It's Linnaeus' Legacy time again! May 5th's edition will be happening at The Ethical Palaeontologist, so get your submissions in to julia (at) ethicalpalaeontologist.com, leave them in the comments here, or use the submission form at Blog Carnival.
We also need hosts for future editions!
Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development4 weeks ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.4 weeks ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
Soft Waxy Scales
The Hemiptera (true bugs) are one of the definite contenders for the insect order containing the most oddballs (Coleoptera and Hymenoptera are probably their competitors). Hemiptera are well marked as a group by their specialised sucking mouthparts, but within the Hemiptera a wide range of body plans have arisen. The scale insects (Coccinea) are perhaps one of the oddest groups of all, and it is one of the scale families, the Ortheziidae, that is our current Taxon of the Week.
Scale insects get their name from the adult females, which have completely abandoned the joys of mobility and live their lives on a single spot, sucking the sap from a host plant. To protect themselves they secrete a covering of sticky wax or a hardened scale. Because of their sedentary lifestyle, indulgences such as legs or eyes are unnecessary, and have become reduced or lost. Only close inspection of the adult, or of the males or nymphs, would identify these creatures as even being insects. Those scales that are significant to humans are mostly plant pests, though some species are used to produce lacquer or the red dye known as cochineal (yep, gramophone records were once made from crushed insects).
Scales of both sexes first hatch out of their eggs as highly mobile nymphs called 'crawlers', with fully developed legs and antennae (Williams, 1991). This is the dispersal phase of their life cycle - not only can they crawl around, but they are also small enough to be easily blown by the wind. Once they find a suitable host plant and moult to the next instar, scale nymphs become pretty much immobile, and lose all the paraphernalia of their youth. While females pretty much remain in this state for the rest of their life, males do things quite differently. They feed for the second and third instars, then enter a non-feeding pupal stage before emerging as the winged adult (the adult males of a few species lack wings). Adult male scales also don't feed and lack mouthparts - they will only live for a short time while they find a mate. Male scales are also one of the few groups of winged insects, in addition to Diptera (flies) and Strepsiptera, to have lost one of the pairs of wings (the first time I ever saw one, I was not yet aware of this and it confused me immensely). Because of their brief lifespan, male scales are relatively rare overall, though I get the impression that they can appear in large numbers in the right season. However, they are also of microscopic size, so are not likely to be noticed.
Scale insects are divided between a number of families. They are often divided into two superfamilies, the Orthezioidea (archaeococcids) and Coccoidea (neococcids) (Koteja, 2000), though other authors combine them all into the Coccoidea. However, the archaeococcids are united only by primitive characters and are assumed to be paraphyletic and ancestral to neococcids. The Ortheziidae (ensign scales) is one of the most basal of the families of Coccinea, and one of the earliest families known from the fossil record, in the Lower Cretaceous (Koteja, 2000) - however, the Coccinea fossil record is extremely poor and should be treated with caution (most female scales are distinguished by microscopic characters not usually preserved in fossils, and the great difference between males and females makes them impossible to identify with each other unless specimens are preserved in the process of mating). Characters giving away the basal position of ortheziids include the presence of abdominal spiracles in the female (lost in neococcids), and compound eyes in the male (in neococcids the compound eye has disintegrated into a row of separate simple eyes). Nymphs and adult females secrete symmetrical plates of wax on their backs, while the female also secretes a wax ovisac at the end of the abdomen in which she incubates her eggs. This is the 'ensign' referred to in the common name.
The Ortheziidae are not a particularly large family by insect standards - about 200 species are known. As with other scales, a number of species have been spread around the world along with infected host plants, and some can cause trouble as pest species.
REFERENCES
Koteja, J. 2000. Advances in the study of fossil coccids (Hemiptera: Coccinea). Polskie Pismo Entomologiczne 69: 187-218.
Williams, D. J. 1991. Superfamily Coccoidea. In The Insects of Australia, 2nd ed. vol. I pp. 457-464. Melbourne University Press.
Experimental Fags
John Lynch at Stranger Fruit has opened a comments thread on the question of LGBT (Lesbian, Gay, Bisexual and Transgender - though to be honest, I always think it sounds like some sort of sandwich) people in science. The query which brought up the question was:
I can quite honestly say that I have never felt culturally pressured to become a fashion designer. Quite the opposite, in fact - unless Suburban Slob Styles have a completely unexpected burst of popularity, I don't think anyone is likely to be asking fashion tips of me. The basic question of "gay under-representation" still is worth addressing at least briefly. However, the question that needs to be asked in reply is, "Are LGBTI people really under-represented?"
I personally think this is a quite different question from that of female underrepresentation. Yes, LGBTI people are definitely in the minority in science, but they are also in the minority in society in general. Unless the proportion of LGBTI people in science is significantly less than in humanity as a whole, it's not really under-representation. However, the next question is a bit of a deal-breaker - "how would we know?" I have had occassion in the past to refer to being gay as belonging to one of the easier targets of discrimination. My reason for this characterisation was that we have a certain degree of choice as to whether we allow others to know our sexual orientation, unlike (e.g.) women or members of other races who are instantly recognisable as such.
Taking science bloggers as representative of science in general (which must be admitted to be a pretty spurious generalisation), I can look at my blogroll to the right and spot Rick MacPherson and Doug Taron as two openly gay bloggers, out of a blogroll of 65. That may look like under-representation, but only by ignoring the nature of blogging. I only know of those two bloggers' sexual orientations because they have chosen to write about them on their blogs. The community of bloggers vary significantly in what they choose to impart about their personal lives - some write extensively on the subject, others give away very little. Having never directly asked anyone on my blogroll what their sexual orientation might be, I have no way of actually knowing. It is the same in society in general - there is no way of knowing whether the question of LGBTI under-representation in science is actually a valid one. All I can offer here is my own experiences as a gay man working in science.
And I have to say, they've pretty much all been positive ones. Once I reached university, I rarely found the need to hide my sexual orientation, and it has been the same in my working career. I have perhaps been fortunate in that regard to be working in New Zealand and Australia, both of which are pretty egalitarian countries where people tend not to try and interfere with other people's personal lives*. Academia also tends to attract people of a pretty liberal disposition. Part of it may also be my own personal attitude towards these things - I don't personally make any effort to inform people of my sexual orientation, though nor do I conceal it in any way. I just generally run under the assumption that it's general knowledge. And I certainly wouldn't feel any hesitation about, for instance, taking my partner to a work do at a new job.
*I have always remembered a segment I saw on a skit-comedy programme in New Zealand many years ago that was headed "Donoghue comes to New Zealand", back in the days when Phil Donoghue had a television talk-show in America where people would come on set and talk about their personal lives. In the comedy skit, the actor playing Phil Donoghue first asks a woman about her painful divorce from an abusive husband, to which the woman replied, "No, there's nothing wrong. What are you asking for?". He then attempts to interview a heavily disabled man about dealing with his disabilities, only to be told not to worry about him, he's fine, couldn't be better.
My point is that in this, as with so many other things, don't assume anything (as an ex of mine used to say, "Assumption is the mother of all fuck-ups"). Just because someone isn't screaming their sexual orientation from the rooftops, doesn't mean they're straight. If they haven't had any particular reason to tell you, they quite possibly wouldn't. And, as Julia Anderson has put it, Don't Be A Dick.
I was wondering if any of you folks at science blogs can discuss the issue of LGBT people in science. Apart from Jim Pollack, Alan Turing and a few others, we seem to be underrepresented. Is it due to something essential or innate in queer people? Is it because there is cultural pressure for gay people to work in other disciplines like fashion etc.?
I can quite honestly say that I have never felt culturally pressured to become a fashion designer. Quite the opposite, in fact - unless Suburban Slob Styles have a completely unexpected burst of popularity, I don't think anyone is likely to be asking fashion tips of me. The basic question of "gay under-representation" still is worth addressing at least briefly. However, the question that needs to be asked in reply is, "Are LGBTI people really under-represented?"
I personally think this is a quite different question from that of female underrepresentation. Yes, LGBTI people are definitely in the minority in science, but they are also in the minority in society in general. Unless the proportion of LGBTI people in science is significantly less than in humanity as a whole, it's not really under-representation. However, the next question is a bit of a deal-breaker - "how would we know?" I have had occassion in the past to refer to being gay as belonging to one of the easier targets of discrimination. My reason for this characterisation was that we have a certain degree of choice as to whether we allow others to know our sexual orientation, unlike (e.g.) women or members of other races who are instantly recognisable as such.
