Biological species and related concepts

This post is part of a series on species. Read the previous parts here and here.

The Biological Species Concept (BSC) is perhaps the most famous of them all. In science, it is one of the things evolutionary biologists Theodosius Dobzhansky and (in particular) Ernst Mayr are best known for. It is basically what most non-scientists would also come up with when asked what a species is, unless they have never given the topic a thought before: species are breeding groups, i.e. groups of individuals that form a reproductive community.

Many colleagues will tell you that the BSC is very popular with zoologists but not so much with botanists, supposedly because it works well with animals but not so much with plants. And indeed I know many well accepted plant species that can interbreed, at least potentially. But that is of course circular reasoning: should they then really be separate species? Maybe botanists are simply splitting species too much.

On the other hand, the idea that some interbreeding or even potential interbreeding already makes two populations conspecific may be a caricature of the BSC as promoted, for example, by Coyne & Orr's book Speciation (which, by the way, is a fantastic resource for those interested in species); really the BSC is often understood to allow for some rare gene flow between biological species.

Botany picture #52: Spathicarpa sagittifolia

Spathicarpa sagittifolia (Araceae) from the Botanic Garden of Göttingen, 2008. The predominantly tropical Araceae are a group of monocots with strongly reduced flowers arranged in a spike. This spike is then usually subtended by a large bract called a spathe which often serves to attract pollinators as a pseudo-petal. Just like most people think that the daisy head is a flower so they also would usually call this complex Araceae-inflorescence of many flowers a flower. Many Araceae look pretty bizarre and alien, and this is one of the strangest I have seen so far. The spike is here fused to the spathe.

What is that "we" incompatibilists are talking about?

Before I continue with writing about species, I would like to address very concisely something that pops up every few weeks or so in a part of the blogosphere that I read: the controversy over determinism and free will. The occasion is a recent post by Jerry Coyne, who linked to a study showing that certain decisions are made unconsciously several seconds before we become conscious of them to argue that, and the following word is where the crux lies, "we" do not really make any decisions at all:

The implications of this research are obvious: by the time we’re conscious of having made a “choice”, that choice has already been made for us—by our genes and our environments—and the consciousness is merely reporting something determined beforehand in the brain.

To summarize the determinism vs free will issue, there are three main positions. The first is held by many religious believers, Cartesian dualists, people with an esoteric bend etc. They believe that in addition to the material world following its physical rules there are souls or spirits or whatever immaterial components to our mind (for the sake of simplicity I will subsequently simply speak of souls), and that those souls are somehow transcending the cause-and-effect of the material world.

Botany picture #51: Cardamine pratensis

Cardamine pratensis (Brassicaceae), Germany, 2008. I am not overly fond of Brassicaceae. Although the family is economically very useful - cabbage, broccoli, rapeseed, radish) - and provides with Arabidopsis thaliana the most important model organism from the plant kingdom, their flowers are pretty boring, and they are one of those families that are generally hard to identify without fruits. In addition I unfortunately hate cabbage with the exception of red kraut. The spring flowering species above I always found quite attractive though.

Tidbinbilla

We made a family trip to Tidbinbilla Nature Reserve today. It is a superb destination for a day trip from Canberra, especially if you are interested in seeing wildlife.

Part of the Nature Discovery Playground; several barbecues are available at the site, and it was quite full with families having lunch.

Hanging Rock peeking out of the Eucalyptus forest. Yes, the rock is as big as it looks next to that tree.

I have never before seen so many turtles as today at the Sanctuary wetlands of Tidbinbilla. They were constantly popping up to take air, then diving back in. Some of them looked at us curiously as if they were expecting to be fed, however.

And another cute little reptile! Presumably a red-bellied black snake?

Finally, something botanical: a frond of Pteridium esculentum, the native bracken, breaking through the bitumen of a footpath. Unfortunately, most of the plants that were in flower were introduced weeds. Autumn is really starting here.

