How periodic cicadas evolved their timing

Every few years, the periodic cicadas come into the news, when they simultaneously complete their life cycles and emerge from the ground as winged adults. They swarm over large parts of the eastern United States and attract both curiosity and alarm from residents and the media. After a few weeks, their mating and egg-laying over, they disappear just as quickly as they appeared. Of course, they are not completely gone: their juveniles live underground, having perhaps the longest maturation of any insect, to emerge as adults after a period of 13 or 17 years.

13-year cicada from Brood XIX. Via Wikimedia Commons.

Why 13 or 17 years? These prime-numbered periods have puzzled more mathematically-minded biologists for ages, with one suggestion being that a prime-numbered life cycle would minimize the number of predator life cycles that could synchronize with it (because a prime number has no factors but itself). But how did this situation evolve?

A new paper published in PNAS (open access) from a group of Japanese scientists looks at the phylogeny and population genetics of the known species of periodic cicadas. The periodic cicadas fall within the genus Magicicada, within which are species partly defined by the length of their period. M. tredecim for example is a 13-year species, while M. septendecim is a 17-year species. Within each species there are also multiple "broods", representing different cohorts have the same emergence and mating cycles. One brood may encompass multiple species. Siva blogged here about one such brood in 2004, the ominously-named Brood X, which had an unusually large emergence (the "X" is actually just a roman numeral). The different species fall within three species groups, each with both 13- and 17-year species.

Contrary to expectations, the old species, defined by morphology and period, do not correspond to the evolutionary history as uncovered by molecular phylogeny and haplotyping. The three big species groups are still supported, representing two evolutionary splits at about 3.9 and 2.5 million years ago (Mya). The splits within the species groups, however, are relatively recent, mostly less than 0.5 Mya. Furthermore, the splits correspond more to geographical regions than to life cycle period. The split between 13- and 17-year periods have also evolved multiple times. To quote from the paper:

Our results are broadly consistent with the previous idea that an ancestor of all Magicicada diverged into three species allopatrically, and later, the three became sympatric and each species independently diverged into 13- and 17-y cicadas. Surprisingly, however, the divergence of 13- and 17-y cicadas was asynchronous among the species groups and occurred repeatedly even within a species group. This finding is all of the more interesting given that each species group shows similar eastern, middle, and western phylogeographic divisions similar to post-Pleistocene patterns observed in other North American taxa, suggesting that the three Magicicacda groups shared multiple refugia during the last glacial maximum.

This is a nice surprise, and as the authors point out, the repeated switching between 13- and 17-year forms suggests that there is a single genetic "switch" involved, because it is unlikely that a complex mechanism could be repeatedly gained and lost in such a manner.

Backyard Naturalists

There's a great article on the BBC website about amateur naturalists who discover new species in their spare time. One would think that the flora and fauna of Europe has been largely cataloged, but new species are still being discovered there, mostly by people who pursue natural history as a hobby.

Much of this new biodiversity is small, especially insects and other invertebrates:

New species are sometimes hiding in plain sight - a new species of wasp was recently discovered by a technician in a car park by his office in Spain. And not long ago, a retired man in Wales came across a new type of slug in his back garden.

The article links to a recent (2012) study published in PLoS ONE, which found that 60% of new species from Europe were described by non-professional taxonomists. As professional expertise in taxonomy moves from the West to emerging economies like those of Latin America and Asia, perhaps this could be a new model for how the study of biodiversity could be kept alive in those regions.

Taxonomists are not going extinct

When talking to people studying biodiversity, one often hears that "taxonomists are a dying breed", an opinion that has been expressed on this blog before.

A newly-published meta-analysis looks at whether science can realistically finish cataloging all the world's biological species before they go extinct:

"Some people despair that most species will go extinct before they are discovered. However, such worries result from overestimates of how many species may exist, beliefs that the expertise to describe species is decreasing, and alarmist estimates of extinction rates. We argue that the number of species on Earth today is 5 ± 3 million, of which 1.5 million are named. New databases show that there are more taxonomists describing species than ever before, and their number is increasing faster than the rate of species description. Conservation efforts and species survival in secondary habitats are at least delaying extinctions. Extinction rates are, however, poorly quantified, ranging from 0.01 to 1% (at most 5%) per decade. We propose practical actions to improve taxonomic productivity and associated understanding and conservation of biodiversity."