Taking science bloggers as representative of science in general (which must be admitted to be a pretty spurious generalisation), I can look at my blogroll to the right and spot Rick MacPherson and Doug Taron as two openly gay bloggers, out of a blogroll of 65. That may look like under-representation, but only by ignoring the nature of blogging. I only know of those two bloggers' sexual orientations because they have chosen to write about them on their blogs. The community of bloggers vary significantly in what they choose to impart about their personal lives - some write extensively on the subject, others give away very little. Having never directly asked anyone on my blogroll what their sexual orientation might be, I have no way of actually knowing. It is the same in society in general - there is no way of knowing whether the question of LGBTI under-representation in science is actually a valid one. All I can offer here is my own experiences as a gay man working in science.
And I have to say, they've pretty much all been positive ones. Once I reached university, I rarely found the need to hide my sexual orientation, and it has been the same in my working career. I have perhaps been fortunate in that regard to be working in New Zealand and Australia, both of which are pretty egalitarian countries where people tend not to try and interfere with other people's personal lives*. Academia also tends to attract people of a pretty liberal disposition. Part of it may also be my own personal attitude towards these things - I don't personally make any effort to inform people of my sexual orientation, though nor do I conceal it in any way. I just generally run under the assumption that it's general knowledge. And I certainly wouldn't feel any hesitation about, for instance, taking my partner to a work do at a new job.
*I have always remembered a segment I saw on a skit-comedy programme in New Zealand many years ago that was headed "Donoghue comes to New Zealand", back in the days when Phil Donoghue had a television talk-show in America where people would come on set and talk about their personal lives. In the comedy skit, the actor playing Phil Donoghue first asks a woman about her painful divorce from an abusive husband, to which the woman replied, "No, there's nothing wrong. What are you asking for?". He then attempts to interview a heavily disabled man about dealing with his disabilities, only to be told not to worry about him, he's fine, couldn't be better.
My point is that in this, as with so many other things, don't assume anything (as an ex of mine used to say, "Assumption is the mother of all fuck-ups"). Just because someone isn't screaming their sexual orientation from the rooftops, doesn't mean they're straight. If they haven't had any particular reason to tell you, they quite possibly wouldn't. And, as Julia Anderson has put it, Don't Be A Dick.
The Most Unread Books
It's been a while since I last bothered with any of the meme things, but I found this one via Stanger Fruit and Evolving Thoughts. Supposedly, this is a list of the 106 top books that people have lying around at home because they think they should read them sometime but have never got around to reading. Needless to say, it's a list that is heavy on the "classics" and other pretentious wank. As John Wilkins did, I've bolded the books that I've read, and italicised the ones that I've started reading but never finished. I don't know how universal the list is, though it's probably largely American - I can't help wondering if a New Zealand list would be much different. Would The Bone People get a look-in, for instance?
There once was a time when I was a very avid reader, and often went through a couple of books in a week. Unfortunately, I rarely find time to read fiction these days, but I may track down a couple of titles from this list I haven't re
Jonathan Strange & Mr Norrell
Anna Karenina
Crime and Punishment
Catch-22 - I've lost count of how many times I've read this book. It's one book that I've found I can pick up any time, anywhere, and still enjoy fully.
One Hundred Years of Solitude
Wuthering Heights - started reading this one, but lost the book about a third of the way through and never picked up another copy.
The Silmarillion - I'll admit that it's harder to read, but I actually have a lot more regard for the Silmarillion that for either The Lord of the Rings or the confused mess that is The Hobbit. The Silmarillion (which was never really considered publishable during Tolkein's lifetime) was where Tolkein indulged his own personal enthusiasms for mythology and linguistics, while one can't help the feeling that The Lord of the Rings has been wrapped in a more commercially-acceptable blanket.
Life of Pi : a novel
The Name of the Rose - I remember running around university trying to find an acquaintance from high school who was studying Latin to confirm what the last sentence actually meant.
Don Quixote
Moby Dick
Ulysses - this barely qualifies to be italicised. The British version of the telly programme Who's Line is it Anyway? used to occassionally have one segment where the competitors had to give an ordinary composition (such as, in the case I'm about to refer to, a chocolate cake recipe) in the style of a famous author. In the chocolate cake example, one of the 'competitors' indicated that he would be constructing his recipe in the style of James Joyce. The host, Clive Anderson, replied, "Well, I'm sure we've all read the first two pages of Joyce". That about sums up my effort. Funnily enough, that's also all I've ever managed of Brian Aldiss.
Madame Bovary - the main problem with Madame Bovary is that it is impossible to like a single character. Flaubert obviously didn't think much of people.
The Odyssey - The Illiad's better.
Pride and Prejudice - I'm rather a fan of Jane Austen, and this was the first of her books I read - I'd say Persuasion was probably my favourite, though I haven't yet read Northanger Abbey or Mansfield Park. If I may be allowed a lowbrow moment, though, I was actually glad to have seen the BBC version of this with Colin Firth before I read the book, because I have to admit that some of it would have gone over my head if I hadn't. In my defense, I was about fourteen at the time.
Jane Eyre
The Tale of Two Cities - I think I managed three pages for this one.
The Brothers Karamazov - I rather liked this one. It does drag on in places, but the ironic gems hidden within it rather make up for it. My favourite example: "You see, I once knew a certain young unmarried woman, back in the last 'romantic' generation, who after several years of mysterious love for a certain gentleman, whom, incidentally, she could have taken to the altar at the time of her choosing with a modicum of fuss, ended by inventing insuperable obstacles, and on a stormy night throwing herself from a lofty bank, resembling a cliff, into a rather deep and fast-flowing river and perished in it really for no other reason than her own caprice, solely in order to emulate Shakespeare's Ophelia; and one might even say that had this cliff, so long ago selected and favoured by her, been not so picturesque, and had there been on its site merely a flat, prosaic bank, then her suicide might possibly have never taken place at all."
Guns, Germs, and Steel: the fates of human societies
War and Peace
Vanity Fair
The Time Traveler’s Wife - never heard of it
The Iliad - I've actually read two or three versions of this - it's quite incredible what a difference the translation style makes.
Emma - apparently, Jane Austen commented in a letter when writing Emma that she had invented a heroine whom no-one was going to like but Austen herself. I must admit that I found the character of Emma more than a little annoying.
The Blind Assassin - don't know this one, either.
The Kite Runner - nor this.
Mrs. Dalloway - watching that absolutely drear piece of cinema, The Hours, rather put me off the idea of reading this.
Great Expectations - If I ever read this one, I'll have to see if I can find the original version. The movie was based on the version with a 'happy' ending, and the happy ending just pissed me off.
American Gods - I'm a great fan of Neil Gaiman's Sandman comic series, but I must admit that his novels don't enthrall me so much. Ditto his movie efforts.
A Heartbreaking Work of Staggering Genius - haven't of this one either. The title rather sets the bar, doesn't it?
Atlas Shrugged
Reading Lolita in Tehran : a memoir in books
Memoirs of a Geisha - the movie was a little tame, but anything that manages to get Michelle Yeoh and Gong Li into the same film has a lot going for it.
Middlesex
Quicksilver - the only Quicksilver I know is the X-Men character
Wicked : the life and times of the wicked witch of the West
The Canterbury tales - I missed this part of high school English
The Historian : a novel
A Portrait of the Artist as a Young Man
Love in the Time of Cholera - wash your hands first.
Brave New World - Aldous Huxley was brother to Julian Huxley, one of the authors of the modern evolutionary synthesis, and grandson of Thomas Henry Huxley, the self-styled "Darwin's bulldog".
The Fountainhead - I read this when I was in high school. Even then, Ayn Rand pissed me off. The 1949 movie version's not bad, though.
Foucault’s Pendulum
Middlemarch
Frankenstein - The Modern Prometheus was not what I expected. It's actually something of a tear-jerker.
The Count of Monte Cristo
Dracula - I read this in high school. It was a lot more boring than I expected. I read it in an omnibus edition that also included The Lair of the White Worm, the 1988 movie version of which (featuring the unbelievably aptly-named Amanda Donohoe - put the stress on the last syllable) is a must-see for lovers of glorious B-grade trash.
A Clockwork Orange - I think it was actually a Nature piece I once saw that referred to a clockwork orange - "to use the phrase coined by Stanley Kubrick". No.
Anansi Boys
The Once and Future King - very nearly. I never quite read about the last twenty pages.