Classifying the species concepts

This post continues a series on species that began with this introduction.

So looking over the literature and the aforementioned list of 26 species concepts, let's try to classify the concepts into different groups:

Synchronous concepts
    Reproductive community concepts
            *Compilospecies
        Biological species
        Cohesion species
        Genetic species
        Genic species (?)
        Recognition species
        Reproductive competition species
    Phenetic and cluster concepts
        Autapomorphic species
        Ecospecies
        Genotypic cluster
            *Agamospecies
        Morphospecies or typological species
        Phenospecies
    Phylogenetic concepts
        Phylogenetic species
        Genealogical concordance species
Asynchronous concepts
    Internodal species
    Composite species
        *Successional species
Incertae sedis
    Evolutionary species

The first division, indicated by bold font, is whether the concepts deal only with species in the here and now or, more generally speaking, with those existing together in one time-slice (synchronous) or whether they have a historical dimension (asynchronous). Note that the latter are rarely of interest for anything beyond theoretical discussion unless we are talking about a group with an excellent continuous fossil record. I am not sure where to place the Evolutionary Species Concept because I may not quite understand it. It sounds a bit like a reproductive community seen from an asynchronous perspective, so I have placed it apart for the moment. (Similarly, I previously understood the genic species to mean something different from how it is described in the list I linked to, so there is a question mark behind it.)

Within the synchronous concepts that deal with delimiting and circumscribing species in the present we have a second division, indicated in italics, where the concepts are grouped by their main grouping and, if defined, ranking criteria. The first group is what we might call the family of the biological species concept, different concepts that attempt to delimit species by the ability or propensity of individual organisms to interbreed. The second group defines species via some kind of character combination or overall similarity. In all these cases, species are groups of individuals that are ecologically, morphologically or genetically more similar to each other than they are to individuals belonging to any other species. In contrast to this essentially phenetic approach, the small third group employs some kind of phylogenetic approach to species circumscription.

I have left out several concepts that are silly or too similar to others. The ones that are further indented and marked with asterisks are also a bit dubious as they appear to represent merely special cases of the concepts directly above them. Even having reduced the number already, it will still be useful to lump them further and discuss, for example, all reproductive community concepts together. On the other hand, it appears useful to take a more granular approach to the phenetic concepts - but that may just reflect my personal biases.

Botany picture #50: Eryngium campestre

Eryngium campestre (Apiaceae), Germany, 2007. The Apiaceae are best known for the carrot and all the spices they provide - fennel, parsley, caraway, anise, etc. - and most of them look kind of the same: deeply divided leaves and small usually white or sometimes yellow flowers arranged in a double umbel. But there are a few more unusual groups that a beginner in botany would not even recognize as part of the family. The genus Eryngium is one of those - many of them look more like thistles, and the South American representatives look much like monocots. Unfortunately I do not have good pictures of the latter, so here is a European representative.

Species (introduction)

We encounter species all the time when reading about biology. Darwin titled his most important work The Origin of Species. Articles about groups of plants or animals boast how many species they contain compared to other groups at the same rank of a classification ("this is the largest order of insects", etc.). Likewise, you can find information on how many species occur in this country as opposed to that. Some species are considered threatened and protected by law, and conservationists design species recovery plans to protect species from extinction. Evolutionary biologists calculate speciation and extinction rates for different groups of organisms, i.e. rates at which species appeared and went extinct in evolutionary history.

Given all that, it may come as a surprise that a good number of biologists would not consider species to actually, you know, exist.

Some time ago a colleague asked that question in our journal club over at the university: everybody here, do you think that species are real? Meaning, are species entities that actually exist out there in nature and that we can reproducibly and objectively discover, or are they merely arbitrary human constructs? And quite a few colleagues answered no, species don't have any (special) reality. My own reaction was to stall. I think it depends on the group of organisms you are talking about, was what I said.

