Thursday, 22 March 2012

Me too! I'm a bony fish.

This week the Blogosphere, Twitterspace, and at least one website have been giving some attention to taxonomic principles.
It all began with an article by Vasko Kohlmayer in the Washington Times that asked "Is Richard Dawkins an ape?".  The correct answer, according to that article, is "No", despite Dawkins's statement that he is indeed an ape.  Kohlmayer went on to say Dawkins can't be an ape because he has all the usual human attributes, and we humans have these because we were created by a god.
That ought to have been the end of it.  The usual scientists' response to such bronze age superstition is to point and laugh and move on.  But biblical creationists aren't the only people who don't like to think of humans as apes.  Quite a few biologists as well are unhappy with the idea that species or groups that are very different from their ancestors should nevertheless be classified with them.  For instance, humans are different from apes, birds from dinosaurs, and termites from cockroaches.  Technically speaking, when we separate out part of a natural group because it looks very different (humans, birds, termites), the left over remnants of the natural group (apes, dinosaurs, cockroaches) are said to be paraphyletic.
So scientists responded to Kohlmayer in different ways.
First, anthropologist John Hawks argued that we use folk taxonomy terms like ape in everyday parlance to mean something other than the formal Latinized names that taxonomists use, and so it's OK for these groups to be paraphyletic because that's what ordinary people understand.  I can see where he's coming from, and not long ago I sort of agreed.
That's because I was aware that Kew botanist Dick Brummitt (2006) had made an argument for recognising paraphyletic groups in an article called "Am I a bony fish?".  Brummitt argued that paraphyletic groups, like fish, have biological meaning and that including mammals and other tetrapods among the fish in order to make fish monophyletic takes that meaning away.
I disagree absolutely with Brummitt that we ought to accept paraphyletic groups in biological taxonomy.  Rather, I think his "I am not a fish" argument is a clever rhetorical device to use in an argument against cladistic taxonomy.  It sounds so self-evident, so intuitively correct, and it can win the day with people who (1) aren't familiar with phylogenetics, and (2) aren't used to stepping outside their comfort zones (something scientists ought to do).  I do agree with Hawks that "fish", like "plant", "fruit", "bug", and even "animal", has a non-scientific meaning that can be different from its scientific meaning. But biologically, the common ancestor of all fish was also my ancestor, and that makes me a fish.  That may sound ridiculous to a non-biologist, and I was inclined to agree with Hawks because it's harder to deny the logic if we simply change the words and ask, "am I a bony vertebrate" instead of fish (the correct term for the bony vertebrates is Osteichthyes).   
But although in part we're arguing about the meaning of words, we're also arguing about whether or not evolution is important.  Creationists say it didn't happen, but even some scientists who accept evolution still think we ought to classify ourselves and other living things according to what we look like, giving less weight to what we're related to.
Evolutionary biologist Jerry Coyne summarised the controversy very well in two posts on his website (here and here). Then another biologist, Brian Switek, weighed in with "I am an ape, and I'm also a fish".  Now I'm ready to put my hand (pectoral fin) up and say, "me too".
So why do I think I am a fish?  Bony vertebrates are defined by their ossified bones and traditionally include fish and tetrapods (amphibians, reptiles, mammals, and birds). The bony fish, as people historically have defined them, have an ossified internal skeleton of bones, but also scales, fins, streamlined bodies, and gills.  If we divide the bony vertebrates into two groups, bony fish and tetrapods, we can make some decidedly odd-sounding statements about evolution, e.g., a coelacanth (fish), is more closely related to a human (tetrapod) than it is to a salmon (fish).  How can a fish be more closely related to a non-fish than it is to another fish?  In a natural group, every member is related more closely to every other member than it is to any non-member.  So if fish doesn't include tetrapods, clearly it isn't a natural group.  And in dividing the bony vertebrates up, we can use natural groups like the ray-finned fish, the lobe-finned fish, and the tetrapods.
What's more, if you look at every fishy feature, like scales, gill arches, and fins, you can find those structures modified in your own body (teeth, jaw & inner ear bones, arms and legs) and so our fishiness is still present in a modified form.  Even the fish's repeated body segments, so obvious when we eat a trout, are present but rather hidden in our own bodies (when I got shingles, it affected just one segment of my body because the chickenpox virus attacks from a single segmental nerve). Yet if you were to take an unrelated group, say insects or echinoderms, you'd not find in yourself such modifications of their characteristics (exoskeletons & spiracles; tube feet).  So it makes sense to think of ourselves as modified fish, modified tetrapods, modified mammals, and modified apes, but full members of all those groups nevertheless.  Neil Shubin's "Your inner fish" covers it well and this is why Dobzhansky's statement "Nothing in Biology Makes Sense Except in the Light of Evolution" is held so dear by biologists.  (However I was quite surprised to read about how that statement came to be written, something biologists who quote it probably aren't aware of).
It's not only about trying to build a classification that reflects evolution.  Another reason is that science should be objective.  If we propose a classification, we can test it by asking how well it aligns with natural groupings.  Natural groupings are those that arose by a natural process, the branching pattern of evolution.  Cladistic taxonomists reject groups that don't pass that test, or more accurately they redraw the boundaries until the groups do pass the test (e.g., by adding humans to apes or tetrapods to fish).
I'm a botanist: why do I care about fish?  Well, first I should care because I'm a biologist, but secondly also because exactly the same arguments occur in botany.  The classification of plants has been going through quite a bit of turmoil lately for the same reasons.  Family membership and names have changed to reflect the desire to classify only natural groups, so hebes and foxgloves have been taken out of the Scrophulariaceae and put in Plantaginaceae with their close relatives the plantains (Plantago), which look very different because their flowers are adapted for wind pollination.  The same thing has happened at the rank of genus: the genus Rhododendron now includes the azaleas, so the names of azaleas now begin with Rhododendron.  That's upsetting for people who have to learn new names, and also for people who are tuned in to the differences between rhododendrons and azaleas, rather than the relationships.
At heart, I also think some taxonomists are uncomfortable with the notion of testing their ideas about classifications.  They are quite coy about this in print, but in lectures, emails, and conversations I often hear "obviously ...", or "it's totally different", or "only a fool would ...", phrases that try to pre-empt a challenge or to beg the question.  I hear pleas for taxonomic judgement to over-ride objectivity, and for intuition to trump tested hypothesis.
My own part in this has been transferring New Zealand hebes and their relatives back into the genus Veronica.  Our hebes aren't a separately evolved (and certainly not created) group that has nothing to do with the northern veronicas.  Rather, they evolved from ancestors that were veronicas, and we can understand how they evolved when we begin to see them as veronicas that have adapted to life in New Zealand.  Most of them are shrubs and have tubular flowers and capsules that are flattened parallel to the partition, but some are still quite like northern veronicas.  To reflect the fact of their origin, and it is a fact, I've provided new names (or resurrected old ones) for all New Zealand's hebes and their relatives; these names all start with Veronica.
Veronica lilliputiana, a New Zealand species that has non-woody stems, blue flowers, and short corolla tubes.
Veronica parviflora, a more typical New Zealand hebe.
I'll give the last word to Professor David Mabberley.  I've just bought his wonderful and authoritative book and was delighted to see this issue discussed in the introduction, including mention of Veronica.  Mabberley is wonderfully uncompromising in his support for classifying only natural groupings.
Writing about modern DNA-based phylogenetics, he says, "I believe that somewhat condescending, tut-tutting scientists and others are seriously underestimating the intellect of the rest of society's building on these bases to appreciate and assimilate the results from modern work. As Darwin predicted, 'Our classifications will come to be, so far as they can be made, genealogies'."
And: "To maintain these and similar examples as separate genera or families, effectively picking holes in the (monophyletic) generic fabric and denying us the framework within which we can not only begin to understand ecological-evolutionary shifts but also marvel at the workings of evolution itself, is to maintain the holey relic as paraphyletic."
And yes, I think the spelling "holey" was deliberate.

