Monday, 30 May 2011

Season of mists and mellow fruitfulness: truffle-like fungi

Truffles are fungi whose mushrooms don't open to release their spores.  Once upon a time they were all thought to be related, but non-opening mushrooms seem to have evolved many times independently, and there are basidiomycete truffles and ascomycete truffles.  (Ascomycetes and Basidiomycetes are the two largest groups of fungi; they include most of the fungi that we're familiar with.)  Typically, truffles have underground mushrooms that are dependent for spore dispersal on animals that can smell them, dig them up, and eat them.  In Europe this relationship is co-opted by truffle-collectors; dogs and pigs are used to find wild truffles in the forests.  In Australia there are truffle-like fungi that are dispersed by marsupial mammals.  Such fungi are often brown or pale in colour; not surprisingly, because most mammals don't have colour vision and rely on their sense of smell.

So what happens in New Zealand, where there are no native land mammals apart from bats and the odd lost seal?  We have a range of truffle-like fungi of various sizes and colours.  At least one, Weraroa erythrocephala, is bright red.  Others are purple, orange, or white.  New Zealand botanist and mycologist the late Ross Beever suggested these might be eaten by birds, which then disperse the spores.

These ones (probably W. erythrocephala) are common in the Wellington Botanic Gardens at the moment, among leaf litter and mulch.  They look for all the world like small fruits of for example pigeonwood (Hedycarya arborea) or creeping Fuchsia (Fuchsia procumbens).  

Something's been gnawing on this one.  It'd be interesting to investigate their scent, and whether weta are attracted to white and purple mushrooms, because Duthie et al. (2006) showed that weta eat some small-seeded berries and disperse their seeds.


Beever,  R . E.  (1993). Dispersal of truffle-like fungi in  New Zealand, in  R . S. Hill  ( ed. ), Southern Temperate Ecosystems: Origin and Diversification  22. Hobart, Australia.

Duthie, C., Gibbs, G., Burns, K.C., 2006. Seed dispersal by weta. Science 311, 1575.

Friday, 27 May 2011

Why are there still monkeys?

Evolutionists laugh at the idiocy of this question, but it's related to a real disagreement in taxonomy.  
Biodiversity evolves by speciation: species split into more species, and this creates a tree-like pattern of life.  Most taxonomists agree that only whole branches of the phylogenetic tree of life should be named as groups; we call them monophyletic groups.  Giving names to groups that are not monophyletic can cause misunderstandings.  “How come there are still monkeys?” is one of those misunderstandings.
Dick Brummitt of the Royal Botanic Gardens, Kew, argued for taxonomic recognition of partial branches of phylogenetic trees in a short paper, famously titled “Am I a bony fish?”.  His argument was that to make bony fish a monophyletic group we’d have to include our own species within it, thus calling ourselves bony fish.  That's a fair enough consequence of recognizing only whole branches.  I think his concern arises not from the requirement that whole branches should be recognised as named groups, but from the historical baggage we associate with names. In fact, the branch that's descended from the ancestor of all bony fish already has a name, Osteichthyes (which translates as “bony fish”).  I think readers were expected to recoil in horror at being called bony fish, much as creationists recoil in horror at being called monkeys.  If only the rules of nomenclature would allow us to invent a non-threatening new name for the whole branch (bony vertebrates would do it nicely), I’m sure people wouldn’t feel so uncomfortable.
If we include humans in the ape clade, or apes in the monkey clade, or tetrapods in the fish clade, or hebes in the Veronica clade for that matter, we get this artificial problem; it’s caused by the baggage we associate with the name of the group in popular culture.  And in the case of humans, that baggage arises because many think our species is special and separate from other animals.  Some even think it was specially created by a god.  The monkey clade has radiated from a common ancestor, and we’re one of the products.  We are humans, and we’re apes, and we’re monkeys, mammals, tetrapods, bony fish, jawed fish, chordates, deuterostomes,  metazoans, all the way down.
But if our concept of apes doesn't include humans, then the taxonomic group "apes" wouldn't be a whole branch of the tree (because the human twig isn't included), and it loses the meaning that evolution brings to biology.  I think it's fascinating to understand our species as a highly modified fish, a true story told so well by Neil Shubin; it's a much more useful and interesting idea than a classification that doesn't even hint at our historical relationship.
The tree-like pattern of life is one of the best pieces of evidence we have for evolution.  We discover essentially the same tree when we use DNA data as when we use morphology, or chemical attributes, and the order of the origins of different branches matches their order in the fossil record.  It makes sense for disciplines of science to be consistent with each other like this; in fact we usually suspect ideas that are inconsistent with other branches of science.  So the coming together of taxonomy and evolution is something we should welcome, even if some of the names we use for groups may make (some of) us feel a little uncomfortable.
Brummitt, R.K. 2006. Am I a bony fish? Taxon 55: 268–269.