They found that it's not true that taxonomists are a dying breed, but that the profession is undergoing a geographical shift from Western countries where modern taxonomy and big museum collections were first developed, to South America and Asia-Pacific countries. They argue that this is a good development because those are the countries where much of the world's biodiversity actually lies.

The number of active taxonomists was estimated by looking at databases to find out who is publishing new species descriptions. It's also not true that the current generation of taxonomists are mostly "one-hit wonders" who only describe one or two new species in their careers; there is not much difference between the previous and current generations of taxonomists in their productivity.

If we want to catalog all the world's biodiversity, declining lack of expertise is then not the problem. What's problematic is that even as we are still in a state of ignorance about the world's biodiversity, species are going extinct at a steady rate due to human activity. We are also victims of our own success: as more and more species have been described, it becomes harder to find new ones among the existing known diversity. It's like being stuck at home for the weekend: after you've read most of the books and watched most of the movies in your house, it's harder to find something new to do (at least before the Internet...).

But what's the point of all this taxonomic toil? Why describe new species? The questions of "how many species on Earth?" and "what is the extinction rate?" are notoriously difficult to answer. Whereas we now have a fair guess at the answer to the first question, estimates of the extinction rate vary widely, reflecting the huge uncertainties involved. As the authors point out: "Taxonomists are not in danger of extinction. They are increasing in numbers and will become more in demand as more species mean more diagnostic challenges to discriminate species, whether they are pests, pathogens, food, ecological keystone, or endangered species." This highlights how knowledge of biodiversity is important, both for its own sake and for the sake of human interests.

Scientific turnover and the fate of old theory

The Arts and Sciences are often seen as non-overlapping complements, as naturally opposed as North and South, or the two sexes male and female. It's therefore surprising to find someone who can make a significant career in both, not just as an amateur but as a paid professional.

Vladimir Nabokov is best known as the author of the novel Lolita, but before becoming famous for his writing in English, he was a professional lepidopterist, an expert on a group of butterflies known as the Blues. An earlier blog post here highlighted some recent research on "his" group of butterflies.

His two careers were also the subject of an essay by Stephen Jay Gould. Gould used Nabokov's example to examine our attitudes to "genius". If Nabokov was a genius in literature, does it follow that his scientific work was also illuminated by the same genius? Was his scientific writing especially fluent or literary, as some literary critics claim? Gould found that, in the opinion of other professional lepidopterists, Nabokov's scientific work was competent and painstaking, but not especially pathbreaking or profound. Nor was his scientific writing unusually poetic or stylistically striking, in the way that his novels were.

In fact, Gould goes as far as to characterize Nabokov as being somewhat of a "stick in the mud." At the time when he was engaged in his butterfly work full-time at the Museum of Comparative Zoology at Harvard, from 1942 to 1948, a revolution was underway in taxonomy. Where previously the morphological characters, such as wing coloration or genital anatomy (a serious preoccupation of much of entomology!) were the means by which new species were defined, the budding science of cytology (the study of cells) had introduced chromosomes as yet another important character. "Cryptic" species with identical morphology were now being defined on the basis of their differing karyotypes (the number and appearance of the chromosomes). Nabokov rejected the use of chromosomes for defining new species, perhaps as a matter of practicality: pinned butterfly specimens in museums only preserve the morphology, so it would be impossible to distinguish karyotype variants in the museum cabinet.

His autobiography, however, seems to belie this depiction of Nabokov as a rigid conservative. Nabokov spoke about "great upheavals... taking place in the development of systematics." The year that Nabokov started working in the Museum was also the year that Ernst Mayr, by then also an emigre to the United States, published his Systematics and the Origin of Species, the book which established the biological species concept, that species (at least for sexual macroorganisms like birds and insects) are defined by their potential for breeding to produce viable offspring. The new emerging school of taxonomy represented by Mayr were strong champions of geographic variation. Species were not immutable, platonic ideals. The variation represented by geographic "races" or subspecies was just as important as the original "type" of a species. Conceptually, this so-called Neo-Darwinian revolution was when darwinism finally became orthodoxy in taxonomy, the field that had inspired it, nearly a century after the publication of the Origin of Species.

