Antho-what-now?

So, after an extended break, normal service is resuming, although the post today will be slightly off the usual topic of the evolutionary journey.

As I mentioned yesterday, I have been writing my bachelor project, and I thought I would share with you a little of the topic I have written it on.

I could write a post which would keep my good e-friend Argyle Sock very happy, with lots of statistical stuff in it, but, honestly, if I see the terms “not normally distributed” one more time, my head may go pop!

Also, the actual topic is much cooler than the stats (even though they are very cool too of course!).

I would like to introduce to a group of pigments called anthocyanins.  These are the reason for the colour of blueberries, blackberries, some grape species, olives and many other fruits, and purple or red colourings in flowers, like these pansies:

Violet pansies: The purple colour is caused by anthocyanins in the petals. Image from Wikipedia

The amazing bright red colours you see in autumn leaves is also down to anthocyanins.

So..why have I spent this last semester writing about pretty red colours?

Well..here is where it gets a little more interesting (not that pretty purple flowers are not interesting of course!)

Anthocyanins are also found in leaves which are not about to fall off the tree.  Some plants have red leaves when they are young, and some plants can turn on and off the red colouring under certain conditions

Sciencey term for the day: This is called phenotypic plasticity….a phenotype is the appearance something has due to certain genes being expressed. If a phenotype is plastic, it means it can change under certain environmental conditions.

So, I have been looking at a particular plant, which is usually green and grows in shallow lakes.  These lakes dry out a bit in the summer (Yes, we have summer in Denmark, sometimes!), and so some of these plants may end up out of the water.  If this happens, 90% of these plants turn red, until the water covers them again.

The reason I have been looking at this plant (with a bunch of other people who are much better at scary maths than me!) is because it is not entirely clear exactly what the red stuff in the leaves does.  In some plants it seems to act a bit like a sunscreen, in others it seems to stop the plant being eaten by insects.

The amazingly awesome Leaf-cutter ants (Several posts on them will come along a bit later in our evolution journey) will not harvest leaves which are red. This may be because insects do not see red the way we do, they do not have the parts in their eyes which can collect red light.

Leaf Cutter Ants carrying leaves off to their underground farm Image from wikipedia

It has also been suggested that anthocyanins can help plants survive during cold or drought conditions, so, there seems to be a whole lot of stuff that this pigment helps with.

The health food industry has even been getting in on it, and you can buy anthocyanin supplements…this is because in plants, they work as anti-oxidants, and we are always hearing about how having free radicals is bad for us, and so we should eat blueberries, or whatever the cool food to eat this week is (its usually the most expensive one!).  I am not entirely sold on this idea, as, last time I checked, I am not a plant.

So anyway, I have been working with an awesome group of my fellow students, and we have been trying to make these poor plants very stressed to see what happens. We grew them under some very bright lights, and then did some tests where we zapped them with..well…an even brighter light, to see what they did.

Personally, I find the plant we have been studying more interesting than the actual pigment we have been looking at, although, that has been fascinating to learn about.  The plant itself has no stomata, which are the holes which plants use for taking in carbon dioxide and giving out oxygen and look like this in extreme close-up:

Stomata on a tomato leaf Image from wikipedia

Because this plant has no stomata, it has to breathe through its roots, which is extremely cool!  This means that it can only live in lakes which do not have a lot of nutrients in them, because, if you increase the amount of nutrients which end up at the bottom of a lake, you decrease the amount of carbon dioxide which is produced by the bacteria eating all the dead stuff at the bottom.

As more dead stuff ends up at the bottom of the lake, the bacteria down there start using up more oxygen than is available, and so the only ones that can live there produce methane (CH4) instead of carbon dioxide (CO2). This is what is found in my favourite land-types, the wetlands, bogs and moors.

Oh, yes, I forgot to show you a picture of the plant!  This is the little thing I have spent 6 weeks growing, and then several weeks cutting up and zapping with bright lights!

