once I have baseline information on the taxonomy of the endemic insects.

What we’ve talked about so far has been general and more or less applicable to any landscape affected by invasion or to any island, but Cyprus still provides an extra experimental and data-gathering arena. What will now follow is a look at the scientific basis for my research.

First off, a purely theoretical look at the background of the main thesis, that increased mutation rates will lead to speciation. The flowchart above shows, generally, how macroevolution proceeds.

The foundational level in macroevolution is the genome – the entire collection of genes and sequences, both those that will be expressed at some point and those that will not. From this collection, a few select parts are activated during development of an organism. These tend to be evolutionarily conserved (indicated by the loop), as screw-ups during development are generally very deleterious.

Development leads to the building of the phenotype, of the individual. The phenotype then has a very tight interplay with ecology – which I lump here with natural history, so including things like behaviour and life cycles, not the least through functional morphology. Ecology in turn can modify the phenotype through environmental effects – more food leads to larger organisms, a preference for colder habitats leads to different phenologies, etc.

As I stressed in my natural selection lecture, the individual is where natural selection acts, because it’s the individual that survives and reproduces, not its genome. But, as the flowchart shows, the individual is itself dependent on development, which is itself derived from the genome. So, in effect, tracing the evolution of the phenotype can be done by looking at the evolution of its development. The action of natural selection on the phenotype and on development leads to an evolutionary response on the genome, making some parts of it invalid, or emphasising the roles of other sections.

This is how macroevolution works, basically. It’s nothing more than a feedback between development, the phenotype, and the genome, with the former two exerting their effect on the latter.

What my project aims to do is subvert this scheme on its head, by asking a hypothetical question: What if the diversity in the genome increases? Will that make the filter of development more porous and lead to higher phenotypical diversity, in turn leading to more ecological diversity and to speciation?

The answer known already is that yes, higher genomic diversity can lead to speciation, as evidenced by studies with gene or genome duplications. Where my project differs is that I am taking the question at a truly fine level, looking at individual mutations, and all in a well-constrained natural arena. The reason I can do this is only because of Cyprus and its geology.

The above picture summarises the geology of Cyprus. It’s split up into four units: the Kyrenia Mountains in the north, the Troodos Ophiolite in the center and west, with the sedimentary succession surrounding it, and the Mammonia Terrane to the west and southwest.

We’re interested in the Troodos Ophiolite. As you can see from the endemic plant distribution map, it’s clear that the endemic plants are mostly found in all the geological units besides the sedimentary one, but the Troodos Ophiolite is particularly well-inhabited – the patch in Mammonia, around the lake in Lemesos, is mostly due to the presence of unique salt marshes there, not due to geology per se.

The diagram on the left shows the structure of the Troodos Ophiolite. An ophiolite is nothing more than a piece of oceanic crust, and this discovery was done in Cyprus in the 1950s, thanks to the impeccable preservation of the Troodos sequence – other ophiolites tend to have bits and pieces of this sequence, in Troodos it’s complete. For orientation, the bottom of the diagram is actually the top of Mt. Olympus, and the top of the diagram is the lowland part of the mountains. So, in effect, when you drive up the mountain, you’re actually going back in time as far as geology is concerned. It’s quite surreal.

A detailed look at this falls outside the scope of the post. Suffice it to say that the bottom of the sequence, from the harzburgites to the plagiogranites, represent the rocks of the oceanic crust, from the deepest ones (subject to high temperature and pressure) to the shallow ones. The sheeted dykes and basalts are lava – the uplifting of the oceanic crust caused cracks to appear, and magma seeped through (sheeted dykes), spreading on the ocean floor (massive basalt) and reacting with the much colder ocean water (fractured basalt). After a certain period of uplift, volcanic action subsided and sediments accumulated on top of the whole thing. For some reason, when it was uplifted, the ophiolitic sequence of Troodos got flipped upside down, resulting in the oldest rocks (harzburgites and lherzolites) being found at the top and the sediments at the bottom.

Diagram source: Edwards S, Hudson-Edwards K, Cann J, Malpas J & Xenophontos C. 2010. Classic Geology in Europe 7: Cyprus.

Geology serves as a basement, and gets eroded and degraded by plants to form soil. Thus, the characteristics of the soil are intrinsically linked to the mineral content of the underlying geology. In this case, we have water reacting with olivine-rich rocks of the oceanic crust and hydrating them – this leads to the formation of serpentine minerals.

The soil derived from this group of rocks and minerals is correspondignly called a serpentine soil, and its main, relevant characteristics are shown on the right. First is very low concentrations of elements typically critical for plant growth, including potassium, nitrogen, phosphorus, and calcium. This means that only specific plants can actually grow here.

Making matters worse for the plants, and gloriously exciting for me, is the second characteristic: high concentrations of heavy metals. Iron and magnesium levels are especially increased, but chrome, nickel, and cobalt levels are also notable. Heavy metals are known to be hazardous as mutagens, and so the pool of plants that can grow on heavy-metal enriched soils increases.

And here Is where the geology ties back to my previous scheme of macroevolution and the question I’m asking. As mutagens, heavy metals will increase the diversity of the genome, and so will provide a natural experimental set-up to test my hypothesis.

There is no data to go on yet for Cyprus – that’s why I’m trying to get the project funded. But there is another region in the world where ecology on serpentine soils is being studied: California. California has an area of ~424000 km². Serpentine underlies 6000 km² of that, so only 1.5%.

Yet, as the graph above shows, the percentage of endemic plant species in this tiny patch is equal to or greater than the percentage of plant species in the rest of California. This is mostly due to the inhibitory nature of the soil, with the high heavy metal concentrations and low critical element concentrations.

Graph source: Safford HD, Viers JH & Harrison SP. 2005. SERPENTINE ENDEMISM IN THE CALIFORNIA FLORA: A DATABASE OF SERPENTINE AFFINITY. Madroño 52, 222-257.

But it is also valid to ask whether higher microevolution rates, caused by the mutagenic heavy metals, can also play a role. My not being a botanist (although with an interest in plant physiology) prevents me from investigating this with plants in Cyprus. However, one of the first lessons in ecology and environmental sciences is about bioaccumulation, that toxicity accumulates the higher up a food web one goes. And the next level is, of course, the myriad insect herbivores, followed by the carnivorous insects and spiders, and all supplemented by the omnivores and detritivores.

So, if any effect on microevolution rates are there, they can just as easily be observed in the associated animals, in which case I can inject my own disciplinary bias and look at the topic as a macroevolutionary problem.

If the effect is not observed, then an equally valid question to ask is “why?”. Why don’t the heavy metals affect the animals and their mutation rates? Do they simply not go up the food web (and if so, why?), or do they do so but physiological mechanisms prevent them from having an effect (if so, what are these mechanisms?).





A Visit to a Vernal Pond

6 12 2011

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