Journal article titles on Pokemon ecology and evolution

Pokemon Go is out in Singapore and is all the craze now. There can be two common reactions by biodiversity science workers to this. One is to ask: What’s that? After all, we’re too busy doing real work… The other is to roll our eyes, and wonder why so few people appreciate the real plants and animals around us.

Some call this passive-aggression. To be honest, I did go on a rant to the wife about how I would absolutely give a student zero if I caught him/her playing Pokemon Go on a field trip.

But the world of Pokemon should be really intriguing to us who search for patterns in the (real) natural world. It led me to think: what research hypotheses would I test using Pokemon Go? Which in turn leads me to fantasize: what would the titles of the papers look like?


1. Excessive use of lures homogenizes Pokemon beta diversity

2. Fourth-corner analysis reveals habitat preferences of Pokemon functional groups

3. A test of temporal niche-partitioning in nocturnal- vs. diurnal-spawning Pokemon

4. Invasive species, or urban commensals? Population control of Rattatas and Pidgeys does not increase Pokemon diversity nor abundance

(On evolution:)

5. A phylogenomic approach to estimating speciation rates in the Eevee clade

(Typical review bullshit:)

6. The role of Pokestops in sustainable harvesting: prospects and challenges

7. Ontogenetic shifts in life history strategies for Pokemon displaying multi-stage metamorphosis

(‘Cos you gotta have one for the taxonomists:)

8. Lectotypification of Nidoran

9. Dynamic occupancy modelling of the amphidromous Magicarp

There are only nine because I could only think of nine. After all, I don’t play the game, so I don’t know enough about their natural history. For those who do, why not grab your nearest/favourite journal article, and think about how you might change it to one on Pokemon! It might help others understand the kind of work we actually do.

Singapore’s MFA on the environment

I was browsing the Ministry for Foreign Affairs website because my flight home from Edinburgh is on Turkish Airlines and transits through Istanbul. Given the coup attempt just less than 48 hours ago, I was wondering if I should (spend an obscene amount of money to) change my flight.

I chanced across a page “Sustainable Development and Climate Change” and professional curiosity caused a momentary digression.

The opening line for the page was:

As a land-scarce and highly-urbanised city-state, Singapore is aware that economic development should not come at the expense of harming the environment or reducing the quality of one’s living conditions.

Gotta hold ’em to it.

Bridging the engagement gap

A relatively old paper, but makes for good and easy reading: Gibbons et al. (2008; Ecological Management & Restoration 9: 182). A figure lists the different motivations of researchers and policy-makers when it comes to collaborating on projects, lightly adapted below.

Researchers are motivated when the projects:

  1. generate information that they can publish
  2. generate resources for longer-term research, e.g., postgrad scholarships or newer funding
  3. have spin-offs for their teaching or training of graduate students
  4. raise their profile in the media
  5. have demonstrable impacts on public policy, e.g., they are formally acknowledged in a policy document
  6. seek objective knowledge rather than support for an existing position

On the other side, policy-makers are motivate by projects that:

  1. are relevant for a contemporary issue
  2. are acceptable to the current government
  3. identify practical solutions
  4. can be used to identify policy options
  5. is demonstrated to work
  6. does not attract controversy
  7. are effectively and succinctly communicable

It ties in with my own experience working on several government-funded projects.

If government agencies want to motivate researchers, they must allow (or even encourage) them to publish and present the work. This also means that the vetting process for publishing and publicising the work, while understandably necessary, cannot be overly onerous. Also, I have found it disappointing when agencies appear to have used our outputs or recommendations without giving credit or acknowledgement. Finally, yes, we are rather wary when it seems like the agency already has a desired outcome in mind, which usually portends conflict as results may just as easily turn out opposite from what is expected.

At the same time, it is clear that the research must address a particular applied problem of interest to policy-makers and/or management. We also often heard the desire for outcomes to be “immediately operational”. Complex solutions, or those that are not popular or politically palatable, usually end up being ignored. And from reading the article, I realize one reason why agencies often reacted negatively to our recommendations: they like to be presented with options going forward, and not be just told what to do, or worse, that they were wrong in something.