Friday, 20 May 2011

Creeping Fuchsia

Fuchsia is mostly a South American genus, with about 100 species.  The three New Zealand species and one in Tahiti (F. cyrtandroides) are distinctive in the genus because they have blue pollen, plus some flower and chemical features that are unique to this group.  The original description of the bellbird said it had a blue patch on its head, but that was a patch of Fuchsia pollen; flowers are pollinated by bellbirds and tuis in New Zealand, and by hummingbirds in South America.  The pollen is distinctive, and has been identified in sediment of Oligocene age in Australia, although Fuchsia doesn't grow wild there now.

Mostly Fuchsias are shrubs, like F. magellanica, which is naturalised in many places; I've seen it often in New Zealand gardens and once as a wild plant in Co. Cork, Ireland.
Fuchsia magellanica, Eastwoodhill, Gisborne.

In New Zealand, we have two unusual species, F. excorticata, which is a small tree, and F. procumbens, which is a softly woody creeping vine.  Fuchsia flowers usually hang down, but if F. procumbens flowers hung down they'd drag on the ground, so instead they're erect.  At this time of year, creeping Fuchsia has large red berries.
Fuchsia procumbens, Karori, Wellington
Like many bird-pollinated flowers, F. excorticata flowers are red, but Lynda Delph and Curt Lively have shown that the birds visit them when they're green, like the one at the bottom of the photo below.  Red colouring seems to be a signal that the flower is old and not worth visiting.
Fuchsia excorticata, Karori Wldlife Sanctuary.

Saturday, 14 May 2011

Pronouncing scientific names

I'm often asked how to pronounce scientific names.  Usually my answer is "I don't care".  Botanical names are mostly in Latin, or at least have Latin form, but some are based on Greek and some on modern languages or peoples' names.  We could get picky and insist on proper Latin pronunciation, but the way the Romans spoke changed over time, and church Latin is different again.  I used to love hearing James Stirling talking about Ruddydendrums.
Euphrasia, Mt Cheeseman, Canterbury

Latin is supposed to allow botanists all over the world to communicate with each other, but we pronounce names so differently that often we don't understand each other.  New Zealanders say "You-frayzia" whereas Germans say "Oy-fraatzia" (Euphrasia).  In Pittosporum, some emphasise the first o, others the second.  Personally, I don't care too much.
Fuchsia excorticata, Port Hills, Canterbury.

What I do try to get right is pronunciation of botanical names that are based on personal names.  So I try to remember Fuchsia is named after Fuchs ("Fooksia", not "Fyoosha"); Dahlia after Dahl ("Daalia", not "Daylia"); Aristotelia after Aristotle ("Aristot'lia", not "Aristoteelia").

Tuesday, 10 May 2011

Lammas flowering

One of the many delightful things about J.R.R. Tolkein's Lord of the Rings is the way he brings in words from other languages or archaic English.  I've never bothered to look many of these up, but I always enjoyed the mystical sounds of them.  One of these words is lammas; the fellowship were given lammas bread by the elves to take with them on their journey.  I never expected to meet this word in my capacity as a botanist.

Lammas is a harvest festival, celebrated in England on August 1st, early autumn there.  It's associated with the bringing in of fruit and grains for the winter.