Monday, 12 March 2012

A new old book

When I started this blog 11 months ago, I introduced it as being mostly about plants and our interactions with them, but I said I'd be posting about my other interests from time to time, including bookbinding.  So far, it's all been about plants except for one brief introduction to my sailing dinghy.  This post's about books and bookbinding.
I'm slowly getting around to buying an e-reader or maybe an i-pad, so I can read electronic books.  I love real books, especially old ones, but they take up a lot of space, and lately I've been borrowing from the library more than buying.  But even better is the pleasure of making my own, and to my surprise it's quite easy.  This one is my facsimile of a rare botanical book that turns out to be quite important: Plantarum Novarum ex Herbario Sprengelii Centuriam, attributed to J. F. T. Biehler, 1807.
 Over two hundred years after its publication, it’s hard to judge the significance of this little book.  It's believed that only a few copies of the original printing remain, mostly in European botanical libraries (Stafleu & Cowan, 1985, “saw no copy” of it, but there is one copy at least at Kew, bound in leather with some related works in one small volume). It was published on 30 May 1807 as a Doctor of Medicine dissertation at the University of Halle, Saxony, now part of Germany.  Botany was an integral part of medicine at the time, largely because of the predominant use of herbs, so it was essential that medical doctors could demonstrate mastery of Linnaeus’s sexual system of plant classification. 
 The 46 small pages of Biehler’s dissertation contain descriptions of 100 plants and lichens, many of them new, from all over the world (listed below).  Thus it has a lingering influence and importance as the place of first description for many plants.
Caucasus & Black Sea
Herbaria, gardens, & unknown
India & Sri Lanka
Mediterranean (incl. Lebanon) & C Europe
N America (mostly Pennsylvania)
North & Central Europe
Siberia and Mongolia
St Helena
The author whose name appears on the title page of this book, Johann Friedrich Theodor Biehler, was born about 1785, and although the date of his death isn't recorded anywhere, I'm pretty sure he's no longer with us.  Apparently he published no other botanical work, and most likely he practiced medicine after he qualified with this dissertation.  