I guess we have to work harder, from both ends. Some more excerpts:

Hamel and Prahalad (1989) noted that many scientists appear to operate under a ‘strategy of hope’, that is, simply hoping that their work will engage management professionals but doing nothing to further that goal… Roux et al. (2006) noted that researchers can be guilty of providing a ‘solution’ with the expectation that it will be embraced and then ‘move on to another project bemoaning the fact that their work was not put into practice.’

How true.

Thoughts on botany from 1959

A bunch of choice quotes from the Gardens’ Bulletin volume 17 issue 2, published in 1959 on the 100th anniversary of the Singapore Botanic Gardens.

The knowledge of the correct names of plants is essential for the ecologist… I believe that ecological studies in the widest sense provide the only sound basis for the preparation of rational plans of land utilisation.

Purseglove, p. 146
“History and functions of botanic gardens
with special reference to Singapore”

The critical name of a plant species is the alpha of botanical knowledge…

Van Steenis, p. 162
“Singapore and Flora Malesiana”

…for the taxonomic progress with living plants and all the impetus to botany, theoretical and applied, which will follow, we must look to the botanical institutes in tropical countries… Western science has led the way to a better appreciation of nature, but the tropical countries must now help their eager students to extend this knowledge in their own rich heritage for the benefit of mankind… On the tropical students now falls the responsibility for writing their biological floras… Theirs will be the responsibility of preserving the native vegetation and the beauty of the country by wayside and in natural park, and of collecting the living assemblage of economic, ornamental, and rare plants for research and recreation in botanic gardens… At present they may lean on outside support, but I look to the time when students from outside will learn in the tropical institutes.

Corner, p. 214
“The importance of tropical taxonomy to modern botany”

The State of the World’s Plants

The Kew Royal Botanic Gardens just released the first-ever State of the World’s Plants (SOTWP). This has been making rounds in various news sites, e.g., The Guardian, the Scientific American, etc., after Kew put out its press release. In another opinion piece in the Guardian, Michael McCarthy writes that the report has made “Kew, at a stroke, a global voice for plants.”

I have a bit of beef, however, with Mongabay’s article on it.

First, the article’s title: “How many plant species are there in the world? Scientists now have an answer”.

This conveys a factually wrong message. Scientists have long had an answer. When I was a graduate student, I read Govaerts (2001; Taxon 50: 1085) and Paton et al. (2008; Taxon 57: 602); just last year, there was Pimm and Joppa (2015; Annals of the Missouri Botanical Garden 100: 170). If anything, a “working list” of plant species, enshrined as Target 1 of the Global Strategy for Plant Conservation (GSPC), has often been commented as the best-achieved among all the GSPC targets, having evolved from the International Plant Names Index to the Kew World Checklist to The Plant List today. It was just a matter of narrowing the range of some 250,000-500,000 by extrapolating the degree of synonymy (i.e., redundant names). From what I’ve read, SOTWP simply updated the number using the same methodology of Paton et al. (2008) to arrive at a point estimate of 391,000, which is really still a “working number” of species just as The Plant List is a working list.

In fact, nowhere in the Kew press release did they trumpet this point estimate as a first-ever estimate. Nor did any of the other news sites I cited above. They all simply stated that this is the first report on the state of the plants, which is quite different from being the first to report something. The title of the Mongabay article is an example of the Chinese saying: drawing a snake and adding legs on it.

More lines from the first few paragraphs that could misrepresent what the report has managed to achieve (emphasis mine):

For the first time ever, scientists have assessed the state of all vascular plants in the world…

The report provides — for the first time — baseline information on all vascular plants…

Reading and taking it at face value, you would have thought that the SOTWP team managed to assess the conservation status and provided baseline information of every single plant species in the world, which would be an impossible feat at this point in time. Only 5% of the world’s plant species have been assessed, and again this is a very well-known problem. The “one-in-five” estimate of the proportion of plant species threatened with extinction reported in the SOTWP is simply citing work done by Brummit et al. (PLoS ONE 10: e0135152) creating a Sampled Red List Index for plants, which as the name suggests randomly chooses 7,000 species for conservation assessment to estimate the degree of endangerment in the global plant species pool.