Yesterday I received an email from my colleague, entomologist George Gibbs, who had observed autumnal flowering in hard beech (Nothofagus truncata) along the Butterfly Creek track, eastern Wellington.  Neither of us had seen this before, although occasional autumn flowers can be seen in quite a few spring-flowering trees and shrubs; I'd especially seen it in Rhododendron in mild autumns.  George followed it up in the literature and reported back to me that Dr Lindsay Poole mentions it in his book Southern Beeches (1987), under the term lammas flowering: "buds can burst at the end of summer in a year in which there is going to be a mast flowering in the following spring.  They ‘are unable to contain themselves …’!    Evidently also occurs in European beeches."
Nothofagus truncata forest, Remutaka Range.
Masting is a phenomenon where some plants flower less frequently than every year.  Usually they flower every three years or some other prime number.  One explanation is that it's a way of avoiding predators by making it hard for them to bulk their numbers up in anticipation of good fruiting years.

Schauber et al. (2002) gathered a lot of information about mast flowering New Zealand trees and came to the conclusion that masting is a phenomenon of plants that lay down their flower buds the season before; if that's a warm summer, the plants will flower spectacularly the following year.  Lammas flowering in Nothofagus supports this idea, as the comment 'unable to contain themselves' implies.  Some of the buds laid down in the warm 2011 summer are tricked into opening early in the mild 2011 autumn.  It shows that next year's flower buds are already present, and we can expect a bumper flowering next spring.

Since I received George's comment, I've noticed lammas flowering in Veronica parviflora on the Victoria University of Wellington campus.  Normally this tree hebe flowers in January/February, but it's flowering right now near VUW Press at the Rawhiti Road entrance to the campus.  I don't think it's a masting species though; it's just that the flower buds are probably laid down the preceding summer.
Veronica parviflora, Johnson's Hill, Wellington
Added 14 May: Wineberry (Aristotelia serrata) is sporadically flowering right now too.


Schauber EM, Kelly D, Turchin P, Simon C, Lee WG, Allen RB, Payton IA, Wilson PR, Cowan PE, & Brockie RE 2002. Masting by eighteen New Zealand plant species: the role of temperature as a synchronizing cue.  Ecology 83:1214–1225.

Friday, 6 May 2011

Identification keys

"When he has learnt that bottinney means a knowledge of plants, he goes and knows 'em.  That's our system, Nickelby; what do you think of it?"
Charles Dickens, Nicholas Nickelby.
Many people characterise botanists as people who know the names of plants, and I’m often asked to identify specimens and, increasingly, photographs.  However, identifying plants is not a widespread skill among us; botany involves a lot more than knowing names.  Even plant taxonomists, who are specialists in the identification, classification, evolution, and naming of plants, sometimes know well only the members of the groups they study.  For ability to identify a wide range of plants on sight, I’d recommend horticulturists, conservation biologists, and field ecologists.
Identifying plants is such a seemingly simple skill that it’s often under-rated and certainly under-valued.  The professional identification of a possibly poisonous plant can be a matter of life and death.  I’ve identified plants for both police and defendants in drug and burglary cases, hospitals when children have eaten berries, vets, farmers, insurance companies, and for disputing neighbours.  Conservation depends on accurate identification of rare plants and the weeds that threaten them.  Identification of a sample opens up the world of information about that plant, which would otherwise be unavailable.
How do botanists identify plants?
The easiest and commonest way is simply to recognise a species you’ve seen before and to recall its name.  The process is the same as the way we recognise our friends, or cars, celebrities, or dinosaurs.  I think humans differ in this ability, and children are often very good at it.  (Incidentally that skill makes some parents believe their child is some sort of prodigy, but I don't think it's a good indicator of scientific ability.)
Anyway, that approach will always fail when you’re confronted with a plant you’ve never seen before; so then you need to draw on the recorded knowledge of others.
The simplest resources are picture books and Google images, although pictures vary in their usefulness.  A clear diagram drawn by a botanical artist can draw the user’s attention to the important features.  Digital photography, especially when layered to improve depth of field, can be amazingly clear and accurate, but it takes both photographic skill and knowledge of the plants to do this well.  A poor diagram or a blurry photo is almost useless.
More scientific books, like Floras, have written descriptions of plants that detail, often in technical language, the attributes of species.  Descriptions alone are precise, but they can be hard to work with, and additionally a picture is worth a thousand words.  
And there’s immediately an efficiency problem with using pictures and descriptions alone.  There are 250,000 species of flowering plants, so if you could compare your unknown plant with a photo or description every 5 seconds, you’d need about two weeks of non-stop comparing before you could check them all.  Even then, there will be a lot of look-alikes that would baffle you.  We need a way to quickly whittle down the possibilities, and that’s where keys come in.
Identification keys are a simple kind of expert system.  They’re written by an expert and so they focus on the characteristics the expert knows to be reliable.  For instance, if you didn’t know that the way leaf edges join in the leaf buds is important for the identification of hebes, you could easily confuse Veronica stricta and V. salicifolia.