The Grapes of Wrath
The Poisonwood Bible : a novel
1984 - I found this book a lot more disturbing when I re-read it a couple of years ago than when I had first read at about age 13.
Angels & Demons
The Inferno - I've read the entire Divine Comedy, though I must admit I somewhat skimmed Il Paradiso.
The Satanic Verses
Sense and Sensibility - seriously, all you people with unread Austen on your shelves should get around to it. If Sense and Sensibility has a significant failings, it's that the ending seems a little contrived. Sense and Sensibility is centered a lot less on a specific romance than the other novels, being rather about the relationship between the two sisters who are the main characters, so when Austen marries them off at the end of the book (as she always does), there doesn't seem much reason for it beyond expediency.
The Picture of Dorian Gray - in places, it has to be admitted, something of a vehicle for Wilde's one-line witticisms. If you read a lot of Oscar Wilde, you can't help noticing that he also used the same lines in a number of different works. One story holds that after someone (I forget who, unfortunately) once made a clever comment in Wilde's presence, Wilde commented, "I wish I'd said that". The original speaker replied, "You will, Oscar".
Mansfield Park
One Flew Over the Cuckoo’s Nest
To the Lighthouse
Tess of the D’Urbervilles
Oliver Twist
Gulliver’s Travels - a very good book, but the obscenely funny Modest Proposal is probably the best of Swift's works.
Les Misérables
The Corrections
The Amazing Adventures of Kavalier and Clay
The Curious Incident of the Dog in the Night-Time
Dune - this book impressed me a lot when I was a teenager, but to be honest it's rather palled somewhat as I grown older.
The Prince
The Sound and the Fury
Angela’s Ashes : a memoir
The God of Small Things
A People’s History of the United States : 1492-present - I don't think there's much reason to expect me to have read this, is there?
Cryptonomicon
Neverwhere - I actually prefer the telly series.
A Confederacy of Dunces
A Short History of Nearly Everything - I'm still not quite sure what to make of this one. At least half of the 'information' in here is utter bollocks, but then the value of Bill Bryson's work for making science more popular probably allows for a lot of forgiveness.
Dubliners
The Unbearable Lightness of Being
Beloved
Slaughterhouse-five - I still think this is a great book. I'm a fan of Vonnegut in general, though Galapagos is probably my favourite (perhaps unsurprisingly).
The Scarlet Letter
Eats, Shoots & Leaves - yeah, I'm a grammar nazi too.
The Mists of Avalon
Oryx and Crake : a novel
Collapse : how societies choose to fail or succeed
Cloud Atlas
The Confusion
Lolita
Persuasion - as I said, probably my favourite of Austen's works (and is it just my imagination, or has every single one of them except Northanger Abbey appeared on this list?)
Northanger Abbey - oh, there it is. We have the complete Austen set!
The Catcher in the Rye - does anything actually happen in this book? At all?
On the Road
The Hunchback of Notre Dame - though there are reasons why I should probably read this one in the not-too-distant future.
Freakonomics : a rogue economist explores the hidden side of everything
Zen and the Art of Motorcycle Maintenance : an inquiry into values
The Aeneid - despite having read a lot of classics, I've never got around to this one.
Watership Down - I loved this one as a kid.
Gravity’s Rainbow - I actually intend to read this one again. Maybe I'll actually work out what the heck's going on the second time around. Maybe not, though.
The Hobbit - I referred to The Hobbit above as a confused mess, and I stand by that statement. Problem is, Tolkein started on The Hobbit as a story for his kids before he realised the possibility of linking it into his "Elven lore" compositions. As a result, The Hobbit doesn't know whether it's supposed to be a light children's story or a serious piece of pseudo-mythology, and there's definite signs of strain.
In Cold Blood : a true account of a multiple murder and its consequences
White Teeth
Treasure Island - one of the possible names I suggested when we got our dog as a small puppy was Flint, because he kept on climbing up onto our shoulders.
David Copperfield - Reader's Digest versions do not count.
The Three Musketeers
There once was a time when I was a very avid reader, and often went through a couple of books in a week. Unfortunately, I rarely find time to read fiction these days, but I may track down a couple of titles from this list I haven't re
Giving Plants the Glove
Today's Nature has got what has to one of the most confusing news items I've read for some time - Swiss 'dignity' law is threat to plant biology. To quote the news item:
And the rabbit hole just goes down from there. Later on we're told:
By this point, I was going a little cross-eyed. But when I got to:
my eyes crossed so far they actually migrated past each other and each fell out the opposite ear. I have had cause to complain a couple of times before about poorly thought-out legislation interfering with legitimate research, but this has got to be about the most downright comical example of which I've ever heard. So what exactly defines a plant's "dignity"? Is a researcher offending a plant's delicate dignity if they spend an unwelcome amount of time leering at their stigmata? Are too many botanical chikan-committers fiddling with Arabidopsis stamens?
Okay, let's calm down a minute and take this seriously - specifically, the latter point that interfering with a plant's ability to reproduce would count as a violation of its "dignity". As pointed out in the Nature article, this could be quite a problem for plant research, particularly research on horticultural significant taxa which are often deliberately bred to be infertile. Not only are seedless fruit often more popular among consumers, but any gardener knows that vegetatively-propagated plants can be relied on to maintain consistent characters while seed-produced progeny are often annoyingly unpredictable. One commenter on the article also points out that infertility can also act as a safeguard when developing, for instance, a genetically-modified variety of an important crop plant, as researchers can feel confident that the novel variety will remain contained until it has been fully tested and its characteristics will not be spread through pollination.
Another commenter seems to have had the same reaction to the story I did:
The Swiss federal government's ethics committee on non-human biotechnology has mapped out guidelines to help granting agencies decide which research applications deeply offend the dignity of plants — and hence become unfundable.
And the rabbit hole just goes down from there. Later on we're told:
All plant biotechnology grant applications must now include a paragraph explaining the extent to which plant dignity is considered. “But scientists don't know what it means,” says Beat Keller of the Institute of Plant Biology at the University of Zurich who is running the first field trial — of disease-resistant corn (maize) — to be approved under the new legislation.
By this point, I was going a little cross-eyed. But when I got to:
The committee has created a decision tree presenting the different issues that need to be taken into account for each case. But it has come up with few concrete examples of what type of experiment might be considered an unacceptable insult to plant dignity. The committee does not consider that genetic engineering of plants automatically falls into this category, but its majority view holds that it would if the genetic modification caused plants to 'lose their independence' — for example by interfering with their capacity to reproduce.
my eyes crossed so far they actually migrated past each other and each fell out the opposite ear. I have had cause to complain a couple of times before about poorly thought-out legislation interfering with legitimate research, but this has got to be about the most downright comical example of which I've ever heard. So what exactly defines a plant's "dignity"? Is a researcher offending a plant's delicate dignity if they spend an unwelcome amount of time leering at their stigmata? Are too many botanical chikan-committers fiddling with Arabidopsis stamens?
Okay, let's calm down a minute and take this seriously - specifically, the latter point that interfering with a plant's ability to reproduce would count as a violation of its "dignity". As pointed out in the Nature article, this could be quite a problem for plant research, particularly research on horticultural significant taxa which are often deliberately bred to be infertile. Not only are seedless fruit often more popular among consumers, but any gardener knows that vegetatively-propagated plants can be relied on to maintain consistent characters while seed-produced progeny are often annoyingly unpredictable. One commenter on the article also points out that infertility can also act as a safeguard when developing, for instance, a genetically-modified variety of an important crop plant, as researchers can feel confident that the novel variety will remain contained until it has been fully tested and its characteristics will not be spread through pollination.
Another commenter seems to have had the same reaction to the story I did:
Please tell me that this is merely a three-week old April Fool's story that somehow slipped by the editors.
The Shrikes of the South
Like them or loath them, there can be little argument that the introduction of molecular methods in the latter part of the last century revolutionised the study of phylogeny and evolution. In many cases, the results of molecular studies supported the theories already proposed about which taxa are related to which, and how. In other cases, molecular data came up with results that strongly contradicted what we thought we already knew. And in some cases, molecular studies gave results that had never been suggested before, but seemed perfectly reasonable in hindsight.