Nabokov was aware of this theoretical revolution - how could he have ignored it? This was a tremendous change from the lepidoptery of his youth, which could well be said to be truly "butterfly collecting". As he observed:

"Since the middle of the [19th] century, Continental lepidopterology had been, on the whole, a simple and stable affair, smoothly run by the Germans. Its high priest, Dr. Staudinger, was also the head of the largest firm of insect dealers. Even now, half a century after his death, German lepidopterists have not quite managed to shake off the hypnotic spell occasioned by his authority. He was still alive when his school began to lose ground as a scientific force in the world. While he and his followers stuck to specific and generic names sanctioned by long usage and were content to classify butterflies by characters visible to the naked eye, English-speaking authors were introducing nomenclaturial changes as a result of a strict application of the law of priority and taxonomic changes based on the microscopic study of organs. The Germans did their best to ignore the new trends and continued to cherish the philately-like side of entomology. Their solicitude for the "average collector who should not be made to dissect" is comparable to the way nervous publishers of popular novels pamper the "average reader"--who should not be made to think. 

"There was another more general change, which coincided with my ardent adolescent interest in butterflies and moths. The Victorian and Staudingerian kind of species, hermetic and homogeneous, with sundry (alpine, polar, insular, etc.) "varieties" affixed to it from the outside, as it were, like incidental appendages, was replaced by a new multiform and fluid kind of species, organically consisting of geographical races or subspecies. The evolutionary aspects of the case were thus brought out more clearly, by means of more flexible methods of classification, and further links between butterflies and the central problems of nature were provided by biological investigations."  

(Speak, Memory: An Autobiography Revisited, pp.122-123)

So it wasn't that Nabokov was a conservative who didn't like change. He had already spanned the era between "hobbyist" and scientific entomology. He was already witness to a revolution (in science, and also in his homeland of Russia). There's a quip I've heard attributed to the physicist Max Planck, that science doesn't progress because people come to accept new theories on the strength of their evidence; it progresses because old scientists who believe the old theories die out. It's certainly an exaggeration, but we are equally certainly products of our education. Every generation in science has its own revolution of understanding, and maybe it's unfair to expect someone to accommodate a second one, just as he or she was getting comfortable with the first!

Battle of the species hunters

Scientists are not the only ones who are hunting for new species. Animal and plant collectors too, searching for new exotic species to add to their collections, pose a threat to the survival of newly-described species. They monitor the scientific literature for new species descriptions, which essentially tell them exactly where to pick up the loot and what it looks like!

That at least is the message of a new podcast from the BBC documentary series One Planet, titled "The New Species Dilemma" (mp3 download). New podcasts are available for 30 days after broadcast.

In some cases, though, scientists are aware of this problem. When the famous Wollemi Pine (which even has its own official website) was discovered in Australia, its location was not made publicly known, and I think that still is the case to this day.

At the same time, proper scientific description requires full documentation, and that includes geographical data. It's an unexpected problem, and I don't think something that most taxonomists have to think about. But if you're working on a particularly "charismatic" group of organisms (and standards for "charisma" vary; some people collect exotic frogs, for instance) it might be something worth giving some thought to!

How many species - why do we care?

How many species are there on Earth? This is one of those simple questions that rapidly unravel when you try to pin down an answer. Despite over 250 years of the Linnaean system being available as a "filing cabinet" for humanity's systematic exploration of life on Earth, the answer is still not clear.

That we lack an answer is far from astonishing - there's plenty of Earth (and plenty of Ocean) to explore. Taxonomists still argue about what exactly is a species and how to recognize one when you see it.

A paper just published in PLoS Biology by Camilo Mora and colleagues has put forward the figure of 8.7 million species. This has been widely reported in the mainstream press (BBC, The Guardian, Today Online), though most omit mentioning that this figure has a generous margin, a standard error of +/- 1.3 million.

What I'm intrigued by is why there is so much attention being paid to this piece of news. After all, estimating the total species count of the planet is not a new endeavour.

Immigration and invasion - biological xenophobia?

One of the hottest political topics in Singapore today is the issue of immigration: your 'foreign talent' may be my 'job-stealer', as the debate continues on just how much immigration is desirable for a small country like ours.

In the field of biological conservation, a similar conflict has popped up, as reported recently in the Boston Globe. Conservationists have traditionally spoken of 'introduced' vs. 'native' species, with the least desirable introduced species being termed 'invasive'. But a number of vocal critics have spoken up to say that this is simply nativism - an unthinking bias in favour of the supposedly native. They contend that the division between native and non-native is arbitrary and unscientific, in part because many familiar species were originally imports from elsewhere, and also because the environment is constantly changing, and species are continually migrating, and to try to freeze a community in time is akin to gardening nature. The author Michael Pollan went as far as to say that species-nativism was "xenophobic".