The word all is not just superfluous, but has also innocuously added another meaning, whether or not the writer intended to. Just delete it and it would be much better.

The nuance might be a bit subtle, and admittedly this is not all that damaging a matter, but it is instructive for science communication. It shows perhaps that there is a unconscious tendency to add an unnecessary, inaccurate spin when we are trying to make our science sound more exciting or more urgently requiring the reader’s attention. Mongabay is a respected website for news on tropical conservation, so they need to be extra careful about this to maintain their standing.

Back to the SOTWP, two things caught my attention: something called “Important Plant Areas”, and a claim that some 5,000 plant species are known to be invasive.

I’ve heard of Important Bird Areas by BirdLife International, but not Important Plant Areas (apparently, by Plantlife International), so this is something new. Checking out the interactive map and the database, however, while much of the Indo-Malayan region is shaded, none of the countries (e.g, Indonesia, Malaysia, much less Singapore) have sites listed in the database.

As for the number of “invasive” plant species, it seems to be simply a compilation of various weed/invasive plant databases, all of which have struggled with the problems of defining what “invasive” is, and the level of evidence required for species to be listed.

I can’t help but feel a little disappointed, but oh well, it’s the first report, which tells us that very much more needs to be done.

Plants with extra-floral nectaries

I have a special interest in Macaranga and Cecropia which leads to an interest in ant-plant relationships.

Many people know that many flowers have nectaries, i.e., glands that secrete sugary solutions, which attract pollinators. Not many people know, however, that many plant species also have such glands outside of the flower tube, such as on leaves or along newly developed twigs. Obviously these will have little use in pollination. (Sometimes these glands secrete oils instead; not sure if these are still called “nectaries”?)

Ants tend to be attracted to plants with extra-floral nectaries, therefore some plants appear to be always covered with ants. Such plants are called “myrmecophiles”. When the ants actually live and form colonies within the plant itself, the plant is called a “myrmecophyte”, or a true ant-plant. Contrary to common misuse of the term, not all Macaranga and Cecropia species are myrmecophytes; many Macaranga are actually myrmecophytes. A telling sign of myrmeco-phily and not -phytism is that the twigs are solid and not hollow.

And anyone with some painful field experience in the tropics will tell you that these ants bite. So this leads to the hypothesis that the ants defend the plants from herbivores, or perhaps even cut away climbers that may otherwise smother the young plant over time. It’s an attractive hypothesis because ant-plants tend to be fast-growing, light-demanding species, like Macaranga and Cecropia. So the benefits of getting rid of free-loaders of such a fast-growth, high-productivity strategy is high relative to the energetic costs of giving away some sweets.

If so, the plants with extra-floral nectaries should have higher fitness, e.g., higher growth rates and lower mortality.

An article just out by Muehleisen et al. (2016; Biotropica 48: 321) tried to test this, but found, after correcting for the phylogenetic conservatism of the extra-floral nectary trait, that there was no evidence for higher growth and survival rates.

Actually, I was more drawn to Figure S2 in the Supporting Information:


At Pasoh, which is nearby in Negri Sembilan, Peninsular Malaysia, the species-rich families with the highest proportion of species with extra-floral nectaries are, in decreasing order: Euphorbiaceae, Dipterocarpaceae, and Ebenaceae. The Pasoh data comes from Fiala & Linsenmair (1995; Biodiversity & Conservation 4: 165).

At the two Neotropical sites (Yasuni in Ecuador and the Barro-Colorado Island in Panama), the legumes (Fabaceae) have the highest proportion of species with extra-floral nectaries.

Legumes here in tropical Asia also tend to have extra-floral nectaries… But we’re not quite as species rich in legumes as in the Neotropics. Other notable families here with extra-floral nectaries are the Chrysobalanaceae and the Salicaceae.

Many Euphorbiaceae (which include the Macaranga but also MallotusClaoxylon, Croton, etc.) in tropical Asia also tend to be disturbance-adapted species, i.e., abundant in forest gaps and along edges. On the other hand, the Dipterocarpaceae are the flagship of climax species here… But actually even among the dipterocarps, there is a gradient from the faster-growing and more shade intolerant to the slower-growing and more shade tolerant. May be worth looking into whether it is the faster-growing, light-loving dips that tend to have extra-flora nectaries?