Lobelia Dortmanna. Image from wikimedia

So, I hope I did not bore you too much with the slightly off-topic post, and next time we will pick up on the evolutionary trail again, with some weird and wonderful creatures. If you prefer plants, hang in there, we will get to them in a few million years or so!

Why mature forests matter..more trouble for the Ash tree.

I wrote a few weeks back about the fungus which is infecting Ash trees in Europe (HERE)

At the time I wrote that  “So far, it seems that the fungus has not managed to infect “wild” trees in the UK, and the government has begun a consultation, which will end on the 26th of October, which could lead to a ban on imports of Ash (and given the severity of the threat, I would hope that a ban is imposed).”

Well, this week it has been announced that the disease has been discovered in  mature forests in the UK, as this Guardian article discusses (HERE).

My last post about this was a bit technical and clunky, so I will try to keep this easier to read.  I want to try to explain as much of the specifics as I can though, because, when I am finding anything out, I like knowing all the details if possible, rather than just understanding the gist of something.

We are going to take a little detour, as I could just tell you that “Mature forests are important” and let you just take that as read, but I would rather run through the reasons behind my claim.

So, firstly, what is a mature forest?

To most of us, a forest is a forest is a forest, but to biologists, and specifically botanists, there is a difference in the type of forest, and it has to do with a term called succession.

Succession can be thought of as the stages of life of an area, whether that is to do with a wetland, a forest, a field etc.

My ecology textbooks define succession as “Replacement of one community by another, often progressing to a stable terminal community called the climax”

To illustrate this I will use the example of how a natural forest progresses, as it is one of the simpler ones to picture, but this also applies to planted forests, although the starting point is different there, as we actually initiate tree growth.

Diagram showing forest succession. Image from the encyclopedia of New Zealand

So, we start out with our bare ground on the left of the diagram, which usually consists of some soil, maybe some grass species (those little guys get everywhere).  This bare ground may be the result of a big event like a glacier retreating, or it could be from the drying up of a lake, or the spread of grasses along a sand dune area.  It can also be derelict land which was previously used as an urban area, things are a little more complex in that case, but the basic order still follows.

If we imagine that we have some rocks on the bare ground, and a few tough grasses to start with.  The rocks provide a nice cosy place for some lichen to start living, whilst the grass roots prevent what little soil or sand there is from blowing away.

The lichen cause damage to the rocks, and small particles of rocks fall off and get trapped on the ground by the grasses, and other particles flying around in the wind also become trapped.  As the lichens and grasses die, or get damaged, they fall to the ground, and begin to form a layer.  Eventually, there is enough of this layer (known as humus) to allow mosses to take hold in the area, and as these die off, they too add to the growing layer of dead stuff on the surface, which allows for bacteria to come in and decompose them, adding nutrients to the new soil.

Over time, the nutrients and soil layer builds up, and small, tough plants can begin to grow there.  These are often other grasses, ferns and very small bushes (Box 2 in the diagram). Microbes, insects, worms etc begin to colonize the young soil.

As the soil quality improves (because the plants there die, and are broken down, and nutrients build up in the soil), and the stability of the soil increases due to the growing number of plants, seeds which are blown in the wind, deposited by animals etc begin to be able to grow, and some of these will be from trees.

Initially, only small, hardy trees can grow, but new species come in and as the conditions continue to improve for plants, taller trees begin to take hold.  These do not grow in the earlier stages as tall trees usually require higher levels of nutrients than bushes, or dwarf trees.

Now we have a young forest, and species of animals and birds begin to colonize the area. Trees begin to grow taller, and form a canopy, this leads to a change in the communities of plants which are on the forest floor, and the ones which die off further improve the soil quality.

Finally, we reach the mature forest stage, where the animal and plant communities are stable, and as a tree dies, a sapling takes its place.  In some ecosystems, trees can stay short, like a new tree, for years until a gap opens up in the canopy, then they all race to be the one to take the place in the sun at the top.  Whilst individual trees may change, the overall structure of the forest stays the same at this point, which provides stability for the animal, bird and insect populations, and leads to the forests which we love to walk in.