Classical examples of species invasions include the rabbit and cane toad in Australia, and the European starling in the USA (for which Shakespeare, bizarrely enough, is to blame). In Singapore, Clidemia hirta or Koster's Curse (a native of the Americas) has a tenacious foothold on forest fringes and clearings, preventing the re-establishment of native vegetation.

However, much of our modern landscape is precisely the product of introduced species. The grand arching wayside tree canopies that provide shade and shelter are often rain trees, Samanea saman, which are native to Brazil. These are perhaps the 'foreign talent' side of the argument.

We justifiably take pride in our native species, and among the popular Science Centre guidebook series is a volume on cultivating native plant species. But for an island as small as Singapore, does it make sense to speak of 'native' species? What hope is there of eradicating non-native species, anyway?

Ultimately, it may simply be a matter of rhetoric. The disagreement is not over the substance of the matter but the language that we use to talk about it. As the Globe article says:

Just as most ecologists accept that only a fraction of non-native species are harmful, the anti-nativists, when pressed, will admit that unequivocally destructive species like the Asian longhorned beetle should be reined in. Their disagreement lies more in how we should talk about the issue, how we justify our interventions and how we label the species we want to eradicate.

That is to say: when we call a species an 'invasive species', it's not enough simply to say that it's non-native and hence must be eradicated for that reason alone. We must be clearer about what 'invasiveness' means, and be able to justify our assertions about their harmfulness and undesirability.

End of a botanical tradition

Botanical Latin is a curious creature, with a grammar and vocabulary very different from classical or medieval Latin. It dates back to the traditional use of Latin in scientific and scholarly works as the common language of learning in multi-lingual Europe. In modern times, it has been restricted to the formal description, called a 'diagnosis', of a newly-published plant species.

As Latin grew less important to general education, however, botanists have had to seek help from other quarters in writing these diagnoses, but because of the independent evolution of botanical Latin for its special purposes:

... when a botanical author thanks a professor of classics for providing a Latin description, this is usually in bad or at any rate unconventional botanical Latin... (W.T. Stearn, Botanical Latin, viii.)

The use of Latin was codified in the International Code of Botanical Nomenclature - a set of rules for keeping the profusion of scientific names in order. It was preserved for both tradition's sake and also because taxonomists have usually argued that a common language is needed to keep communication possible amidst a profusion of vernacular languages. The parallel Zoological Code, however, did away with Latin descriptions a long time ago.

New editions of the Code are voted upon at meetings of the International Botanical Congress, and at the latest meeting in Melbourne, Australia, this tradition of botanical Latin may have met its demise (Nature news and editorial). Attendees have voted for several amendments to the code (full list of proposals here), including dropping the requirement for botanical Latin in new descriptions, and allowing the publication of new species names in electronic journals. The full congress will have to ratify these amendments before they become permanent.

The demise of botanical Latin might have been just a matter of time, but the issue of electronic publication is a relatively new one. Electronic-only journals have been proliferating, but for taxonomy, which is concerned with permanence and record-keeping rather than rapid communication of information, they have distinct disadvantages. There is no guarantee that a server crash or corrupted computer file may not wipe out a species description forever, resulting in a book-keeping nightmare when species names have to be revised or updated. The zoological Code, for example, still requires that a number of hard paper copies be sent to libraries around the world as an insurance against that possibility. This is what the Raffles Bulletin of Zoology, which is published in Singapore as an online journal, does to fulfill the requirements of the code.

So does this mean that William T Stearn's classic reference book, Botanical Latin, will become obsolete immediately? Not necessarily. A big fraction of the historical botanical literature, especially the earliest works from the time of Linnaeus onwards, are written exclusively in Latin and no translations exist for them. We also owe much of our technical nomenclature to Latin and Greek. Botanical Latin may be newly dead, but it still lives on.

Spellchecker to Weed Out Botanical Typos [Updated]

[Update 17/6/11]
Following the comments by araygoza to this article (see below), I ran my list of misspelled plant names through the TNRS spellchecker and voila! it works!

That's really cool! The new URL is here.

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Scientific nomenclature - the business of giving names to organisms - is a huge book-keeping exercise that is notoriously error-prone. Not only may one species be given multiple binomials, as scientists argue whether it should be classified one way or another, but misspellings and typos are easy to make.