Veronica stricta
Veronica salicifolia
Keys work by ruling out possibilities with pairs of contrasting statements, so that whole groups of plants can be quickly eliminated without having to compare them all.  For instance, consider the following couplet:
1.         Seedlings with 1 cotyledon ………………………….2
Seedlings with 2 cotyledons …………………………n
You’ll see the two contrasting statements in this couplet can’t both be true for an unknown plant.  The upper lead eliminates all the eudicots and basal angiosperms (what we used to call the dicotyledons; nearly 200,000 species), whereas the lower lead eliminates all the monocotyledons (about 60,000 species).  That’s a lot more efficient than comparing every one with your unknown.
Each lead of the couplet directs the enquiry to the next couplet, no. 2 in the case of monocotyledons, n in the case of the remainder of flowering plants. Couplet 2 should similarly divide the monocotyledons into two groups, maybe based on whether they have showy petals (e.g. lilies) or not (e.g. grasses).  In the end, no further division is possible and instead of a lead to another couplet, a name is presented.
You might immediately spot a problem with the example above: how can this couplet help if your sample isn’t a seedling?
It’s helpful to the user if we can add some supporting characters to cover that situation, rewriting couplet one:
1.   Seedlings with 1 cotyledon; leaves without petioles; leaf veins usually parallel; flower parts in threes or multiples of 3; taproot absent at maturity ..............……….2
      Seedlings with 2 cotyledons; leaves with or without petioles; leaf veins usually forming a network; flower parts mostly in 4’s or 5’s or multiples thereof; taproot often present at maturity …………………………………………….………………n
You can see though that I’ve had to add some weasel-words to cover exceptions, words like usually, mostly, and often.  Character states like these, which are not universal in the group concerned, make the key less accurate, even while making it more helpful.  In principle, we should focus on character states that are:

  • likely to be present, 
  • easy to observe without a microscope, 
  • easily understood by the user, 
  • qualitative rather than quantitative, 
  • and non-overlapping.  

For instance:
Leaves 10—60 mm long …………………..Veronica hulkeana
Leaves 20—150 mm long …………………. Veronica stricta
is not as useful as:
Leaf margins toothed …………………..Veronica hulkeana
Leaf margins entire …………………. Veronica stricta
Veronica hulkeana 
Veronica stricta
In a good key, the two statements of a couplet should be exactly comparable, using the same characters in the same order.  As a contrived bad example, consider the following, which uses useful characters for these two species, but not in a way that's helpful because the user isn't told the states for the other species:
Leaves toothed; flowers in terminal panicles ……..Veronica hulkeana
Corolla lobes erect; capsules acute ………………. Veronica stricta