Which leads me to a point about the approach in the paper. To be honest, I only glanced through the methods and the graphs, but I suspect the fitness advantage of extra-flora nectaries will not be evident in a simple test using mean growth or mortality rates, because it is confounded by the trade-offs in specific plant strategies. The Pasoh, Yasuni, and BCI multi-hectare plots that were used in the analysis are more-or-less intact forests. In such communities, you can expect that coexisting plant species is, on the average, already occupying close to the optimal fitness conditions that its ecological strategy is suited for. Naturally, those that don’t need extra-flora nectaries where they are growing will be doing well without them, and vice-versa; otherwise, if there is a residual fitness advantage, you would have expected species with extra-floral necatries to displace those without, over time. It’s a basic paradox of species coexistence and dynamic community equilibrium at the ecological time scale.

A better approach, I think, would be to break it up into two hypotheses:

(1) Species with extra-floral nectaries tend to have more ants (or some other “defenders”) on them.

(2) Plants with more ants on them tend to grow faster and survival better, all else constant.

The first may sound a bit duh, and is probably already documented somewhere. I am guessing that the second is, too. The crux is all else constant: the basis of comparison must be the same. For example, you could take both categories of plant species out of their comfort zone, i.e., put plants without extra-flora nectaries in the places where plants with extra-flora nectaries occur, and vice-versa. Or you could exclude ants from plants with extra-flora nectaries (e.g., taping sticky traps around the base of the stem and trimming off any plants that might serve as bridges for ants) and add fake nectaries to plants without (e.g., sweets??).

Other improvements could be to further break down (2) into two steps that reflect the hypothesized link to better fitness, which in this case could be herbivore attack or climber infestation. I think boldly stating these mechanistic links is the way to go. Also, in ant exclusion/sugar addition experiments, one may need to account for the ontogenetic shift in growth/mortality rates over time/size classes, which are obscured by averaging growth rates. Pioneers tend to show a distinct peak in maximal growth rates at small-to-intermediate size classes, while climax species show a more flat growth-size relationship. Ants may be more necessary in the early stages of rapid growth, and not so much when the pioneer tree is already shading out the undergrowth below but slowing down in growth. Likewise, mortality is U-shaped with respect to age/size class: highest for the youngest, and then gradually increasing again to claim the old.

Too many genera

Chistenhusz et al. (2015; Botanical Journal of the Linnaean Society 178: 501) surveyed the users of botanical classification on whether to split or lump a number of contentious groups. In closing, they reproduced a comment from one of their respondents:

Emperor Joseph: Well, I mean occasionally it seems to have, how shall one say? How shall one say, Director?

Orsini-Rosenberg: Err. too many notes, Your Majesty?

Emperor Joseph: Exactly. Very well put. Too many notes.

Mozart: I don’t understand. There are just as many notes, Majesty, as are required. Neither more nor less.

…In reply to E.J.H. Corner’s complaint of the Sapindaceae that there are ‘too many species and far too many genera,’ many a specialist would echo Mozart and say that there are just as many genera as are required; neither more nor less.

The exchange was regarding Emperor Joseph’s reception of Mozart’s The Abduction from the Seraglio.

Australia: 5 months

The wife came over to spend the past five weeks with me in Brisbane.

We visited the Glass House Mountains up north:

20160317_102302 labelled

Members of the Glass House Mountains as seen from a look-out. Names and heights taken from the information panels at the look-out.

And we visited Lamington National Park down south, as urged by Alvin Lok.


Epiphyte-laden tree limb, seen from climbing up a ladder to a deck, along a tree-top walk near the Lamington National Park visitors’ centre and resort.

The in-laws came over for the fifth week, and we went to Tasmania. We started with Launceston (which I think is pronounced “lawn-sass-tehn”), the second-largest city in the state.


The Cataract Gorge at Launceston.

Then we went to Cradle Mountain National Park (which apparently in Chinese would be called 摇篮山). In fact, we went up to it twice, because it was drizzling rather badly the first time. A cold place, with delightful wombats lumbering around in the scrub.