Typos directly affect scientific research, which often relies on analyzing data from species databases. For example, a simple count of how many species are present in a certain place may be inflated because some name records have been misspelled. For botanists, there is now a possible solution available online. A team from several institutions has launched the Taxonomic Name Resolution Service, which uses technology similar to spell-checking software to detect erroneous names and suggest corrections.

I decided to give the system a try (click on "Try it now!" on the main page), using the names of four common plants with single-letter misspellings, listed below:

• Cocos nuciferra
• Samana saman 
• Pterocarpus indicum
• Ficus grossulariodes

The results showed that these names were not found in the database, but it couldn't suggest any possible matches, which was a disappointment. Just in case they weren't actually in the database (it's based on TROPICOS, which focuses on plants from the Americas), I ran the correctly-spelled names through the checker and got a 100% match on each one.

From this small trial, which admittedly is not very thorough, I would say that the fuzzy-logic system for suggesting correct names is not really effective right now. However, the batch-check function is useful if one has a large database of records to sort through for validity. They have posted their source code and also are developing an API (application programming interface) for the service, so developers (or botanists with some computing savvy) can readily plug in their own systems.

(Via Nature News.)

Latest named cat species actually two subspecies

The Sunda clouded leopard (Neofelis diardi) was recognized as a distinct species, separate from the mainland Southeast Asian clouded leopard N. nebulosa, in 2008. Both are Vulnerable species, according to the IUCN.

Based on molecular genetic data, researchers suspected that the Sunda clouded leopard might actually represent two different subspecies, and this has been confirmed by a combination of molecular genetics and skull/dental features. There may be additional differences in coat patterning, but the number of specimens available for inspection is not enough to make a definitive statement.

The two subspecies are geographically separated: the Sumatran subspecies (N. diardi diardi) and the Borneo subspecies (N. diardi borneensis). They were probably isolated from each other after Sundaland land bridges were cut off when sea levels rose after the last ice age.

The BBC has a good summary article including a rare video of the animal from Dermakot National Park in Sabah, Borneo.

History of Amazon Basin Shaped by Andes

Here's something that has relevance to the name of this blog. The traditional model for the history of Amazonian biodiversity held that much of it weathered the Pleistocene period in forest fragments, or refugia, and from there spread out again to repopulate the basin when the climate again became amenable. These so-called diversity centers, however, have been shown to be artifacts of sampling, rather than a real biotic phenomenon, pushing back the origins of diversity in the Amazon to earlier periods of geological history.

Amazonia today. From Hoorn et al. 2010 (Link)

A recent review in Science magazine synthesizes what is known about the geological and biological past of the Amazon, to reconstruct a scenario where the uplift of the Andes mountains, which are relatively young, is responsible in part for the present-day patterns of diversity in the basin. Prior to the Andes uplift (which began in the Paleogene after the end-Cretaceous 65 Mya, and continues to the present day), the geology of Amazonia was 'cratonic', i.e. it was dominated by the rocks of the continental center. The rising mountain range changed both the climate, e.g. by intensifying rainfall to the East of the range, and also the landscape, as sediment eroded off the mountain faces and came to be deposited in the basin below. Extensive, inland wetlands (the Pebas system) first appeared in correlation with intensified uplift and then disappeared, replaced by a riverine, fluvial landscape.

The present-day biota of the Amazon is very much terrestrial. Therefore, the disappearance of the extensive wetlands, which formerly fragmented the terrestrial forests, was a prerequisite for the appearance of modern Amazonian fauna and flora. Furthermore, diversity as measured today for both mammals and tree species is highest where the soils are of Andean origin (swept down by erosion and deposited by the rivers), as opposed to where the original cratonic soils remain at the surface. Perhaps the nutrient levels are linked to both forest productivity and resultant diversity, but the climate engendered by the topographic relief may also have a role in patterns of diversity.

This is very much a 'big picture' review, and is worth reading to think about how the literal shape of the Earth has a role in defining the life that dwells as a thin film on its surface.

Formosan Black Bears

Hwang Mei-hsiu (黃美秀), assistant professor at National Pingtung University of Science and Technology, Taiwan relates the challenges to study the ecology of Formosan Black Bears in a dialogue with President Ma Ying-jeou.

