Nature

09 November 2017: the eighth great ape and the problem with ‘species’

Until recently, only seven species made up the group of primates known as the great apes, or Hominidae. Two orangutan species (Sumatran and Bornean), two gorilla species (eastern and western), two chimpanzee species (chimpanzees and bonobos), and us.

But in a report recently published in Current Biology, an international team of scientists announced a new hominid with fewer than 800 members, Pongo tapanuliensis, found just south of Lake Toba in Sumatra. To save your tongue twisting around that particular binomen, we can call it the Tapanuli orangutan.

The scientists compared skull, jaw and dental characteristics of a Tapanuli specimen with those of the Sumatran and Bornean species, and analysed 37 orangutan genomes as a second line of evidence.

Orangutan

Three species of orangutan: from left, Bornean, Sumatran, Tapanuli. Photo credits: Eric Kilby, Aiwok, Tim Laman

The report gained a great deal of media attention: not only because we humans had a new cousin, but because the Tapanuli is an endangered species.

However, there were dissenting voices. In an interview with the ABC, for example, Lee Christidis from Southern Cross University pointed out that the analysis had been carried out on only one specimen and that the DNA evidence was at best ambiguous.

It’s only fair to point out that it’s often the case that a species will be described by a single representative organism, or, as happens frequently in palaeontology, those fragments of a single organism that have been fossilised or otherwise survived over many millions of years.

The report also generated discussion about what we mean by the word ‘species’. Jerry Coyne, professor emeritus at the University of Chicago and author of the excellent Why Evolution is True, wrote in his blog:

‘Not only do I see this new “species” as merely an isolated and genetically differentiated population (as are many human populations regarded as H. sapiens), but I’d also contend that there is only one species of orangutan overall, with these three groups all being subspecies. Sadly, a lot of systematists don’t see it that way, as they seem to think that any isolated population, if it can be told apart morphologically or genetically from others, warrants being named as a new species. Yet to evolutionists, a “species” is not an arbitrary segment of nature’s continuum, but real entities that maintain their “realness” because they don’t exchange any (or many) genes with other such entities where they cohabit in nature.’

But is this indeed the definition of species with the greatest currency among most biologists?

To start with, there has to a definition that works across all fields. A primatologist cannot have a different concept of species from, say, an entomologist, or the whole point of taxonomy – the orderly classification of living things that demonstrates their evolutionary relationships – starts to fall apart.

This doesn’t mean that definitions in biology – or any scientific endeavour, for that matter – are written in stone. As our knowledge of the world around us grows, the language we use to explore, explicate and explain that knowledge must also grow.

The definition I was taught at school is not dissimilar to Coyne’s quoted above, and is based on what is called the Biological Species Concept (BSC), developed by Ernst Mayr and Theodosius Dobzhansky in the early 1960s (Coyne did some graduate work under Dobzhansky at Rockefeller University). As Colin Groves, professor emeritus at the Australian National University, wrote, ‘This concept states that under natural conditions a species ‘should not exchange genes with other species’[i]. Groves goes on to point out that ‘ … the popular idea that two species are “unable” to interbreed is  a misunderstanding: it is not that they cannot interbreed, it is that they do not.‘

The BSC was further refined by Mayr and Jared Diamond in a paper on Melanesian birds in 2001, and then in 2004 by the aforementioned Jerry Coyne with H. Allen Orr in a book about speciation called, appropriately enough, Speciation.

Groves argues that the modified definition of BSC risks different standards of comparison in different taxonomic groups: it’s a definition that won’t work across different fields, in other words.

Groves again: ‘If a genus contains a pair of sympatric[ii] sibling species (species that differ only slightly, inconspicuously), the standard for species recognition will be set much “lower” than in a genus in which sympatric species pairs are grossly different. It is the search for objective standards – for an operational means of distinguishing species – that has been responsible for the controversies that marked taxonomic discussions over the past 15 or 20 years.’[iii]Taxonomy

Many biologists now use what is called the Phylogenetic Species Concept (PSC), developed by American biologist Joel Cracraft from the early 1980s. Put very simply, in this concept a species is the smallest population of organisms that is measurably different from other populations sharing the same ancestry. Note that this concept says nothing whatsoever about species sharing genes, such as happened between Homo sapiens and H. neanderthalensis around 100,000 years ago.

It’s important to note that both the BSC and the PSC are attempts to operationalise the evolutionary concept of species; that is, that a species is an evolutionary lineage.

While the report in Current Biology describing the Tapanuli orangutan as a new species of great ape has, for the most part, been received positively, the fact that many distinguished scientists question the findings shows that the debate about what constitutes a species is ongoing.

[i] Groves, Colin. ‘Speciation in hominin evolution’; African Genesis: Perspectives on Hominin Evolution; ed Reynolds, Sally C. & Gallagher, Andrew; Cambridge University Press; Cambridge; 2012, p 46.

[ii] Sympatry occurs when two or more species live in the same geographic area.

[iii] Ibid.

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22 May 2016: Crows got smarts

Corvus_corax_tibetanus

Corvus corax, the common raven. Photo: Pkspks [CC BY-SA 4.0]

It’s no secret that corvids – crows and ravens – are exceptionally smart for birds, especially at problem solving. Now an experiment carried out with ravens provides evidence they may have a basic Theory of Mind as well; this means they have an ability to attribute mental states they experience to another raven.

In a paper published in Nature in February, researchers Thomas Bugnyar, Stephan Reber and Cameron Buckner from the universities of Vienna and Houston, carried out an ingenious experiment that tested how ravens caching food behaved when they thought they were being seen by another raven.

There is increasing evidence that the Theory of Mind exists in chimpanzees, bonobos, scrub jays and ravens. How equivalent the experience of a ToM is between species is, so far, untestable, but the strong possibility that some form of ToM exists in different animals provides yet more evidence of the complexity of the mental life of species apart from humans.

Not only does this add weight to calls that humans should reconsider the way they relate to other animals, especially the often appalling way we treat farmed and domesticated animals, but firmly places Homo sapiens as the product of the same evolutionary process that produced ravens, dogs and garden slugs.

02 November 2014: But I discovered the meaning of life!

Who’d have thought that in a competition between scientific research papers on the wonders of sex, the bizarre mini-universe of quantum physics, the age and size of the cosmos, the last universal common ancestor, the wingspan of giant condors and the implications of relativity, the top three most cited papers would be about proteins?

The most recent issue of Nature, one of the world’s leading academic journals, has a fascinating article about the most popular papers in science.

The top three – and here you need to take a very deep breath – are “Protein measurement with the folin phenol reagent” (1951), “Cleavage of structural proteins during the assembly of head of the bacteriophage T4” (1970), and “A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principles of protein-dye binding” (1976).

I didn’t even know “quantitation” was a word, let alone part of the title of a scientific articles that has over 150,000 citations.

For the full wherefore and whyfore, go read the article. In the end, as it generally does in science, it all makes sense.