I have spoken elsewhere about the new picture of oscine (songbird) phylogeny which has arisen from molecular studies of the group. I'd recommend reading the second and third paragraphs of the post I've just linked to for the background to what I'm just about to talk about. Let it suffice to say that most of the Holarctic families of oscines belong to a clade called Passerida, which is nested within a series of mostly Australo-Papuan clades. Of these Australo-Papuan clades, the most diverse is the Corvoidea, which also includes a number of taxa that have dispersed outside of Oceania such as the crows and orioles (the proper Old World orioles, that is, not the American birds known as 'orioles' which are not orioles at all but members of the Passerida). Also included in the Corvoidea are the shrikes, Old World birds with hook-tipped bills that are more predatory than your average songbird.
In 2004, Barker et al. published a phylogeny of the oscines that resolved a number of clades within the Corvoidea. Among the most interesting clades identified by this study was one that united the bush shrikes (Malaconotidae) and helmet-shrikes (Prionopidae) of Africa (both previously counted as subfamilies of the Laniidae) with the woodswallows (Artamus) and butcherbirds (Cracticidae) of Australia. This was definitely one of the third class of molecular results that was unexpected but sensible, as the cracticids are in many ways the shrikes of Australia. The new clade, which lacks a name but which for convenience I'll dub the 'malaconotoid clade', therefore combines many of the world's shrike-like birds in one convenient package. The notable exceptions are the true Eurasian shrikes of the stripped-down family Laniidae, which are Corvoidea but whose affinities seem to lie elsewhere as the sister group of the crows, and the Asian shrike-babblers of the genus Pteruthius, which Reddy and Cracraft (2007) showed to be corvoids related to the American vireos.
Comparison with the other corvoids suggests that the malaconotoids had an Australian origin, a suggestion corroborated by the fact that the basalmost split in the group seems to be between the Australian taxa on one side and the African taxa on the other (Barker et al., 2004; Moyle et al., 2006). As with all good scientific theories, this brings up a further question - how did the malaconotoids get from Australia to Africa? To answer this question, it turns out that a collection of small southern Asian families also fall into the malaconotoid clade - the Platysteiridae, the ioras of the genus Aegithina, and the unusual Bornean bristlehead (Pityriasis gymnocephala). The reasonable suggestion might therefore be made that southern Asia was used as a corridor by the malaconotoids on their way to Africa. Unfortunately, the evidence is a little more equivocal in this regard. It is true that the Asian taxa sit on the African side of the malaconotoid clade (Moyle et al., 2006 - Fuchs et al., 2006, found Aegithina to be sister to the Australian taxa, but with low support), but there is no clear division between taxa from the two continents. Instead, the African and Asian taxa are mixed together, suggesting more than one dispersal between the continents and also unclear whether dispersal was from Asia to Africa or vice versa.
The other significant dispersal in the history of the malaconotoids was from Africa to Madagascar, where an ancestral malaconotoid gave rise to the vangas (Vangidae). The vangas were one of the very few oscine groups to reach Madagascar, and once there they formed an island radiation comparable to the honeycreepers of Hawaii or the finches of the Galapagos. While there are only twenty-one species of vanga, the group is spectacularly diverse ecologically, as shown above in a figure from Yamagishi et al. (2001) - so much so, in fact, that many of the species had been assigned to separate families and were only recognised as vangas recently (see Don Roberson's page on the family for further details). Notable in this regard are the handsome sickle-billed vanga (Falculea palliata), the coral-billed nuthatch (Hypositta corallirostris) which bears an uncanny resemblance to the unrelated true nuthatches, and the large-billed helmetbird (Euryceros prevostii).
REFERENCES
Barker, F. K., A. Cibois, P. Schikler, J. Feinstein & J. Cracraft. 2004. Phylogeny and diversification of the largest avian radiation. Proceedings of the National Academy of Sciences of the USA 101: 11040-11045.
Fuchs, J., J. Fjeldså & E. Pasquet. 2006. An ancient African radiation of corvoid birds (Aves: Passeriformes) detected by mitochondrial and nuclear sequence data. Zoologica Scripta 35 (4): 375-385.
Moyle, R. G., J. Cracraft, M. Lakim, J. Nais & F. H. Sheldon. 2006. Reconsideration of the phylogenetic relationships of the enigmatic Bornean bristlehead (Pityriasis gymnocephala). Molecular Phylogenetics and Evolution 39 (3): 893-898.
Reddy, S., & J. Cracraft. 2007. Old World shrike-babblers (Pteruthius) belong with New World vireos (Vireonidae). Molecular Phylogenetics and Evolution 44 (3): 1352-1357.
Yamagishi, S., M. Honda, K. Eguchi & R. Thorstrom. 2001. Extreme endemic radiation of the Malagasy vangas (Aves: Passeriformes). Journal of Molecular Evolution 53: 39-46.
Spiders Losing their Lungs
The current Taxon of the Week arguably has a pretty poor claim on the title, because it is no longer recognised as a valid taxonomic grouping. As I have explained before, modern spiders can be divided into three suborders or infraorders or what-have-you. The Mesothelae or Liphistiomorphae (segmented spiders) are a small group distinguishable from all other spiders by their obviously segmented abdomens. The Mygalomorphae (vertical-fanged spiders) have fangs that move straight up and down, and include the trapdoor and funnel-web spiders and American tarantulas. The largest group of spiders by far is the Araneomorphae (cross-fanged spiders), with fangs angled towards each other, including orb-weavers, cobweb spiders, jumping spiders, wolf spiders, and pretty much any other spider family you're likely to be familiar with. However, some older references may list a fourth group, the Hypochilomorphae, and it's with the latter that we're dealing today.
The 'hypochilomorphs' include three small families, the Hypochilidae, Austrochilidae and Gradungulidae, that are now regarded as basal members of the Araneomorphae. Like other araneomorphs, they possess fangs that are angled towards each other rather than parallel. Where they differ from other araneomorphs is in the number of book lungs they possess. Book lungs are the ancestral respiratory structure for all arachnids, and evolved from the gills of their aquatic ancestors as they adapted to life on land. They are little more than gills recessed into the underside of the animal and covered over to prevent moisture loss, and the name "book lung" refers to their appearance in cross-section like leaves of a book. The ancestral number of book lungs in arachnids is four, though many arachnids (particularly the smaller forms, and including some spiders) have independently replaced the book lungs with tracheae, or lack any specialised respiratory structures entirely. Most araneomorphs with book lungs have lost the posterior pair and only have two book lungs. Hypochilomorphs retain the posterior pair, demonstrating their basal position to other araneomorphs and causing them to all too often be damned with the execrable title of "living fossil". However, because this is an ancestral feature rather than a derived one, it does not indicate that hypochilomorphs form a group exclusive of other araneomorphs, and other features make it clear that Austrochiloidea (Grandungulidae and Austrochilidae) are more closely related to the other araneomorphs than they are to Hypochilidae (Griswold et al., 1999). The remaining araneomorphs have usually been presented as a single clade (the Araneoclada), though at least one species of Filistatidae, Kukulcania hibernalis, possesses posterior book lungs as a juvenile, suggesting that family lost the posterior book lungs independently of other araneomorphs, and Lopardo et al. (2004) suggested that Filistatidae may be outside the Austrochiloidea + Araneoclada clade.
The Hypochilidae are large spiders found in Asia and North America. They construct a unique web for snaring prey, often referred to as a "lampshade web" in reference to its shape, though if the description in Forster & Forster (1999) holds for all hypochilids, then the photo on the Wikipedia page for this family is quite possibly upside down. According to Forster & Forster, Hypochilus builds its web on the underside of an overhanging rock, with a tightly woven upper section flaring out around the lower circular edge. Hypochilids are mostly montane species.
The Austrochiloidea are restricted to Southern Hemisphere continents - the Austrochilidae are found in southern South America and Tasmania, while the Gradungulidae are found in eastern Australia and the South Island of New Zealand (Forster & Forster, 1999). The Austrochilidae build large horizontal webs, but many Grandungulidae have abandoned web-building and become active hunters. The Gradungulidae are characterised by the significant increase in size of one of the claws on the legs, which is used to great effect in seizing prey. In one of the Australian web-building species, the cave-dwelling Progradungula carraiensis, a long, sparse web is built between the ground and an overhang, up to and exceeding a metre in height. The spider itself sits head downwards at the base of the web, low enough that the front legs are near the ground. Any suitable prey that walks by the spider is grabbed with the front legs and bitten. The prey may be eaten where it is caught, or carried up to the top part of the web that also serves as a retreat for the spider. One of the New Zealand species, Pianoa isolata, has abandoned the web but hangs down among strands of dense moss, catching its prey in a similar manner to Progradungula. A New Zealand cave-dwelling species, Spelungula cavernicola, shown above in a photo by Paddy Ryan, is an active hunter but often feeds on its prey suspended in mid-air from a silk dragline. The round egg-sacs are also hung from draglines, probably as protection from potential predators.