Whilst the exact age at which a forest is defined as mature varies (depending on the types of trees which are present), a mature forest is several decades old.  If these forests are able to continue developing, they eventually are classified as Ancient Woodlands, which in the UK means forests which have been there for 400 years or so (the current definition of an ancient forest in the UK is forests which have existed since 1600).

EDIT FOR UPDATE: I have found out that one of the woodlands affected is actually an Ancient Woodland, which is believed to have been in place for around 1000 years. Info about Ashwellthorpe HERE

Ok, so now you know why I feel that mature forests are important.  They provide a stable habitat for wildlife and other plants, and due to the length of time which it takes for them to develop, they are not something which is easily replaced.  They also play a role in preventing soil loss from rain or wind erosion.

Now, you are probably wondering why Ash trees are so important, and why the media have been giving this so much attention.

Ash is the fourth commonest tree in the UK, and many forest areas have it as the dominant species. (source: Woodland Trust). Birds such as woodpeckers and owls live in Ash trees, as they are easy for them to hollow out, and they provide food and a habitat for a diverse range of animals, insects, mosses and lichens (For more info, see the Royal Forestry Society link HERE)

Ash woodlands are part of the UK Biodiversity Action Plan, and are listed as a priority habitat in the plan. (See page 60 in this PDF), and they say:

“Mixed ashwoods are amongst the richest habitats forwildlife in the uplands, notable for bright displays of flowers such as bluebell.. primrose..wood cranesbill and wild garlic . Many rare woodland flowers occur mainly in upland ashwoods, such as dark red helleborine.., Jacob’s ladder.., autumn crocus.., and whorled solomon’s seal … Some rare native trees are found in these woods, notably largeleaved lime… and various whitebeams…. Upland mixed ashwoods also harbour arich invertebrate fauna, which may include uncommonor declining species. The dense and varied shrub layer found in many examples can in the southern part of the types range provide suitable habitat conditions fordormice… The alkaline bark of old ash (and elm where it still survives) supports an important lichen flora…. ”  (Latin names have been removed, hence the dots)

Aside from the ecological importance, it has a long history in the UK and Northern Europe, it is suggested as  the “world tree” from Norse Mythology (Yggdrasil) and Ash has been used in the UK since early history, as everything from spears to walking sticks, furniture etc.

So, seeing as these woodlands are on the Priority habitat list, you are probably thinking that the government has taken immediate action on this, and had in fact begun to assess this threat as soon as they heard of it.  Well….not quite.  George Monbiot over at the Guardian has pointed out that the government were made aware of the threat to the Ash tree in the UK some time ago, before the imported infected trees were discovered, and that even importers of Ash trees were recommending that action be taken (link HERE)

So, what is the government in the UK doing?  They have announced that a ban is being implemented starting Monday (link HERE).  Bear in mind this fungus was first found in the UK 8 months ago (February)…. Would it have taken so long for action to be taken if we were talking about infected livestock?

I apologise for the very long post, but I feel it is important that I explain exactly why we need to make sure that we do not lose our Ash trees the way we lost our Elms, and I am very angry at the government response.

Leaves, keys and fungi

So, there was this story yesterday in the Guardian about how ash trees are at risk from a fungus: http://www.guardian.co.uk/environment/2012/oct/04/deadly-fungus-ash-tree-imports?intcmp=122

This topic has been in the media a fair bit lately, but very few of the stories have gone into the mechanisms and details, so I thought I would write briefly about those, as they are fascinating, and can help with understanding the problem better.

Most of the stories in the media have just said that it affects leaves, which is a very vague description.

So, first of all, to make sure we all know the tree we are talking about, this is an Ash tree, otherwise known as Fraxinus excelsior:

Fraxinus excelsior, the common Ash. Image from Wikipedia

And here is it’s close-up (It doesnt get red-eye like I do, and is always photogenic!)

Close up of the leaves and “keys” (fruit) of the common Ash. Image from Wikipedia

So, now we have met the victim, lets meet the perpetrator (Sorry, I am catching up on CSI episodes at the moment, so excuse me if I go a bit Horatio Caine).