But Biehler wasn't actually the author.  Academic practice in northern Europe at the time was for a doctoral candidate to defend a dissertation that was written by his professor, and this is borne out by the publication, a few months after Biehler’s dissertation, of Novarum Plantarum ex herbario meo Centuria by K.P.J. Sprengel, professor at Halle (Sprengel 1807).  The text of Sprengel’s book is identical with Biehler’s.  Thus Sprengel should be identified as the actual author of the Biehler work, where the publication of many new names is first effected.
Sprengel (1766–1833) followed Johann Reinhold Forster as professor of botany at Halle (Stafleu & Cowan 1985); and he married one of Forster's daughters.  This is the New Zealand connection. 17 of Forster’s plant collections from Cook’s second Pacific voyage (1772–1775) are included in this work and many of these were formally described here for the first time (Garnock-Jones 1986), at least in a format that meets the requirements of the International Code of Nomenclature for algae fungi and plants.  These plants were already known to the botanical world through the well known Primitiae Florae Novae Zelandiae of Solander, and George Forster’s Florulae Insularum Australium Prodromus (Forster 1786).  However, Solander's work was never formally published, and some of the names he coined were later misapplied by Forster.  To make matters worse, Forster only listed those Solander names, so although his book was properly published, these are names without descriptions (quaintly called nomina nuda by botanists). Some of them were not properly published until Sprengel. For Forster's misidentifications, those names were published in a sense that's different from what Solander intended, e.g., Epilobium hirtigerum (Garnock-Jones 1983).   So this little book has more importance than its author might have expected.
The work is also important for other regions, e.g. North America, Europe and SW Asia and many of the names first published here are still in use.
Many years ago I typed this out laboriously, and proof-read the Latin text as an electronic file for printing.  Then a couple of years ago I was given a nice introductory book on bookbinding and decided to make it into a real book. The single signature in the book block is sewn with dental floss. I have been careful to match the pagination and layout of the original, but it's not printed on the original paper size in this version (the text block is the correct size however). The typeface is the IDC Founder’s Caslon family, a close but not perfect match to the original.  Symbols such as those for male and female are in Alchemy type face, as on my favourite page, the description of Lethedon tannensis.

 The boards are covered in fancy paper that unfortunately wasn't waterproof, so it's lost a bit of colour in the gluing.  The bookcloth on the spine is made from scraps of our curtain material, backed with brown paper.  I like the bright yellow endpapers, but really these should have been marbled paper.
You can read the whole book at Victoria University of Wellington's Electronic Text Centre.
Candolle, A. P. de, 1817.   Regni Vegetabilis Systema Naturale 1.  Paris.
Forster, J. G. A. 1786.  Florulae Insularum Australium Prodromus.  Göttingen.
Garnock‑Jones, P.J. 1983. Proposal to reject the name Epilobium junceum Spreng.  (1807) (Onagraceae).  Taxon 32: 656–658.
Garnock‑Jones, P.J. 1986. South Pacific plants named by K. P. J. Sprengel in 1807.  Taxon 35: 123–128.
Sprengel, K. P. J., 1807. Mantissa Prima Florae Halensis.  2. Novarum Plantarum ex Herbario Meo Centuria.  Halle.
Stafleu F. A. ; Cowan , R. S.  1985.  Taxonomic Literature (2nd ed.) Vol. v.  W. Junk, The Hague.

Sunday, 11 March 2012


I saw this while I was walking home through Kelburn last week (just where the mobile library pulls in on Upland Road, if you're local).  Chicory, Cichorium intybus, is a member of the sunflower family Asteraceae, and it gives its name to a distinctive subfamily of that family, the Cichorioideae.  Within Cichorioideae it belongs in the lettuce tribe, Lactuceae.

Lactuceae are distinguished by having just one type of floret in their heads (what looks like a flower in this family is really a cluster of tiny florets), and these are called ligulate florets.  Each floret has five petals joined into a tube and then split down one side to form a flat strap with five teeth at the tip.  In the centre is a style with two stigmas, surrounded by a tube of five anthers (dark blue in the photo above).

Chicory is used as a livestock food in New Zealand and sometimes escapes onto waste land.  The roots are sometimes roasted and ground as a coffee substitute.