REFERENCES
Forster, R. R., & L. M. Forster. 1999. Spiders of New Zealand and their Worldwide Kin. University of Otago Press: Dunedin (New Zealand), and Otago Museum: Dunedin.
Griswold, C. E., J. A. Coddington, N. I. Platnick & R. R. Forster. 1999. Towards a phylogeny of entelegyne spiders (Araneae, Araneomorphae, Entelegynae). Journal of Arachnology 27: 53-63.
Lopardo, L., M. J. Ramírez, C. Grismado & L. A. Compagnucci. 2004. Web building behavior and the phylogeny of austrochiline spiders. Journal of Arachnology 32: 42-54.
The Importance of Vouchers: Even Molecular Workers Need Herbaria
Those of you who have seen the Monty Python movie The Meaning of Life may recall a scene near the beginning where a woman is brought into a hospital to have a baby, only to have attention to her condition overshadowed by the attention lavished by the hospital staff on their expensive equipment and machines going "ping". Part of the joke, of course, is that a lot of their flashy machinery is completely unnecessary under normal circumstances, considering that women have been successfully having babies without it for as long as there have been women to have babies. The other part is that while we all see the ridiculousness of the situation in the movie, we still all fall for the flashy expensive option in real life. If we go to hospital ourselves, we still damn want the machine that goes "ping".
The proposed closure of the Utrecht Herbarium is actually just another example of a general trend of recent years towards the downsizing and reduction in prestige of natural history collections everywhere. In these days of biochemical assays and gene sequencers, many people, unfortunately including many university and museum directors, seem to find specimen collections just a little antiquarian and hokey. Surely modern genomic and proteomic techniques have rendered such things obsolete? No, they haven't. Molecular investigations don't remove the need for physical specimen storage. Indeed, they make it even more important than before.
Yesterday, I wrote on the importance of conserving type specimens. Type specimens are a special type of voucher specimen, and I thought I'd enlarge today on the significance of voucher specimens in general. A voucher is a representative specimen of the organisms used in a study, such as the specimen used as the source of DNA for a molecular study or a specimen collected as part of an ecological survey. Like type specimens, voucher specimens allow for the confirmation of the identity of the species referred to in the study. They therefore provide a backup against misleading results due to such things as misidentification, changing species concepts, etc.
Apparently one of the projects that has been going on at the Utrecht Herbarium involves the identification of native medicinal plants used in Suriname, so I'll take that as a hypothetical example. Imagine that a researcher working on one of these medicinal plants, call it the "big-leaved bungleflower", manages to extract an active compound from it that he dubs "ifeelfantasticin", and which shows a great deal of promise in medical tests. The problem is that no-one else is able to extract that compound from the big-leaved bungleflower, despite much effort. Despair seems inevitable, until someone decides to check the voucher specimens that the original researcher deposited from his original study. At that point, it becomes clear that the original researcher was not using specimens of big-leaved bungleflower as he had thought, but actually the similar purple-leaved bungleflower. Focus switches to the latter species, ifeelfantasticin is recovered once more, and medical history is made.
Without the voucher specimens, the error would have never been corrected so easily. Griffiths and Bates (2002) report on a real life example of voucher specimens allowing the explanation of unusual results, when a molecular study on New World vultures was seemingly unable to distinguish between greater (Cathartes melambrotus) and lesser (C. burrovianus) yellow-headed vultures. Re-examination of the original specimens indicated that some had been misidentified, including one specimen that had been deposited in a collection before the two species were recognised as distinct.
Unfortunately, all too many researchers still fail to deposit vouchers for studies (Agerer et al., 2000; Wheeler, 2003). Dennis (1960, as quoted in Agerer et al., 2000) commented that "records that cannot be verified are mere waste paper". The need for proper natural history collections remains as strong now as ever.
REFERENCES
Agerer, R., J. Ammirati, P. Blanz, R. Courtecuisse, D. E. Desjardin, W. Gams, N. Hallenberg, R. Halling, D. L. Hawksworth, E. Horak, R. P. Korf, G. M. Mueller, F. Oberwinkler, G. Rambold, R. C. Summerbell, D. Triebel & R. Watling. 2000. Open letter to the scientific community of mycologists: “Always deposit vouchers”. Mycorrhiza 10 (2): 95-97.
Griffiths, C. S., & J. M. Bates. 2002. Morphology, genetics and the value of voucher specimens: an example with Cathartes vultures. Journal of Raptor Research 36 (3): 183-187.
Wheeler, T. A. 2003. The role of voucher specimens in validating faunistic and ecological research. Biological Survey of Canada (Terrestrial Arthropods) Document series no. 9. Ottawa.
The Significance of Type Specimens, and More on Utrecht
Last week I brought up the topic of the Utrecht Herbarium, which faces imminent closure as of June 1. Since then I have been in touch with Renske Ek, who started the petition against the closure. The closure of the herbarium is primarily a cost-cutting measure, and has been under consideration for some time, though it was not announced officially until the 26th of March. The most significant question you might be asking, though, is what is to become of the collection after the closure?
Let me remind you that, as well as over 800,000 specimens, the Utrecht Herbarium holds over 10,000 type specimens. What, some of you may ask, is a type specimen? When a new species is described, the author will select one of his/her specimens (or sometimes, a collection of specimens) of that species to act as the 'type'. That specimen then becomes the definitive example of that species. From that point, if the question ever arises, "What species does "species name X" refer to?", the answer essentially is, "The species that "type specimen X" belongs to". The type specimen also allows the identification of the species if the original published description turns out to be inadequate somehow. Imagine that a taxonomist working on ants describes a new species. He describes the new species' colour, ornamentation of the body, shape of its head, and calls it "species 1". Many years later, another ant taxonomist discovers that the area where the earlier taxo got his specimens from is actually home to two very similar species. One is the earlier author's "species 1", the other is a new "species 2". The problem is, the two species are identical in colour, body ornamentation and shape of the head. They can be distinguished by the shape of the antennae, but the earlier taxonomist, not realising that the shape of the antennae was going to turn out to be significant, never included it in his original description. How is the later taxonomist to work out which of the two species he has on hand is "species 1"? That is where the type specimen comes into play - even if the original description didn't include the appearance of the antenna, the later taxonomist can always look at the type specimen and fill in the missing details.
The type specimen means that a species name is not just a vague philosophical concept, but is tied to a real tangible object. As a result, it is critical that any type specimen is preserved and remains accessible to future researchers. If a collection is locked away from visitors, the specimens are unable to serve their purpose. Also, a locked collection does not simply sit intact until such a time as it is ever opened. Biological collections require constant maintenance and monitoring. After all, these are pieces of dead plant and animal matter we're talking about - their natural tendency is to decay. Alcohol and other preservatives can evaporate, dried insects or plants may be eaten by beetles, and when the collection finally gets opened up again, all that is left is unrecognisable dust and mush. The collected specimens, and type specimens in particular, have failed in their purpose.
Unfortunately, at present there seems to be no clear plan for what is to happen to the Utrecht herbarium collection after closure. Plans to transfer it to the Universiteit Leiden appear to have been shelved due to lack of funding. It seems to have been hoped that the Nederlands Centrum voor Biodiversiteit (Dutch Centre for Biodiversity) currently being put together would offer a permanent home for the collection, but it is unlikely that the Centre will be up and running before the herbarium closes.
Whatever is to become of the Utrecht Herbarium itself, it is imperative that the collection, particularly the type specimens, remains curated and accessible somewhere. Failure to ensure this would be an unforgivable tragedy.
Postscript: David Shorthouse of iSpiders has also commented on the situation.
Let me remind you that, as well as over 800,000 specimens, the Utrecht Herbarium holds over 10,000 type specimens. What, some of you may ask, is a type specimen? When a new species is described, the author will select one of his/her specimens (or sometimes, a collection of specimens) of that species to act as the 'type'. That specimen then becomes the definitive example of that species. From that point, if the question ever arises, "What species does "species name X" refer to?", the answer essentially is, "The species that "type specimen X" belongs to". The type specimen also allows the identification of the species if the original published description turns out to be inadequate somehow. Imagine that a taxonomist working on ants describes a new species. He describes the new species' colour, ornamentation of the body, shape of its head, and calls it "species 1". Many years later, another ant taxonomist discovers that the area where the earlier taxo got his specimens from is actually home to two very similar species. One is the earlier author's "species 1", the other is a new "species 2". The problem is, the two species are identical in colour, body ornamentation and shape of the head. They can be distinguished by the shape of the antennae, but the earlier taxonomist, not realising that the shape of the antennae was going to turn out to be significant, never included it in his original description. How is the later taxonomist to work out which of the two species he has on hand is "species 1"? That is where the type specimen comes into play - even if the original description didn't include the appearance of the antenna, the later taxonomist can always look at the type specimen and fill in the missing details.