This is where it can appear a bit confusing, because this fungus actually has two names:  The one most mentioned in the media is Chalara Fraxinea and it looks like this when it is grown in a lab:

Chalara fraxinea, politely posing in a petri dish. Image from Federal Institute of Technology Zurich

This is the fungus mentioned in the Forestry Commission factsheet about this problem (See further reading for link).

This is what is known as an anamorph, which means it is the asexual reproductive phase of this fungus.

I think the reproduction of plants, fungi and small micro-organisms is really cool, so I am going to explain it a bit here as it can seem a bit confusing (I remember getting tied in knots trying to revise this for functional biology!)

The asexual reproduction of fungi such as this species involves producing spores (from the greek spora, which means seeding, or sowing), which you might know from the puffball mushroom, when you kick it, it gives off a load of dust-like stuff, which is actually the spores for the next generation of the fungus, which looks like this:

Puffball mushroom releasing its spores. Image from wikipedia

Each of those spores is a potential new fungus, provided it lands in a suitable environment for growth.  This method of dispersal is very haphazard, and this is why these organisms produce so many spores.  It is a bit like closing your eyes and throwing a handful of seeds randomly out on a bit of ground and hoping for the best.

They are formed by mitosis, which is also how our cells in our body are replaced and is in itself a really really cool process (especially when you see slides of it), and which I will cover in depth in a later post.

As I mentioned earlier in this post, this fungus has two names, the asexual form C.fraxinea and the sexual form Hymenoscyphus pseudoalbidus. Now, maybe it is just me, but I found it a little confusing initially to understand how one organism can have two names, or even two life cycles when I first started reading about this.

This image shows the life cycle of an Ascomycete, which is the group of fungi which this particular one belongs to.  The asexual cycle is the loop off to the left of the diagram.

General life cycle of an ascomycete. Image from Penn State University

From what I gather from reading several journal articles on this species, it seems that the asexual form is on the leaf litter, and dead wood on the forest floor, and this is not infectious (or pathenogenic to use the sciencey word).

It all goes a bit nasty for our Ash trees when it is in the sexual form, H.pseudoalbidus .  It is called “pseudoalbidus” because there is another species called H.albidus which is not responsible for this problem in Ash trees, but appears physically similar.

This is what the fungus looks like:

H.pseudoalbidus on a branch. Image from Institute of Technology, Zurich

This confusion with two different names for the sexual and asexual form of fungi will be less confusing soon, as in 2013 they are changing the naming structure, so that there is one name for a species of fungi, regardless of which stage of the life cycle it is in.

As you can see from the diagram, the asexual form of the fungus only refers to the spores,  everything else within its lifecycle is classified as H.pseudoalbidus. Calling this C.fraxinea in the media is quite confusing, but understandable, as many journals refer to this fungus as C.fraxinea.

The cycle of infection appears to be, that the spores remain in the litter, or on dead branches over the winter, and then, in the summer, it germinates, and becomes the white mushroom thingies.  These release spores, which are spread by the wind, and some end up on the leaves of Ash trees, and on the branches.  These form structures known as mycelium which are basically a mass of threads, and it is these which are responsible for the damage to leaves and branches, if they get into a gap in the bark, they form lesions like on this branch:

Necrotic lesions on a branch. Image from EPPO (European Plant Protection Organisation)

These are also known as cankers, and result from the death of the tissues.

The fungus also damages the leaves, as shown in this image:

Leaf dieback as a result of fungal infection. Image from EOL

The dead branches and leaves then fall to the floor, and the cycle begins again.

This is a relatively new infection in Ash trees, first being noticed in the mid 1990s.

There are ongoing discussions as to why this has arisen, as this fungus has been known since the late 1800s, but as the non-infectious H.albidus.  There is discussion about whether climatic stress has weakened the trees resistance to infection, or whether the infectious version of this fungus is better suited to the milder climate conditions over recent years, or whether this new infectious form is a mutuation which has arisen recently.