Some people argue that each couplet should divide the remaining species equally, rather than separating off one species at a time.  The argument is that each couplet presents an opportunity for error, and with an unbalanced key, some species will require a large number of couplets to reach the answer.  In a balanced key, all species will require the same number of couplets to be compared.  However, on average, they’re both the same, and an efficient key will need n–1 couplets, where n is the number of species, whatever its symmetry.  You might argue that an unbalanced key that keys out the commonest species in very few couplets is more efficient over time.  There’s no right answer to this one, but I believe it’s usually better to sacrifice elegance and efficiency for accuracy and reliability.
Sometimes when you go astray in a key, the questions don't seem to make any sense for your plant.  That's a clue that you've strayed into a part of the key that's dealing with a group of species that doesn't include your sample.
When you reach an answer after working through a key, it pays to check if you’re right.  Compare the sample with descriptions, diagrams, or photographs; even better if you have a herbarium (a systematically organised collection of pressed samples).
Keys have evolved over time.  The early ones often had more than two options (polytomous), where we now have paired couplets (dichotomous).  A disadvantage of polytomous keys is the user didn’t know how many to expect and often overlooked some possibilities, but sometimes they cover the available options more accurately.
The layout of keys varies.  Most nowadays have numbered couplets, but some are indented, a system that uses up a lot of page space.  Most people prefer to have the two comparable statements close together; they can be pages apart in long indented keys.
Note the syntax of the statements in keys.  Typically they don't have verbs; they're merely a noun followed by some adjectives or measurements.  This efficient shorthand has evolved from the use of Latin in biology a couple of hundred years ago.
What about the future?  Computerised keys (DELTA, LuCID) get around some of the problems of written keys.  In particular they can get around the problem of a sample that doesn’t have every life stage.  If fruits are absent on your sample, just answer the questions you can; eventually you’ll get to an answer anyway rather than getting stuck as you would in a traditional key.  Computerised keys are often more efficient too, because they require fewer decisions before you get to an answer.
Image recognition is also a future possibility, so that by entering a photograph of an unknown into a computer network it can be matched with stored images.  Finally, DNA barcoding is a developing system for biological identification.  It relies on the presence of portions of the genome that are universally reliable for the identification of species.  There are practical problems with it so far in plants, but I have no doubt the concept is a good one and we’ll see it in everyday use reasonably soon.

Tuesday, 3 May 2011

Stormy weather.

The tornado that tore through parts of Auckland yesterday, and last week’s strong winds in Wellington, got me speculating about plants and storm damage.  In the tornado, whole trees were uprooted, and some were smashed into houses and cars.  In the Wellington storm, I noticed that some tree species were easily damaged, while others seemed immune.  Most of the small leafy twigs that littered the footpath the following day were mahoe (Melicytus ramiflorus) and large-leaved species of Coprosma (like C. grandifolia).
Coprosma grandifolia
Mahoe (Melicytus ramiflorus)

Pretty much every man-made structure in the path of the Auckland tornado was damaged in some way.  There’s no doubt architects and engineers could build houses and shopping malls that can withstand a tornado, so why don’t they?  The answer is in the cost: tornados are rare in New Zealand and the chance of one striking your town is so small that it’s simply not worth building a reinforced concrete bomb shelter for a house.  In parts of the USA where tornados are more common, many houses have underground shelters in their basements.
I suppose it’s possible that plants could resist tornados too.  They’d need stronger and deeper roots, which might not be as efficient (per kg of root tissue) at taking up water; wood with fewer vessels and more fibres, which wouldn’t conduct water so well; and thick strong leaves, which probably wouldn’t be so efficient at photosynthesis.   
So why do trees get flattened in a tornado, just as houses do?  When tornados are rare, over-strengthened individuals are handicapped every day by the extra resources needed to produce those strong roots, stems, and leaves.  The carbohydrates and proteins they have to invest in strength can’t be used to make flowers and seeds, so in most years, such plants leave fewer offspring, and so their traits get rarer in the population.   True, those trees that survived the Auckland tornado of 2011 might leave more seedlings next year than those that were damaged, but unless there’s a tornado there every year, the over-strengthening costs will kick in and those stronger offspring will again be at a disadvantage. 
There seems to be an analogy here between the design of a house and the structure of a plant that some people claim is proof that living things have a designer, just as houses do.  The triumph of evolution by natural selection is that it explains instances of apparent design without the need to invoke an unseen designer.
Additionally, if the features that allow some plants to survive a tornado aren't heritable, then they can't be passed on and they'd be unable to evolve.  Plants grown in windy sites like Wellington often grow stronger than those in more sheltered places.  That’s why a 120 km/h gale in Wellington does less damage to trees than the same wind in Hamilton.  Most of this is due to plasticity, where a plant is capable of responding to different environments by producing different growth forms, but the specific response itself isn't inherited.  Such plasticity might itself have evolved if a plant’s dispersal range includes diverse environments, such that offspring that can respond to whatever environment they land in will be able to leave more descendents than those whose growth form is fixed.