Other members of the tribe are dandelion, lettuce, catsear, sow thistle (puha), and that serious pest in New Zealand, Hieracium.  Nearly all of them have yellow florets, but a few have orange or purple.  The sky blue florets of chicory are very unusual.
Native dandelion, Taraxacum magellanicum, flowers, Remarkables Range, Otago.
Native dandelion, Taraxacum magellanicum, fruits, Remarkables Range, Otago.
Catsear, Hypochaeris radicata.
Hieracium lepidulum is a serious weed in Otago and Canterbury.
A capitulum (flower head) of Hieracium lepidulum.
Orange hawkweed, Hieracium aurantiacum.

Apart from having all ligulate florets in their capitula, another thing the species in this tribe have in common is milky juice or latex.  The juice is rich in sesquiterpene lactones, which give it a bitter taste and probably deter grazers.  That's why lettuce are sometimes bitter.  Dandelion is a diuretic, with explains its common name in France, piss-en-lit.

Botanically, the best known member of the family is Tragopogon, goat's beard or vegetable oyster.  T. porrifolius is a minor vegetable, but the genus's fame results from its role in evolution research.  American botanist Marion Ownbey discovered that three introduced European species of Tragopogon had hybridised in America to make two new hybrid species.  These are the classical examples of an evolutionary process called allopolyploidy, where a sterile hybrid doubles its chromosome number, restoring fertility and making an instant new species.  It's a common process in plants, but Tragopogon is the best known example.  One surprising thing is that it's happened more than once.  Lately the genetics of allopolyploidy in Tragopogon have been studied in great detail by a team led by Doug & Pam Soltis in Florida.  Jennifer Tate and Vaughan Symonds, now at Massey University, were part of a team that duplicated this process in culture.  The three parent species, T. porrifolius, T. dubius, and T. pratensis, all occur in New Zealand, so one day we might find it has happened here as well.

Saturday, 3 March 2012

More tiny flowers

New Zealand seems to be well-endowed with tiny flowers, and we don't know a lot about what visits and pollinates them.  Only a few approach the theoretical minimum for a functional flower, including this one:

The photo shows both flowers and fruits.  Each flower has 4 sepals, no petals, a single stamen and a single carpel with one ovule.  The fruit is a single seed, enclosed in the ovary, enclosed in the calyx; there's one lying on its side just above and to the right of the middle of the picture.  The mature fruiting calyx is 1.5–2 mm long, and about 1 mm wide; at flowering it's a bit smaller.
Scleranthus uniflorus, Mt Robert, Nelson Lakes National Park.

This plant is Scleranthus uniflorus, and you might have trouble believing that it's in the carnation family (Caryophyllaceae), though it's more closely related to the chickweeds than the carnations.  Scleranthus is a small genus found in Europe, West Asia, Australia, and New Zealand.  In all three New Zealand species, S. biflorus, S. brockiei, and S. uniflorus, the plants form cushions, but in the other two the flowers are paired at the top of each stalk.

There's an Australian Scleranthus naturalized in the Wither Hills in Marlborough, one of the driest parts of the country (Garnock-Jones 1988).  That one is interesting because for years it was thought to be the same as S. biflorus.  It was first described as Mniarum fasciculatum by Robert Brown, but pretty soon another great British botanist Joseph Dalton Hooker had opined that it was no different from S. biflorus, even though he had earlier transferred it to Scleranthus.  It seems nobody doubted Hooker's word for over 100 years; such is the nature of authority.  By the time botanists in Australia started noting that this was different, its original name had faded into obscurity, and we came pretty close to describing it again as a new species, before I happened to see some of the early collections in the Kew herbarium in England).  Interestingly, at least three Australian dry-land grasses are also naturalized in the Wither Hills, so perhaps they all came together with sheep and/or grass seed from Australia.

My first PhD student, Rob Smissen, did his dissertation on Scleranthus.  Using DNA sequence data to discover the evolutionary history of the genus, he showed it was likely the genus has crossed the Tasman Sea twice by long-distance dispersal (Smissen et al., 2003).  However, these little 1-seeded fruits have no obvious means of getting around.  They join a number of other plants that seem to have dispersed, but for which we have no idea how.

Garnock-Jones, P.J. 1988: Caryophyllaceae.  In Webb, C.J.;. Sykes, W.R; Garnock‑Jones, P.J.  Flora of New Zealand Vol. 4 Pteridophytes, Gymnosperms, Dicotyledons. Botany Division, DSIR, lxviii + 1365 pp.

Smissen, R.D.; Garnock-Jones, P.J.; Chambers, G.K. 2003: Phylogenetic analysis of ITS sequences suggests a Pliocene origin for the bipolar distribution of Scleranthus (Caryophyllaceae)Australian Systematic Botany 16: 301 - 315.