Prof Hwang describes the difficulties of studying the black bears in the remote mountains of Taiwan and rarities of sighting the illusive animals. She responded regretfully that she has no exact population figure despite 15 years of research. With initial estimates of about several hundred for the island, she added that the viable population figure should be 2,000. This reflects the endangered status of the bear in Taiwan

Watch the enchanting "making of" clip with Willy the Bear-tracking Dog. This canine is trained to search for bear droppings!

Note: clips in Chinese.

The Elephants' New Tree

Top (L to R): African Savannah Elephant, African Forest Elephant, Asian Elephant

Bottom (L to R): Woolly Mammoth, Mastodon

Source: Wikimedia Commons (click through for source pages)

African Elephants have big ears, Asian Elephants have small ears - that's how we usually learn to tell these two apart. The "African Elephant", though, actually comprises two species in the genus Loxodonta, the Savannah elephant (L. africana) and the Forest elephant (L. cyclotis). The Asian elephants are not as closely related as these two, and are in the genus Elephas. Whether the two species of African elephants are really distinct species, however, has been a subject of debate ever since they were first described by zoologists. New research, however, shows that they are indeed different species, and that this divergence is an ancient one. What's more, the Asian elephant is a closer relative to the woolly mammoth than it is to the extant African elephants!

A scientific team led by researchers from the Broad Institute at Cambridge, Massachusetts and the Max Planck Institute for Evolutionary Anthropology in Leipzig have used DNA from the three extant elephant species as well as ancient DNA from the Woolly Mammoth (Mammuthus) and the Mastodon (confusingly called Mammut) to reconstruct the Proboscoidean family tree. What's really novel about their methodology is that they have used tens of thousands of nucleotides of DNA sequence data, spanning several hundred loci (genes) on the nuclear genome of these elephants. Most phylogenetic studies (i.e. research that aims at reconstructing the genealogy of organisms) generally looks at only a handful of genes because large quantities of data are expensive (money-wise) to produce and computationally expensive to crunch through. They took advantage of the Broad Institute's expertise in next-generation pyrosequencing, where DNA is "sequenced by synthesis", based on technology that is fundamentally different from the decades-old Sanger sequencing technology that we learn about in school.


Their results are based on nuclear genes, but show a conflict with previous results obtained by analyzing the mitochondrial genome (mtDNA) of these elephants. mtDNA suggests instead that the African elephants share a relatively recent common ancestry, within the past half-million years or so. What could be happening is that mitochondrial and nuclear genomes are evolving under different circumstances, because the mitochondria are inherited only through the maternal line. The authors hypothesize that this difference is caused in part by the matriolcal behavior of elephants - matriarchal herds stay more or less in the same place, while waves of male migration spread out and fertilize herds elsewhere, displacing nuclear genes but not mitochondrial ones.


The value of ancient DNA is now well-recognized, and has entered the mainstream in science, where previously it tended to be viewed askance as a fringe endeavor more associated with science fiction than real science (think Jurassic Park). What I'd like to see this research group do in the future is to obtain sequences from a larger pool of animals. At present they have DNA sequences from only one or two individuals of each species. A larger data set would allow us to see how well-supported the nuclear-mtDNA divergence really is, and what degree of variation is present at the populational level for this species. As sequencing costs and computational costs go down, it will certainly be cheap enough, one day, to do large-scale population genetics at hundreds of loci. Also, it would have been valuable to see what tree topologies they would obtain using other tree-building methods, because neighbor-joining is known to produce branch lengths that are difficult to interpret, and information is lost when compressing data into distance metrics.

Highlights from BBC's Decade of Discovery

A new program, "Decade of Discovery", by the BBC showcases the 'greatest hits' from the past 10 years of natural history exploration, including the first live images of the barreleye fish (which can only look up and has a transparent dome over its head), the world's longest stick-insect, and more. Some video clips are available on the BBC's YouTube channel or from the TV program's webpage linked above, and the Guardian newspaper has a picture gallery of highlights if you're in a hurry.

Tuataras!

Natalie Angier, a science writer at the New York Times, has written a great feature article on the tuatara, a 'living fossil' that is the only remaining representative of its group, the sphenodontids. All other lizards and snakes are members of a group called the Squamata, which is distinct from the Sphenodontidae (see a reptile phylogeny at Tree of Life).