Whatever the cause, the result is devastating. Denmark has lost around 90% of its Ash trees since the infection arrived, and other European nations are reporting large scale losses of Ash trees.  The infection appears to have arrived in the UK (Which is usually protected from these types of infection because of its island status) by importing of young trees which were carrying the fungus.

So far, it seems that the fungus has not managed to infect “wild” trees in the UK, and the government has begun a consultation, which will end on the 26th of October, which could lead to a ban on imports of Ash (and given the severity of the threat, I would hope that a ban is imposed).

Further Reading: (Most are very easy to read, with the exception of the journal article at the end, they are mostly from the Forestry Commission, and similar bodies)

http://www.eppo.int/QUARANTINE/Alert_List/fungi/Chalara_fraxinea.htm

http://www.ethlife.ethz.ch/archive_articles/100408_eschenpilz_per/index_EN

http://www.fera.defra.gov.uk/plants/plantHealth/pestsDiseases/documents/chalaraFraxinea.pdf (Rapid Risk Assessment)

http://www.forestpathology.ethz.ch/research/Chalara_fraxinea/index_EN

http://www.forestry.gov.uk/pdf/pest-alert-ash-dieback-2012.pdf/$FILE/pest-alert-ash-dieback-2012.pdf

http://www.forestry.gov.uk/chalara

http://www.guardian.co.uk/world/2012/oct/07/disease-killing-denmarks-ash-trees

Krautler & Kirisits: The ash dieback pathogen Hymenoscyphus pseudoalbidus is associated with leaf symptoms on Ash species (2012) http://www.academicjournals.org/jaerd/PDF/Pdf%202012/14MayConf/Kraeutler%20and%20Kirisits.pdf

 

 

To pea, or not to pea

Ok, so, as I mentioned in the last post, I have just been on a botany field course, and so taking a little diversion from the evolution of life on earth to write about plants. (Got a bit distracted on the course, so forgot to finish writing this post, so apologies for the delay!)

This is a pea, we all know and eat these regularly, across the whole range of dining experiences, from high end restaurants to mushy peas and chips.

A pea plant (img from wikipedia)

This is the pea within the pod

Peas in the pod, ready to be eaten! (img from wikipedia)

The final image is of a pea plant in flower.

A pea plant (Pisum sativum) in flower. Image from Encyclopedia of Life

Peas are in the family Fabacae (from latin “faba” meaning bean, the word became fava over time, and broad beans are known as fava in Italy, they are also the type of bean that Hannibal Lector likes!)

In English, this family is known as the Pea Family, and the fruit they produce (the pea pods in the picture above) are known as legumes.  An alternative (less used now, but more common in the past) name for this family is Leguminosae.

This family is quite a big one, there are 19000 or so species (specific plants) within it.  I found one of the most interesting parts of the course I was just on was looking at a plant and thinking “How the hell did they know that was in the same family as this other plant”, and I am going to try to illustrate that a bit with this post, as well as try to explain how to recognise when a plant is in this family.

This family of plants has been around since the Paleocene era (approx 65-56 million years ago), and the 3rd and 4th images below show a modern Fabaceae plant, and a fossil one from the Paleocene.

Fossil plants compared with modern versions. The centre two images show a modern pea family plant, and a fossil one from the end of the Paleocene era. Image from American Journal of Botany

The modern species within this family are very diverse, and the following images are all of various plants within this family.  The first one is the gorse bush (Ulex europaeus, Ulex is the term Pliny the Elder used for heather (Pliny was an Ancient Greek guy who wrote one of the books which is on my very geeky “Must own this” list, Naturalis Historia) and europaeus means it is found in Europe), which is found on heaths, sandy dunes, and is an extremely annoying plant if you start wandering through some countryside and don’t spot the fallen thorns on the ground around it, or do not notice little bushes of it sprouting up as you climb through the edge of a forest.

Gorse Bush, very pretty, but very prickly! Image from http://www.cavinguk.co.uk/holidays/Pain2006/

This next picture is of course, the peanut (Arachis hypogaea,  hypogaea meaning underground), which, surprisingly is in the pea family!  The image afterwards is of the peanut plant in flower.