That was then, and since then I have given the topic a lot more thought, which is why I want to write about it in the next few posts (exempting the usual botany pictures and whatever else may come up). I am certainly not an expert on the theory but as a taxonomist I need to deal with species all the time. I also do this in part to order my thoughts in preparation for some teaching I expect to be involved in later in the year.

Botany picture #49: Bomarea angustipetala

Bomarea angustipetala (Alstroemeriaceae), a twining petaloid monocot from the Colombian paramo of Chingaza, 2007. I really should read up on the current systematics of petaloid monocots one of these days.

Lifeline book fair

The Lifeline book fair takes place every six months at the exhibition park across the road from us, once in spring and once in autumn. It is a fantastic institution. People donate books that they don't want anymore, and they are sold to help finance the eponymous crisis telephone.

It is an odd mixture of old and new, crappy and good, nonsensical and valuable. I was slightly annoyed to find some creationist literature in the natural sciences section. On the other hand, I was amused that, as seen in the photo below, Left Behind was in the fantasy and science fiction section, something that would probably have annoyed Christians who (like the authors themselves!) actually believe the rapture described in that novel is going to happen and would expect it to be part of the religion section at least.

Ah well. As my wife remarked, there are so many books that the volunteers probably only take one superficial look at most of them to decide where they should go.

The fair starts on Fridays, when masses of people compete to grab the rarest and most interesting books. We came today, on its last day, when they start lowering prices, but that also means that the best may already be gone. Still, we picked up a lot of nice things: An Indian cookbook, the plays of Goethe (in German), Martin Millar's The Good Fairies of New York, three of Jule Verne's novels in one volume, children's books, games and even a nicely illustrated plant anatomy textbook as well as volumes two to four of the Flora of South Australia. Volume one wasn't there, sadly, and obviously being published in the forties and fifties the flora is pretty out of date. But it is nice to have it for my private use, and the most frequent species were usually already described then.

So why is incomplete lineage sorting not an issue at higher taxonomic levels?

When I wrote about incomplete lineage sorting some time back, my main point was that it is an often neglected problem at lower taxonomic levels. One cannot assume that one will infer the true species phylogeny based on only one sample per species and/or only one gene region because many species may have inherited some ancestral polymorphism. Different genes and different individuals may tell conflicting stories. (A good example is the publication from a year ago that found a good portion of the gorilla genome to be more closely related to that of humans or chimpanzees although the overall evidence clearly shows the latter two to be sister species.)

I mentioned also that incomplete lineage sorting is not a problem at higher taxonomic levels, such as when we want to figure out whether a genus or subfamily of plants is monophyletic. The same was recently stated confidently when I was meeting with a few colleagues over lunch.

But why, actually? One might wonder how a problem that makes it harder to infer the true relationships of closely related species A, B, C and D, with some genes saying ((A,B),(C,D)) and others saying ((A,C),(B,D)) would suddenly disappear fifteen millions later. Surely if we want to infer the phylogenetic relationships of four clades A', B', C' and D' that have descended from those four species we will run into precisely the same problem?

Well, I guess so: if these four most closely related species all diversified into clades over those fifteen million years that are happily alive today, then the problem remains because all information that is available to infer the relationships of A'-D' is the information that we could have used to infer the relationships of A-D when they were still only four closely related species. A gene that was fixed in the four lineages so that it tells the story ((A,C),(B,D)) although the real species phylogeny is ((A,B),(C,D)) would mislead us equally in both situations.

No, the real difference between the two situations becomes clear when we think about the likelihood of four species from fifteen million years ago all surviving - it is vanishingly small. Most of everything goes extinct. Just as most seeds do not get to be mature plants and most eggs do not get to be mature animals, most species do not diversify into clades but instead go extinct, and most small clades do not diversify into large clades but instead go extinct.