The type specimen means that a species name is not just a vague philosophical concept, but is tied to a real tangible object. As a result, it is critical that any type specimen is preserved and remains accessible to future researchers. If a collection is locked away from visitors, the specimens are unable to serve their purpose. Also, a locked collection does not simply sit intact until such a time as it is ever opened. Biological collections require constant maintenance and monitoring. After all, these are pieces of dead plant and animal matter we're talking about - their natural tendency is to decay. Alcohol and other preservatives can evaporate, dried insects or plants may be eaten by beetles, and when the collection finally gets opened up again, all that is left is unrecognisable dust and mush. The collected specimens, and type specimens in particular, have failed in their purpose.
Unfortunately, at present there seems to be no clear plan for what is to happen to the Utrecht herbarium collection after closure. Plans to transfer it to the Universiteit Leiden appear to have been shelved due to lack of funding. It seems to have been hoped that the Nederlands Centrum voor Biodiversiteit (Dutch Centre for Biodiversity) currently being put together would offer a permanent home for the collection, but it is unlikely that the Centre will be up and running before the herbarium closes.
Whatever is to become of the Utrecht Herbarium itself, it is imperative that the collection, particularly the type specimens, remains curated and accessible somewhere. Failure to ensure this would be an unforgivable tragedy.
Postscript: David Shorthouse of iSpiders has also commented on the situation.
My First Tardigrades
Well, the lab course I've been tutoring reached the point yesterday that I'd been waiting for ever since I found out I'd be tutoring it - I've now seen my first tardigrades! I covered the generalities of tardigrades last year, but as I've noted before, there is nothing to compare with seeing an organism that you've previously only known from the literature in real life. And I have to say - tardigrades are just as adorable as I'd always imagined them to be. If not more so.
While I couldn't tell you exactly what species they were, but they looked much like the photo (from here) at the top of this post. Little sausage-shaped animals with four pairs of little stumpy legs, on which they bumbled about in a decidedly endearing manner. I wasn't the only person impressed, either - I heard more than one student exclaiming aloud how cute they were when they looked down the microscope. When you've been trying a week previously to encourage enthusiasm in students about nematodes, it's certainly nice to have an organism that pretty much sells itself.
If you'd like to see your own tardigrades, collect some moss or lichen and sit it in a petri dish with some water (use distilled water or rainwater, not tap water). Leave it there for enough time for the tardigrades to become active and crawl out of the moss. (While they may be found in terrestrial habitats, tardigrades require at least a film of water to move in. If they dry out, they either die or enter a dormant resistant stage known as a tun.) After 3-24 hours, pipette some water out of the base of the dish (tardigrades don't swim, so they settle to the bottom) into another dish or watchglass. Place your pipetted sample under a stereo microscope, and you should be able to see the tardigrades crawling around on the bottom! (As well as other small organisms such as rotifers, nematodes and possibly protozoa.) If you want a closer look, you can transfer a tardigrade onto a slide using a micropipette. A drop of alcohol added to the slide will knock the tardigrade out. Take a look at the Microbial Life page for more details.
However, in the interests of safety, I feel I must draw your attention to the warning given by www.tardigrades.com (from whence comes the Victorian-style illustration above):
Please note the following mental and health risks: in some case addictive behaviour towards tardigrades has been noted. And, even worse, young people showed an increased interest in non-commercial, zoological and even philosophical topics. As a rule excited readers can be successfully calmed down by means of scholarly biology lectures, e.g. featuring the properties of allium cepa or the difference between mitosis and meiosis. Please note that it might be unwise to mention tardigrades in presence of those biology teachers who have never heard of them. We do not want to be held responsible for nervous breakdowns or any other possible consequences that might be caused by tardigrade abuse.
On Carnivalia
A number of carnivals have appeared over the last couple of weeks:
Linnaeus' Legacy #6 is up at From Archaea to Zeaxanthol, as is Circus of the Spineless.
Carnival of the Blue is up at Zooillogix.
The Boneyard, lucky # 13, is up at Greg Laden's Blog.
Enjoy!
Linnaeus' Legacy #6 is up at From Archaea to Zeaxanthol, as is Circus of the Spineless.
Carnival of the Blue is up at Zooillogix.
The Boneyard, lucky # 13, is up at Greg Laden's Blog.
Enjoy!
Banana-eating Birds that don't eat bananas
This week's highlight taxon is the Musophagidae, a uniquely African family of birds that contains the turacos (or should that be "turacoes"?), also spelt "touracos". Turacos are about 20 species of medium-sized frugivorous (fruit-eating) birds. The name of the type genus, Musophaga, means "plantain eater", which is also used as the vernacular name for some of the largest species, though it seems that they rarely, if ever, actually eat plantains (plantains, for those not in the know, are bananas eaten baked when they are still fairly green and contain more starch). Figs seem to a much more favoured food. Rutgers & Norris (1972) mentions them also feeding on leaves, insects and occassionally even meat, though it is unclear whether turacos actually eat the latter in the wild.
Turacos are best known for their brilliant coloration, and not without reason. The red turacin and the green turacoverdin are unique among bird pigments in being metal-bearing porphyrins, the same class of compounds as the heme found in haemoglobin, though the turaco pigments contain copper rather than iron. Turacin is unique to turacos, while there is evidence that turacoverdin (or a very similar compound) is also found in the jacana (Jacana spinosa), the blood pheasant (Ithaginis cruentata) and the roulroul (Rollolus roulroul), a species of partridge (Dyck, 1992). Turacoverdin (and the pigments in the latter three species, if they are distinct) is also notable as the only truly green pigment known from any bird. Green coloration in other birds is the result of structural coloration (from the crystalline structure of the feathers), or the combination of yellow pigment and blue structural coloration (Hill & McGraw, 2006). Rutgers and Norris (1972) mention a persistent belief that turacin is water-soluble, and actually washes out when the bird bathes. While this belief is untrue, turacin is soluble in more alkali solutions.
Turacin and turacoverdin are found in four of the six or seven genera of turacos. The genera Crinifer and Corythaixoides (together forming the subfamily Criniferinae) lack both pigments and are mostly grey. Species of Corythaixoides are also known as "go-away birds" after the sound of their calls. These two genera, as well as the great blue turaco (Corythaeola cristata) which is placed in its own subfamily, are referred to as the grey turacos. Corythaeola is also mostly grey, but does have small patches of turacin (the vent) and turacoverdin (a small breast-stripe). The remaining turacos, referred to as the turacin-bearing turacos, are included in the subfamily Musophaginae (Veron & Winney, 2000). Over half the species of turaco belong to the genus Tauraco, which are mostly a spectacular green. Tauraco, the purple-crested turaco (Gallirex porphyreolophus)* and the Ruwenzori turaco (Ruwenzorornis johnstoni) contain both turacin and turacoverdin (the latter two species may be included in the genus Musophaga). The remaining species of Musophaga in the strict sense lack turacoverdin and are a brilliant blue colour, with bright red crests coloured with turacin.
*Gallirex is a very neat genus name - it means "king of the chickens".
The relationships of the turacos to other birds have long been problematic. The most common position attributed to them has been as sister taxon to the cuckoos (Cuculidae), but other suggested relationships have been with the Galliformes or Opisthocomus (the hoatzin). The morphological analysis of Livezey and Zusi (2007) supported the traditional position, while the molecular analysis of Ericson et al. (2006) placed both Musophagidae and Cuculidae in a grade of largely terrestrial birds, also including the Grues (cranes and rails) and Otididae (bustards), sitting at the base of the mostly aquatic "higher waterbird" clade, but was unresolved to whether the two families formed a monophyletic group.
REFERENCES
Dyck, J. 1992. Reflectance spectra of plumage areas colored by green feather pigments. The Auk 109 (2): 293-301.