Dove Lake up the Cradle Mountain, seen from the Glacier Rock, on the second visit when the weather was better.

Next we headed to Bicheno, a small seaside town.


Rocky shore at Bicheno at sunset. The red algae on the rocks is probably the same one that covers the rocks at the Bay-of-Fires up north, which we skipped.

We didn’t see any penguins making landing that night. But it was really more of a rest stop for visiting Freycinet National Park next. So Freycinet is pronounced “fray-sin-nay”. So I guess the genus Freycinetia should be pronounced “fray-sin-nay-sure”.


Wineglass Bay. Tip: this look-out is not a good spot for morning selfies without a flash. The sun is behind the peak, casting a shadow over this side of the slope. My guess is that in the afternoons, the sun will be glaring right into the camera lens.

Finally, Hobart, the state capital. Can’t get away without paying a visit to a nature spot too.


Evening view of Hobart from the peak of the towering Mount Wellington. Very very high up, but you can drive all the way; felt like I was driving into the sky, and the legs were turning to jelly on the accelerator. Very strong winds and very cold.

The wife has just gone back and I’m all alone again. 😦

Residents vs. municipal authorities vs. trees

Just up the road from where I currently stay, there are a few large Ficus elastica trees. I noticed them the first time I came down the street to view the house before renting it; For a couple of years Chow Khoon and I monitored bi-weekly the phenology of some Ficus elastica trees in Singapore, so I recognised them instantly.

The species is sometimes called the Indian rubber tree because the thick white latex was once experimented with as a source of natural rubber. It is also a popular horticultural import all over the world, perhaps because of the large, dark green leaves and long red stipules. It’s “Indian” because its native range includes India, and stretches east and southwards to Java, Indonesia. However, it’s not native to Singapore; in the wild, it may prefer more seasonal climates such as in Java, India, Indochina, etc. The wasp species that was known to pollinate the figs went extinct, leading EJH Corner to declare Ficus elastica one of the “living dead” species, but we discovered a healthy population of another wasp species happily pollinating the cultivated trees in Singapore, leading to ripe figs and successful escape of the species from cultivation. That’s another story, and not the point of this one.

It’s also certainly not native to Brisbane. In Brisbane, as far as I could see, the trees are less exuberant in displaying the strangling habit as they do in Singapore.

When I came back from Singapore to Brisbane last December, I saw that white boards with words had been put up around the trees near my home, slamming the Brisbane City Council (BCC).


From left to right:

These trees survived last year’s horrendous storm. But they can’t survive the BCC.

Why can’t these trees be maintained by the BCC when others can?

More superb community consultation by the BCC… not!

BCC playing the “safety card” again to take away our character!


From right to left:

In a matter of hours this December, these trees will be destroyed by the BCC.

These are significant landscape trees. Cooling and a safe home for wildlife. The removal of these trees will result in a hot embankment of mismanaged plants and weeds. Just look elsewhere to see.

No expense spared to save City Hall. Problem tree? “Just chop it down.”

Slipping in another sneaky decision at Christmas time. BCC the Bad Santa!

There is no emergency! Our rates have increased above the Brisbane average. Stop the destruction now and involve the community in the discussion! It’s only fair.

Brings to mind some of the recent conflicts over cutting down trees in Singapore to widen roads, etc. The Singaporean version is considerably more mild and passive-aggressive, of course.

Does it matter that this fig species non-native? And that, if the wasp species we found pollinating the cultivated population in Singapore (which is also present elsewhere as well) somehow gets introduced to Brisbane, this fig may run wild as some fig species have elsewhere around the world? Would people change their perceptions when they have such information?

Lamarckian illusions

Modern physics views Newtonian mechanics as an approximation that holds at low speeds but fails to accurately describe physical relations between objects at speeds close to that of light. By analogy, regarding [multicellular] organisms as units of evolution is an approximation that does not hold at the microbial and molecular scales, where a gene-centered perspective must be adopted to fully explain certain events.

Weiss (2015; Trends in Ecology and Evolution 30:566)

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