Because of that, it is quite unlikely that the crown groups of the deeper clades whose relationships to each other we want to infer today are derived from a group of very closely related species (their stem groups necessarily are, by definition, but that is besides the point because we cannot sample anything but the crown group). Instead of clades A'-D' in a relationship of

((A',B'),(C',D'))

what we will mostly find are clades A'-D' in a relationship of

(0,(0,((0,(A',((0,(((0,0),((0,(0,(0,0))),(0,(0,(0,0))))),(0,0))),((0,(0,(0,(0,(0,0))))),((0,(0,(0,(0,(0,(0,(0,(0,(0,(0,(0,(((0,(0,(0,(0,0)))),((0,(0,0)),((B',0),(0,0)))),(0,(0,0)))))))))))))),(0,(0,0))))))),(((0,(0,(0,0))),(0,0)),(0,((0,0),(((0,((0,0),((((0,0),(0,0)),(0,(0,(0,0)))),(0,(0,(0,(0,((C',(0,0)),(0,(0,0)))))))))),((0,(0,(0,((0,(0,0)),(0,0))))),((0,0),(0,(0,0))))),(((D',0),(0,(0,0))),(0,0)))))))))

with "0" representing all the related species that have gone extinct over those fifteen million years and thus will never turn up in a molecular analysis.

Clades (sections, genera, tribes, etc.) that are alive today are in most cases derived from ancestral species that were far enough apart on the phylogeny to have accumulated additional synapomorphies along the branches studded only with extinct side lineages. Ultimately, it is not the completion of lineage sorting over time, i.e. the extinction of gene families within species, but instead the extinction of entire species that ensures that incomplete lineage sorting is not a problem for inferring higher level relationships.

Botany picture #48: Loiseleuria procumbens

Loiseleuria procumbens (Ericaceae) from the European Alps, 2004. A cushion-forming dwarf shrub with a wide northern hemsipheric distribution in alpine and arctic areas. The flowers are mostly 5merous but there is the odd 4merous one.

Botany picture #47: Catalpa

Inflorescence of a Catalpa (Bignoniaceae) in the Botanic Garden of Göttingen, Germany, 2004. Bignoniaceae are a family of mostly tropical to subtropical woody plants - trees, lianas or shrubs. They are often quite stunning, with some trees in dry tropical areas covered in massive displays of flowers even while leafless in the dry season. Obviously, many species are ornamentals such as this one.

I still fondly remember how exasperated our Swiss plant anatomy lecturer was when she was asked by some tourists whether the tree depicted in this photograph was an orchid. I mean, it stands to reason, doesn't it? Pretty flower = orchid, that's all the botanical knowledge one needs, durr...

Unfortunately, another equally pretty Catalpa tree in the same botanic garden was knocked over by a storm around the same time (2005?), right towards the botanical institute, and the branches smashed several windows.

Plagiarism, humanities and sciences

My home country has recently seen a distressing profusion of cases of plagiarism among politicians with academic degrees. It all started, as far as I know, with then defense minister Guttenberg who from what has been reported appears to have plagiarized most of his dissertation. What was new about the case was that the dissertation was, after the first few discoveries by academics, thoroughly and publicly examined by numerous contributors to a wiki ("GuttenPlag") in a crowdsourcing approach. From there on, activists started to examine the dissertations of other high-ranking politicians with doctorates, and soon several more cases of plagiarism were found (and one person was charged but then exonerated).

There are two interesting patterns here. First, those politicians are generally conservatives or liberals* as opposed to social democrats or greens. I can only speculate why that is so. An obvious suspicion that has of course been advanced in discussion threads on the internet is that the anti-plagiarism activists selectively target right wing politicians. Said activists seem keenly aware of that charge and take pains to stress that their work is not party-political.