Some fun facts include their 'third eye' (the pineal eye), a primitive light-sensing organ in the center of their head which has been lost in most living reptiles, and their longevity - individuals in the wild may routinely reach 100 years or more, and continue to reproduce despite their advanced age.

Her article highlights research that shows how certain parts of the tuatara genome are evolving at a rapid rate, despite their apparent morphological 'stasis'. This questions our popular notion of what a 'living fossil' is - although they may appear to be quite similar to fossilized relatives from millions of years ago, we shouldn't forget that these organisms have had corresponding millions of years of evolution since that time, and so morphological stability may conceal other advanced specializations. It would be a mistake to think of these organisms as 'primitive' in the common sense of backward and inadequate.

Panthers and Leopards in the Malay Peninsula

The term 'panther' has a confusing history - it's been used to refer to any big, black (i.e. 'melanic') cat, usually the leopard in particular. Leopards and panthers used to be thought of as different species, but they are in fact merely different color variants, and this so-called melanic coat coloration is a recessive Mendelian trait. To complicate matters, the four big cats - leopards, tigers, lions, jaguars - have been grouped in the genus Panthera, based on the same etymological root.

In Southeast Asia, the leopard Panthera pardus exists in two color morphs: the usual spotted variety, and the melanic 'panthers'. However, a recent evaluation of camera-trap data could not find any spotted leopards South of the Isthmus of Kra; all the animals that were photographed by these traps were black leopards. Anecdotal evidence from interviews with aboriginal peoples living in national parks also found that they were unfamiliar with the spotted leopards but could recognize the black ones. Although 'absence of evidence is not evidence of absence', it does show that spotted leopards are at the very least rare in Malaysia. The authors of this study suggest that this trait has become genetically fixed because of a bottleneck event sometime in the history of this population. This is a neat intersection between basic natural history and genetics, having implications for the genetic variability of the Malayan leopards, and hence their conservation viability.

Extinct species back to life - for now

Just as new species are being discovered, some extinct species occasionally do get rediscovered. A group led by Diana Fisher at the University of Queensland has surveyed rediscoveries of mammalian species thought to be extinct, among them the Guadalupe fur seal of Mexico and the Bahian tree rat of Brazil. Their conclusion? Stop wasting time by trying to look for charismatic, but dead-as-a-dodo, species like the Australian thylacine, and concentrate efforts on smaller, often well-concealed, species that are more likely to be alive.

Despite these rediscoveries, the news is not very hopeful, though. Most of these species persist as small populations in refugia which might eventually be destroyed because of clearing and land conversion. This piece of news by no means should be taken to mean that species are recovering, only that our knowledge of the natural world is incomplete, and this incompleteness extends to the extinct as much as it does to the extant.

DNA Barcoding and Taxonomic Tangles

DNA barcoding is an intuitively compelling idea - since every species's DNA is unique, why not use it as a 'barcode' to identify it? In this way, we might be able to catalogue all life on Earth. It sounds so simple that it might surprise some people that such a catalogue is not already in place.

Despite some detractors - I've heard one person mutter "there's more interesting things to do with that data than just species identification" - barcoding initiatives are now well under way around the world. A new review in PLoS Biology looks at the state of barcoding today (and gives links to the major consortia carrying out barcoding projects), and some issues that surround it, including the politically sensitive problem of 'genetic resources'.

Many countries, especially developing countries with rich biodiversity, have laws protecting biological resources, including genetic information, reasoning that bioprospectors might profit from them without paying their dues to the country from which the resources are taken. This review argues that genetic barcodes must be recognized as 'non commercial' research, not least because it is a valuable tool for conservation.

Barcoding also has potential to address one problem that faces biology today: the lack of taxonomists to classify organisms. Biology programs in universities no longer produce as many students with taxonomic expertise, and the ones already out there are either retiring or dying off. As a result, there are groups of organisms for which only a handful of people might be able to identify new species or sort out existing ones. This problem is widely acknowledged, and there are some initiatives, such as the PEET program of the US National Science Foundation, for addressing it. However, the ubiquity of molecular techniques in biology labs today (most biologists now know their way around a micropipette even if they can't tell a calyx from a corolla) makes barcoding potentially an easier way to get a quick ID or to pin down an ambiguous specimen.

That all depends, of course, on the quality of barcoding databases. They're only as good as the specimens and data put into them. This means that whoever is matching scientific names to molecular sequences had better know what he or she is doing, because misidentifications can propagate themselves indefinitely if no one has the expertise to recognize the mistake. Misidentifications are definitely a problem on GenBank and other public sequence databases.