Ericson, P. G. P., C. L. Anderson, T. Britton, A. Elzanowski, U. S. Johansson, M. Källersjö, J. I. Ohlson, T. J. Parsons, D. Zuccon & G. Mayr. 2006. Diversification of Neoaves: integration of molecular sequence data and fossils. Biology Letters 2 (4): 543-547.
Hill, G. E., & K. J. McGraw. 2006. Bird Coloration. Harvard University Press.
Livezey, B. C., & R. L. Zusi. 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society 149 (1): 1-95.
Rutgers, A., & K. A. Norris (eds.) 1972. Encyclopaedia of Aviculture vol. 2. Blanford Press: London.
Veron, G., & B. J. Winney. 2000. Phylogenetic relationships within the turacos (Musophagidae). Ibis 142 (3): 446-456.
An Endangered Herbarium
A message that came through yesterday on the TAXACOM mailling list informs us that the University Board of Utrecht University in the Netherlands has announced plans to close the university herbarium as of the 1st of June, with access to the collections by researchers to cease immediately as of that date.
The Utrecht Herbarium holds a collection of over 800,000 specimens, including more than 10,000 type specimens. The central focus of research at the university is on plant biodiversity in tropical South America, particularly Suriname. Among the current research projects is investigation of the taxonomic identity of medicinal plants used in Suriname, information that will be vital in developing wider applications of the species involved.
The Utrecht Herbarium is part of the Nationaal Herbarium Nederland, which also includes branches at the Universiteit Leiden and the Wageningen University, and would have also been an significant part of the integrated Netherlands Centre for Biodiversity currently being developed. There are currently four PhD students among the staff at the herbarium.
For more information on the significance of the Utrecht Herbarium, and a petition against its closure and, go here. The website of the Utrecht Herbarium is here, and that of the Nationaal Herbarium Nederland is here. Other blog reactions to the closure can be found at Myrmecos and The Other 95%. I will endeavour to keep you all abreast of further developments.
The Utrecht Herbarium holds a collection of over 800,000 specimens, including more than 10,000 type specimens. The central focus of research at the university is on plant biodiversity in tropical South America, particularly Suriname. Among the current research projects is investigation of the taxonomic identity of medicinal plants used in Suriname, information that will be vital in developing wider applications of the species involved.
The Utrecht Herbarium is part of the Nationaal Herbarium Nederland, which also includes branches at the Universiteit Leiden and the Wageningen University, and would have also been an significant part of the integrated Netherlands Centre for Biodiversity currently being developed. There are currently four PhD students among the staff at the herbarium.
For more information on the significance of the Utrecht Herbarium, and a petition against its closure and, go here. The website of the Utrecht Herbarium is here, and that of the Nationaal Herbarium Nederland is here. Other blog reactions to the closure can be found at Myrmecos and The Other 95%. I will endeavour to keep you all abreast of further developments.
Giants of the Silurian
Compared to life in the water, life on land got off to a decidedly slow start. The seas had been swarming with life for hundreds of millions of years before the first tentative colonisation of the previously barren continents by small algae and plants in the Ordovician about 470 million years ago. Even then, it wasn't until about the middle part of the Silurian, about 430 million years ago (give or take) that the first vascular plants and anything bigger than a moss put in an appearance. These early plants were still small by modern standards - one of the larger forms, Cooksonia, was practically a giant at heights of nearly a metre. The first really large land organism made its imposing appearance in the late Silurian.
Reaching heights of up to eight metres, Prototaxites would have loomed over anything else around at the time - something that is made pretty clear in the reconstruction above from Hueber (2001) (obtained via Hans Steur's palaeobotany page, which has a far better analysis of Prototaxites than I'm about to give you). Prototaxites is known from fossils reminiscent of the trunk of a tree, and was originally described as such in 1859. However, the internal structure of Prototaxites is very different from that of any tree. Rather than the vascular cells of a tree, Prototaxites is composed of long filamentous tubes - large unbranched tubes that probably supplied structural support, and much smaller multi-branched tubes that ran among and around the skeletal filaments and probably held the structure together. This structure was compared to the filamentous structure of a number of modern algae, and for many years Prototaxites was considered a giant alga, probably related to the modern brown algae.
However, all known algae are aquatic, while Prototaxites was found in association with terrestrial organisms and was undoubtedly terrestrial itself. In cross-section Prototaxites also lacks the orderliness of structure found in brown algae, with filaments arranged randomly in the trunk with no clear division between pith and cortex. Hueber (2001) therefore made the suggestion that instead of being an alga, Prototaxites might be a gigantic fungus. He compared it to the living perennial bracket fungi, which have a rigid structure and can also reach notable sizes (up to a metre in diameter) through cumulative growth over many years.
The main barrier to accepting Prototaxites as a fungus lies in the size of the filaments (which would then be hyphae). The skeletal filaments reach a diameter of up to 50μm while modern fungi will rarely be more than 10μm. The other major issue, of course, is its size overall. Where did such a large saprobic fungus gain its nutrients from? Despite the plausability of Hueber's (2001) model of perennial growth, and his comparison with the gigantic size attained by hyphal masses in other modern fungi such as a specimen of Armillaria bulbosa covering an area of 15ha, Selosse (2002) pointed out that the modern taxa live in an environment with a much larger overall biomass. A purely saprobic Prototaxites would have required far more nutrition than could be supplied by the meagre vegetation of the Silurian. Selosse (2002) therefore suggested that, rather than being purely fungal, Prototaxites might have been a photosynthetic lichen-like symbiosis. The large skeletal filaments, he suggested, might still represent an algal form, contained and protected by the surrounding fungal hyphae. The idea of an eight-metre-tall lichen is still pretty amazing, but not incredible when we consider that there would have been relatively little competition in the Silurian compared to the modern environment. Prototaxites may have been a slow and inefficient grower, but there was little to exclude it. Hueber (2001) identified supposed reproductive structures on Prototaxites that he held indicated a position for it among the basidiomycetes, which include the bracket fungi. However, as pointed out by Selosse (2002), the reproductive nature of these structures is unconvincing.
No convincing evidence has been found for branching in Prototaxites. Many authors interpreting Prototaxites as a plant or alga have suggested that the flattened fossil Nematothallus found in the same deposits, which also has a filamentous structure, might represent leaves or leaf-like appendages of Prototaxites. However, the two have never been found directly attached. Graham et al. (2004) noted a similarity between Nematothallus and semi-decayed modern liverworts, and suggested that Nematothallus might belong to the latter group.
Prototaxites was around for about 50 million years, a quite impressive amount of time, but it eventually became extinct during the Devonian. Perhaps as the terrestrial environment increased in complexity, the window of low competition that Prototaxites had occupied closed. More efficient plants supplanted Prototaxites, while increased numbers of herbivores may have eaten down growing hyphae faster than the organism could regrow them. Prototaxites' time had come to a close.
REFERENCES
Graham, L. E., L. W. Wilcox, M. E. Cook & P. G. Gensel. 2004. Resistant tissues of modern marchantioid liverworts resemble enigmatic Early Paleozoic microfossils. Proceedings of the National Academy of Sciences of the USA 101 (30): 11025-11029.
Hueber, F. M. 2001. Rotted wood–alga–fungus: the history and life of Prototaxites Dawson 1859. Review of Palaeobotany and Palynology 116 (1-2): 123-158.
Selosse, M.-A. 2002. Prototaxites: a 400 myr old giant fossil, a saprophytic holobasidiomycete, or a lichen? Mycological Research 106 (6): 642-644.
Your Little Friends that are With You Always
At all times, you are surrounded by life. Micro-organisms swarm on your skin, swim in your gut, and set up shop in your organs. Indeed, at any one time, there are considerably more microbial cells around your person than there even are of your own cells. The micro-organisms are not living on you - you are living among the micro-organisms.
They're not all bacteria, either. I just thought that I'd briefly introduce you to one of the more distinctive micro-organisms that you are almost certainly carrying about with you - the follicle mite. I also challenge you to keep from scratching yourself while reading this.
Demodex, the follicle mite, is a specialised inhabitant of the follicles and pores of mammalian skin. A significant number of species appear to have been described from different hosts, ranging from humans to dogs to cattle to marsupial mice to honest-to-goodness mice. The most distinctive feature of Demodex is its elongate body shape, which allows it to live head-first inside the follicles of its host, feeding on cells within the follicle. Humans are actually inhabited by two species, Demodex folliculorum and D. brevis (Desch & Nutting, 1972). The more elongate D. folliculorum lives in the follicles themselves, and feeds on the epithelial lining. The rarer D. brevis is shorter, and is found within the sebaceous gland on which it feeds. Demodex brevis is found on less people, and also at lower numbers - multiple D. folliculorum may be found in a single follicle (as shown below in an image from here), but usually only one D. brevis.