At least part of the answer might be that conservative and liberal politicians are simply more likely to have doctorate degrees. Here is a statistic for the German federal parliament listing the number of doctorates the members from each party have, and the greens have the lowest proportion, followed by the social democrats. This is probably not because academics are more likely to be conservatives - it is actually the German green party that has the most educated supporters. But there might be a cultural issue here about conservatives placing greater value on official titles. Surely a career politician does not actually need a doctorate to be successful in their chosen career, so the only motivation to obtain one that makes sense to me would be the prestige associated with it. But I will be the first to admit that this is speculation.

The second interesting pattern is that the dissertations in question are generally from the humanities as opposed to the natural sciences. Karl-Theodor zu Guttenberg obtained a doctorate in jurisprudence, Annette Schavan in theology and philosophy, Silvana Koch-Mehrin in macroeconomics and history, Margarita Mathiopoulos on what sounds like a historical topic (?), Jorgo Chaitzimarkakis in political science...

It appears logical to assume that politicians would on average have a preference for the humanities, especially sociology, law, politics and history, but not in all cases. The current German chancellor, Angela Merkel, is famously a physicist. So there are natural scientists in politics, but still so far it appears that plagiarism may not be such an issue among them.

And if you follow the news, and look beyond German politicians and at actual career scientists worldwide, you will notice that plagiarism is simply not a relevant issue in the sciences. Of course there is some fraud, but it isn't plagiarism; the frauds committed by scientists are usually (1) inventing data and (2) manipulating data to produce convenient or spectacular "results". The reason is surely down to a fundamental difference between what scholars in the humanities and natural scientists do.

More from the ANBG

We had another nice walk through the Australian National Botanic Gardens today, together with friends.

You may remember the recent botany picture, Azolla pinnata. This is the second native species of this interesting genus, Azolla filiculoides.

Azolla filiculoides differs from A. pinnata in the less regular branching pattern and in its unbranched roots. Personally, I find A. pinnata more attractive.

Many Banksias are just starting to flower. This is Banksia aemula (Proteaceae).

Lambertia formosa, also of the Proteaceae, a shrub found in coastal heath of New South Wales.

I just realized that this is my hundredth blog post. Hooray!

Botany picture #46: Salix x rubens

Male inflorescence of the hybrid willow Salix x rubens (Salicaceae), if I identified it correctly. Willows are one of the very few genera that are really diverse and hard to identify in botanically impoverished central Europe. You can actually find creeks that you can walk along and find four or five species of the genus in a few minutes. The Rothmaler flora of Germany contains three different identification keys: one for female plants, one for male plants, and one for sterile material. Still, identifying these plants is not easy, not least because they hybridize like crazy. Here in Australia a few species of willows are aggressively invasive weeds, and you don't really want to see them, but they are one of the few genera that I miss a bit (others are Papaver and Allium).

Botany picture #45: Helichrysum arenarium

The paper daisies (Gnaphalieae) comprise about half of the ca 1,000 native species of daisies (Asteraceae) in Australia. Until about 30 years ago, many of the species were placed in the then massive genus Helichrysum but then it turned out that they were only distantly related to the real Helichrysum species from Africa and Eurasia. Since then, they have been segregated into numerous mostly small genera. Because I am currently conducting research on some of those Australian plants formerly erroneously placed in Helichrysum and have just produced the first results, my thoughts are also drawn to the "real thing". Unfortunately, I have a picture of only one of the species, H. arenarium, Germany, 2007. Gnaphalieae are mostly southern hemispheric so you find very few of them in Europe.

Jason Rosenhouse's Among The Creationists

Recently I finished reading through Among The Creationists by Jason Rosenhouse, a mathematician blogging at ScienceBlogs. The book was not quite what I expected, it was certainly unusual, and it thus seems best if those interested in reading it approach it with the right expectations. Despite the idea one could get from the title, it is not a collection of amusing anecdotes presented to the reader as an invitation to point and laugh, nor is it a point by point refutation of creationist arguments.