Which brings me around to the taxonomic tangle: a Yale paleontologist has found that a dinosaur specimen in the American Museum of Natural History is actually a genus new to science, but had lain undetected (despite being on public display) for decades because the partial specimen had been restored to look like an existing genus that it resembles.

Mr. Longrich has made a career out of digging through museum collections and tying up loose ends left by previous generations of paleontologists, avoiding the more glamorous but expensive work of digging up new fossils out in the field. Two of his previous discoveries were made in this way, and he said he has two more in the works.

“I’m just kind of doing mop-up work,” Mr. Longrich said.

As the molecular revolution in biology starts to move beyond well-characterized model species, we need a good mop-up crew now more than ever.

"New Marvels" from Costa Rica

New species discovered in Costa Rica, including a dwarf salamander no longer than a thumbnail. Research was conducted by scientists from the Natural History Museum, London funded by the Darwin Initiative. Press release from the NHM.

are species really disappearing?

This article made me really angry today.

The author, one Michael Duffy, begins by relating his personal experience with Greenpeace. He was a member of the organisation until they asked him for money with the claim that 30 000 species were going extinct every year. When he asked them where they got this figure from, they couldn't come up with a good answer and he quit. He goes on to criticise the method of extrapolation used to come up with such estimates of extinction rates, and then extends his criticism to include models used to predict climate change. He gives various examples of models that didn't work, and quotes various experts saying that inconsistencies appeared between models and how things really played out. In short, he's saying that the method of computational modeling tends to over-reach, is being used to come up with policy without sound proof, and is largely a house of cards.

He concludes his article by condemning a whole branch of science:

"We often hear that the predictions accepted by the Intergovernmental Panel on Climate Change are based on "the science". It's important to realise that this is often a very different type of science to other science, the sort that explains why a jumbo jet won't fall out of the sky or why a certain treatment will cure a certain disease."

His false dichotomy of the sciences: woolly-headed models versus hard and concrete laws, falls flat in his choice of examples, which betray his lack of knowledge of how things work. It is precisely computational modeling that is used to design jumbo jets. Engineers are unable to come up with a simple explanation for how jets fly. Planes are designed not with a few computations on paper, or even by building simulations on computers, but by building models and putting them in wind tunnels because that's the only reliable way to figure out how a certain shape of airframe will behave in the air, precisely because our knowledge of fluid mechanics is insufficient to allow us to predict this reliably from first principles. By Duffy's reasoning, then, we shouldn't fly in planes because they are designed with the use of models, which is not 'real science' in his eyes. One can point to examples of planes which failed or almost failed, like the Comet airliner of the '50s and '60s, to support this foolishness.

Bringing the issue back to the environment, we cannot deny that there are species being lost. The numbers thrown around by NGOs and environmentalists vary, and personally I feel that they should be more responsible with where they get their numbers from and their sources' reliability, but species are going extinct and there is empirical evidence for this. Brook, Sodhi, and Ng's paper in Nature (424: 420-426 (24 July 2003). doi:10.1038/nature01795) for instance used species checklists over the period of Singapore's colonial occupation to the present day to determine what used to be found here and is no longer present, and from these known records extrapolated them to estimate species losses for groups of organisms which were not so well documented. But even if we ignore the inferred species extinctions ('inference' being the concept which Duffy finds so difficult to understand or accept) the recorded extinctions alone are high: more than 40% for mammals, 25% for plants, 35% for butterflies.

Furthermore, it is a logical fallacy that Duffy commits (commonly known as 'association by hand-waving') when he segues from taking issue with extinction rates to questioning climate change; as if they are both part of some great conspiracy by environmental groups to misinform the public. This gives environmentalists credit for more public and policy influence than they do have. Duffy says that we should not trust these predictions,

"...because virtual science is ripe for manipulation, usually unconsciously, by virtuous scientists. Few people are aware of the large element of subjectivity, not only in the design of immensely complicated general circulation models, but in the data that goes into them. Even basic information such as contemporary temperatures is often incomplete or uncertain and tweaked by those who operate the models."

There is not much that one can say in response to this, because it's not about evidence any more but whether one trusts the evidence and those who gather it. Well, if one cannot trust the predictions, one should at least trust the observations. If one yet refuses to trust observation, then nothing will satisfy one's critical eye.