The question of whether Demodex causes any harm to its human host is a difficult one. The sheer universality of Demodex within the human population implies that its presence is usually of no concern to the host. However, another species, D. canis, is widely connected with mange in dogs, and Demodex has been connected with skin disorders (demodicidosis) in a number of humans. The difficult question is whether Demodex is a direct causative agent or not. As one might reasonably expect Demodex to be present anyway, it's mere presence at an infection site does not automatically indicate its responsibility for the infection. It seems likely that Demodex may be a facultative agitator of problems arising from other ultimate causes, such as a suppressed immune system (Jansen et al., 2001) or an already-damaged follicle (Pena & Andrade Filho, 2000). It is noteworthy in this light that prevalence of demodicidosis varies seasonally (it is most common in spring), but the prevalence of Demodex itself does not (Desch & Nutting, 1972). Demodex folliculorum may cause damage when more than six individuals are present in the same follicle (Desch & Nutting, 1972).
REFERENCES
Desch, C., & W. B. Nutting. 1972. Demodex folliculorum (Simon) and D. brevis Akbulatova of man: redescription and reevaluation. Journal of Parasitology 58 (1): 169-177.
Jansen, T., U. Kastner, A. Kreuter & P. Altmeyer. 2001. Rosacea-like demodicidosis associated with acquired immunodeficiency syndrome. British Journal of Dermatology 144 (1): 139–142.
Pena, G. P., & J. de S. Andrade Filho. 2000. Is Demodex really non-pathogenic? Revista do Instituto de Medicina Tropical de São Paulo 42 (3): 171-173.
Horns and Guts
This week's feature taxon will, I'm sure, be familiar to most of you. Even kids in the depths of urbania will usually learn at some stage that cows say "moo" and sheep say "baa". Today's subjects are the Ruminantia, the primary group of large herbivorous mammals on the planet today. Including such animals as sheep, cattle, goats and deer, ruminants are also one of the most significant groups of animals in modern human lifestyles.
Modern ruminants fall into six families. The vast majority of modern ruminant diversity is contained within two of those families, the Cervidae (deer - 16 genera) and Bovidae (cattle, goats, antelope, etc. - 48 genera), particularly the latter. The Tragulidae (chevrotains or mouse deer) are two or three genera of small inhabitants of Old World tropical forests. The Giraffidae includes just two genera - the giraffe (Giraffa) and okapi (Okapia johnstoni). Finally, two genera are assigned families of their own - the pronghorn (Antilocapra americana) and the musk deer (Moschus). Fossil-wise, there are a whole host of extinct families, mostly of small deer-like animals, and some of the smaller living families - notably the Giraffidae and Antilocapridae - were much more diverse in the past than they are now.
Ruminants are best-known for their impressive digestive systems, which are regarded as the secret of their current success. Most other mammals living mostly on low-grade plant matter (i.e. browsers and grazers) are what are called "hindgut fermenters" - the beginning of the large intestine forms a large chamber where bacteria break down the cell walls of the plants eaten, releasing the nutrients that would otherwise be locked within into the digestive system. Hindgut fermentation is a fairly simple system, but the problem is that it is relatively inefficient. By the time the plant matter has reached the large intestine, it has already passed through most of the digestive system, leaving only a relatively short distance in which the released nutrients can be absorbed. Most hindgut fermenters compensate for this inefficiency by being very large, their concordantly large guts allowing more time for digestion*. A good example of this can be seen in the gorilla (Gorilla sp.), a specialised folivore (leaf-eater) that is considerably larger than its close non-hindgut-fermenting relatives.
*One exception to this pattern is the Leporidae (hares and rabbits), which have a different method of getting around the limitations of hindgut fermentation - they eat their own faeces, so passing their food through the digestive system twice.
Ruminants, in contrast, are foregut fermenters. In ruminants it is not the large intestine but the stomach that has become enlarged and subdivided to contain fermentative bacteria (the so-called "four stomachs" of cattle - Janis & Jarman, 1984a). Ruminants also complement the digestive process by regurgitating and further chewing their food ("cud-chewing") when not directly grazing. Because the plant cell walls are broken down before passing through the majority of the digestive system, ruminants are able to derive far more nutrients from their food than hindgut fermenters. They are also able to subsist on feed on lower quality, which lead to their taking over as the dominant grazers when the climate cooled and grasslands spread during the Miocene.
Phylogenetically, it is well-established that the Tragulidae are the basalmost of the living ruminant families, the remainder forming a clade called the Pecora. Chevrotains have a less-developed rumination system than other ruminants - while they have four stomach chambers as in other ruminants, the third chamber is poorly developed. Within Pecora, relationships are more controversial. While it seems that Cervidae, Moschus and Bovidae form a clade to the exclusion of Giraffidae and Antilocapra, it is unclear whether the latter two taxa form a sister clade to the other pecorans, or a paraphyletic series. It also has recently been suggested that Moschus may be sister to Bovidae, in contrast to its traditional position closer to the Cervidae (Hassanin & Douzery, 2003). Were one to broaden the investigation to cover the various extinct taxa, the situation just degrades to a hopeless mess.
Part of the reason for this confusion is that homoplasy seems to be rife within the ruminants. The most intriguing feature of the group for me is the repeated evolution of horns or antlers (technically, cranial appendages). Four of the five living pecoran families have some form of cranial appendage, and indications are that they have arisen independently in each family. This is reflected in the different structure of the appendages in each family (Janis & Jarman, 1984). Bovids have permanent horns of bone covered with a layer of keratin. In Cervidae, the antlers are deciduous bone, and are shed and regrown annually. Giraffids have ossicones of permanent bone covered with a layer of skin. The horns of Antilocapra are permanent bone as in Bovidae, but the outer layer of keratin is shed annually. The Tragulidae and Moschus, which lack horns, both have enlarged canines (the above photo of a musk deer by Ben Cooper shows just how enlarged). Enlarged canines are also found in the deer genera Hydropotes (the Chinese water deer) and Elaphodus (the tufted deer), which have small antlers (Elaphodus) or lack them altogether (Hydropotes). There seems to be a rough inverse relationship between enlarged canines and cranial appendages, where the development of the latter is generally (though not invariably) correlated with the loss of the former. Interestingly, recent phylogenetic analyses indicate that Hydropotes is actually nested among antlered deer, indicating that it regained enlarged canines as the antlers were lost (Gilbert et al., 2006).
Again, when the extinct taxa are factored in, the picture becomes even more complicated. For instance, the Climacoceratidae are an extinct family that dental features indicate is related to the Giraffidae, and which had ossicones similar in structure to those of the giraffids (albeit long and branched in some forms, so similar in appearance to a deer's antlers). However, the basal members of the Climacoceratidae lack ossicones, indicating that they were evolved independently in the two families (Morales et al., 1999). The most dramatic armament among fossil ruminants was perhaps that found on the Mediterranean endemic Hoplitomeryx, found in the Miocene on what is now Monte Gargano on the eastern coast of Italy, but was then a separate island (Hassanin & Douzery, 2003). Hoplitomeryx, as shown in a reconstruction above from Scontrone, had a grand total of five horns on its head, as well as long dagger-like canines (providing an exception to the horns vs. canines rule mentioned above). It has been suggested that the overdone armation of Hoplitomeryx may have evolved as a defense against the large birds of prey that would have been its major (indeed, its only) predators on Gargano.
REFERENCES
Gilbert, C., A. Ropiquet & A. Hassanin. 2006. Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography. Molecular Phylogenetics and Evolution 40 (1): 101-117.
Hassanin, A., & E. J. P. Douzery. 2003. Molecular and morphological phylogenies of Ruminantia and the alternative position of the Moschidae. Systematic Biology 52 (2): 206-228.
Janis, C., & P. J. Jarman. 1984a. The hoofed mammals. In All the World’s Animals: Hoofed Mammals (D. Macdonald, ed.) pp. 28-39. Torstar Books: New York.
Janis, C., & P. J. Jarman. 1984b. Even-toed ungulates. In All the World’s Animals: Hoofed Mammals (D. Macdonald, ed.) pp. 58-59. Torstar Books: New York.
Morales, J., D. Soria & M. Pickford. 1999. New stem giraffoid ruminants from the early and middle Miocene of Namibia. Geodiversitas 21 (2): 229-253.
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