It is instead a rather unusual mixture of (nonetheless amusing) anecdotes from Rosenhouse's visits to creationist conferences and institutions that show the creationists with all their human dimensions, a quasi-ethnological examination of the creationist subculture in the USA, and carefully formulated thoughts on the compatibility of science and religion as well as evolution and religion, plus a very personal chapter in which the reader can learn, among other things, that the author dislikes mayonnaise, a sentiment that I personally can understand quite well.

The book has two related major take-home messages:

• Creationists are not idiots, they are people like you and me, and their motivation for rejecting evolution is understandable given the things they hold dear.
• The workarounds generally suggested by well-meaning liberal Christians and science communicators, such as "why don't you just believe that god created life through evolution" are not as simple as they look because evolution, while not decisively disproving a creator god, does have extremely unfortunate implications for such a god's character.

The first one shows that Rosenhouse is a much better person than I am. He is clearly able to develop real empathy for fundamentalist believers, and that allows him to explain their motivation and to examine the controversy in a deeply insightful and very useful manner.

Myself, I find it unfortunately very hard to feel such empathy and virtually impossible to really understand such a worldview. My instinct is to consider somebody who starts from the assumption that a certain superstition is true and who then rejects all contrary empirical evidence to be, yes, and sorry, an idiot. And I know that that is a character flaw. They did not chose to be born into a religious subculture. They did not chose to be told throughout their childhood and youth by the people they trust most, by everybody they trust, that a certain belief system must be protected at all cost or all that is good and holy will collapse. If I had been born into such a life, what would I believe today, how would I reason?

And that is ultimately why I would also recommend this book to others. There are intriguing insights into the workings of creationist conferences, it is amusingly written in some parts, I find much to agree with on the parts dealing with philosophy of science, but what I found really most valuable was the empathy it conveyed. The real strengths of Among The Creationists are that it shows the human side of the people the author nonetheless strongly disagrees with, and that it shows how and why they are so fiercely dedicated to creationism despite it being so much at odds with demonstrable fact. And it may just help me to develop a kinder and more tolerant attitude towards them and other fundamentalist believers.

Botany picture #44: Taxodium

Further to our trip to Lake Ginninderra last Sunday, this is a nice picture of cypress knees, parts of the root system of swamp trees that stick out above the ground. It is frequently assumed that they help supply the roots in the waterlogged soil inhabited by these trees with oxygen, but apparently there is still some doubt about their true function.

And this is the tree to which the roots belong, a Taxodium or swamp cypress from North America, here grown as an ornamental tree in an Australian park otherwise well stocked with native Casuarina and Eucalyptus. Taxodium and a few related genera of conifers once formed their own small family but have recently been sunk into the large Cupressaceae family (cypresses, junipers, Thuja and relatives).

What is science, continued

In the previous post with the same title, I wrote that I consider science to be best defined as the use of empirical data to critically test ideas, regardless of what specifically the ideas are about or how exactly the test looks like. The important thing is to work with observations from the world around us (as opposed to abstract concepts, for example) and to ask yourself how you would know if your idea could be disproved. If you don't do the former but the latter, you are doing non-science but you may still be dealing with a legitimate academic endeavor such as philosophy. If you do the former but not the latter, you are a pseudo-scientist.

It could be asked whether my definition is not a bit too lax - after all, aren't we all using observations to test our ideas? And indeed that has been part of the controversy between people who favor a wide circumscription of science (like myself) and those who favor a narrow one. For example, developmental biologist PZ Myers made the point that we are all daily surrounded by trivial mysteries that are best solved using basically the same approach as a scientist, stressing that "science is simply a process for examining the world, and anyone can do it, even if you don’t have a lab coat." In a similar vein, evolutionary biologist Jerry Coyne once compared science to plumbing because plumbers also use empirical observations and hypotheses in their work, prompting ridicule from philosopher/biologist Massimo Pigliucci. However, I do not consider the equivalence of scientific practice and everyday commonsense problem solving to be an absurd conclusion, as Pigliucci seems to think, but instead an interesting observation.