Peanuts. Image from Wikipedia

Peanut plant in flower. Image from Purdue Agriculture

The peanut is not actually a nut, it is a pod, like the pea pod, but it grows underground.  Once the flowers of the plant have been fertilised, the petals fall off, and the remaining part (the ovary, containing the seeds) develops a spike, and grows towards the ground, burying itself a few centimetres into the ground.  The picture below shows what remains of  a peanut flower after fertilisation.  The reddish brown pointy part is what will dig into the ground, and the whitish bit above it (wider than the stalk) is the ovary, and is where the peanut will develop from.

A Peanut plant after fertilisation, showing the end of the ovary growing towards the ground. Image from Wikipedia

The next picture is of the peanut just after harvesting, so you can see that the peanuts actually come up along with the roots.  It is a common idea that the peanut is part of the root, and not the fruit of the plant.  It is easy to see why people think this, because it does look exactly like that.

Peanut plant after harvesting. It is easy to see why many think the peanut is part of the roots. Image from Sagesite.com

Other plants that you may not expect to be in the pea family are liquorice, and clover (image below is of White Clover, the most common type, Trifolium Repens (Trifolium meaning 3 leaves, and Repens meaning creeping)).

White clover, known for its 3 leaves, and the difficulty in finding 4 leaved versions of it! Also associated with leprechauns. Image from Informedfarmers.com

So, I promised I would try to explain how you can tell something is in the pea family. Having just spent 5 days staring at lots of this family, when I was inserting the images for this post I thought “I cannot put these in, it is obvious that they are all in the same family”, but then I thought that it may not be so obvious if you have not just spent the best part of a week getting “pea-blindness” (Like snow-blindness, but caused by staring at various members of this family for too many hours a day with too little sleep the night before!)

So, the skeptical squirrel guide to identifying pea plants:

Firstly, hopefully it has a flower on it, this makes it very much easier!  Even with something like a clover, which does not initially look like it has the same flower, each clover head is made up of lots of small flowers, which have the same characteristics as other flowers from within this family. They look a bit like a side-on face with a sticking out tongue…..ok, maybe only a little bit, but definitely after some beers, and in the right light, they look like that!  The picture below shows the side view of a flower from this family, along with a diagram showing the parts of the flower.

Side view of a pea plant flower, and systematic diagrams. Image from Ohio State university

So, to be a bit more technical, you are looking for a flower with 5 petals, 1 large one at the top (the banner), 2 smaller ones sticking out in the middle (the wings), and 2 small ones at the bottom, forming a boat(ish) shape (the keel).  The Fabaceae  family has what are known as bilaterally symmetrical flowers, this means that if you cut them top to bottom, each half looks the same.  These flowers are very very distinctive, so once you know what they look like, if you see another one, you will recognise it immediately!

The other very distinctive feature of this family is the pods in which the seeds are held, they look like, well…., a pea pod.

Finally, if you have neither flowers nor seed pods, then it gets very annoying (and gave me a lot of headaches on the field course!), but, some plants within this family have very distinctive leaves, so can be recognised easily from those too.

Clovers, as mentioned earlier, have 3-leaves, or more correctly, a trifoliate leaf, which means it is one leaf, divided into 3 smaller leaflets, and the ones on clovers are very easy to spot.

Many Fabaceae plants have what are known as pinnate leaves, which means there are lots of small leaflets arranged along a small stalk, like in the picture below

A pinnate leaf. Image from UBC Biology 324 blog

At the end of the leaf in the picture above, there is a long curled stalky thing.  This is a tendril, and it is what the plant uses to climb. It wraps around another plant, a pole, anything it can grab onto.

A member of the Fabaceae family (Vicia sativa, or Common Vetch), the tendril is visible on the far right of the picture, extending from the leaf stalk. Image from wikimedia

This is just a very rough guide to how to spot a Fabaceae plant, but hopefully it is a bit helpful.  Tomorrow will be back to Cnidaria, plants will be in later posts, but, the land plants come along a whole lot later in our journey through evolution.