Botany picture #43: Azolla pinnata

Today we went to the parks around Lake Ginninderra in Belconnen. Very nice playground, lakes with many water-birds, a creek with impressive rocks along it, so all in all we made good use of the fine weather. The plants floating on the small lake in the park seen above are the topic of today's botany picture post.

Several lineages of land plants have independently evolved representatives that are adapted to floating on the surface of lakes or slow-moving rivers. The best known are duckweeds which are flowering plants in the Araceae family even if one would not know it from looking at them; their morphology is drastically reduced to a small flat or bulbous thallus, and in two of the five genera even the roots have been lost. Another lineage that has produced a similar floating representative are the complex thalloid liverworts, with Ricciocarpus natans. The photo above now shows a member of a third lineage to independently evolve this habit, the ferns. There are two small genera of free-floating ferns, Azolla and Salvinia, and this is Azolla pinnata (Salviniaceae).

These water-ferns are exceptional among ferns in that they are heterosporous. While most other ferns have only one kind of unicellular spores, the water-ferns produce many small male and fewer large female spores, and the development of the prothallium (gametophyte) takes place inside the spore. That is the first step towards the evolution of true seeds, and the seed plants must have gone through the same stage in their evolution hundreds of millions of years ago. Another interesting thing about Azolla specifically is that it forms a symbiosis with a cyanobacterium that fixes atmospheric nitrogen for its host so that Azolla can grow in more nutrient-poor water than most other floating plants.

Perhaps the most remarkable thing about Azolla is the "Azolla event": congeners of the plants pictured above are hypothesized to have played a crucial role in carbon sequestration 49 million years ago.

Puzzled about online first and print publication in different years

Recently I noticed a slightly confusing aspect of the move towards online first or early view publishing of scientific papers. It is about how to cite a paper. It was all easier when journals were simply a batch of print issues collecting dust on a library shelf; you had the time between acceptance and print, when you would cite the paper as

Blinckhorn N, in press. Molecular phylogeny of the genus Planta (Plantaceae). Some Botanical Journal.

and then you had the time after print, when it would change to

Blinckhorn N, 2002. Molecular phylogeny of the genus Planta (Plantaceae). Some Botanical Journal 19: 34-41.

(That or very similar is how we write reference lists in my area. It might be different in yours but the principle is the same everywhere.)

Now, however, papers actually have two dates of publication, once as online first or early view when they appear as PDFs on the journal's website and then again when they are finally printed, and the problem is really what to do when the two publication dates are in different years. In the above case, the researcher might want to update their staff website or publication list, or a colleague could decide to cite their paper, once it is available online. They would then write something like this:

Blinckhorn N, 2012. Molecular phylogeny of the genus Planta (Plantaceae). Some Botanical Journal. DOI: 00.0000/sbj.0000

It was published in 2012, you can cite it, and the Digital Object Identifier (DOI) allows you to find it online. But then a few months later, the paper comes out in print. It now occupies page numbers in a certain issue of the journal and if somebody wants to cite it in it is suddenly

Blinckhorn N, 2013. Molecular phylogeny of the genus Planta (Plantaceae). Some Botanical Journal 30: 107-114.

So, what is it, 2012 or 2013? Will that cause confusion? Speaking for myself, I think it already has caused me some in a few cases. And consider the not infrequent cases where a funding agency or employer wants a scientist to submit a list of their publications "in the last five years". How about counting the same paper as published (online first) in 2012 when asked for such a list in 2012 and as published (in print) in 2013 when asked for such a list in 2018, whatever serves you best at any given moment?

As more journals move to online only, this will become less of an issue because they will only have one publication date again.

Botany picture #42: unidentified fungus

And another picture from Australia, from the same holiday trip in 2011 as the orchid. Never having been trained in mycology, I have no idea even what genus this fungus belongs to and thus cannot tell you anything about it. I simply found it cute.