Evolution

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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07 October 2017: New evidence suggest we are much older than 300,000 years

In a recent blog I wrote about new dates for skulls found in the cave of Jebel Irhoud in Morocco in the 1960s. Originally assessed as belonging to Homo neanderthalensis (an assessment that was soon challenged), a reappraisal published in Nature this year confirmed they were in fact H. sapiens skulls; the great surprise was that the reappraisal determined them to be at least 300,000 years old.

Jebel Irhoud

Cast of Jebel Irhoud 1 from the Australian National University. Photo: Simon Brown

New work done by scientists in Sweden and South Africa, and reported in Science, have now dated DNA obtained from a 2000-year-old Khoe-San skeleton apparently unmixed with Bantu or Eurasian DNA, as having separated from other H. sapiens sometime between 260,000 and 350,000 years ago.

The San are the First People of South Africa, Botswana and Namibia. Indeed, they may be the First People, the ancestral group all modern humans are descended from, or at the very least very closely related to them.

The San are the most genetically diverse of all humans living today. In an episode of Catalyst on the ABC about her research on San DNA, Professor Vanessa Hayes said, ‘There’s more similarity between myself and a Han Chinese than between two San people.’

Bushman

San hunter/gatherer

As reported in Science, the recent work on San DNA involved several ancient individuals, but the standout dates were given by DNA from the genome of a hunter-gatherer boy known as Ballito Bay A. The scientists concluded that, ‘ … our results show that the deepest split among modern humans (the estimated latest time for the emergence of H. sapiens) occurred at between 350 kya and 260 kya.’

Given that the skulls found in Morocco have been dated to at least 300,000 years ago, it would seem not unreasonable to consider the older dates for the emergence of H. sapiens – 350,000 years ago – being closer to the mark than the lower date of 260,000 years ago.

This new evidence also adds weight to the theory that our species may have partly evolved in South Africa.

In the last eight months, we have seen conservative estimates for the age of our species jump from 190,000 years old to almost double that. It’s been an extraordinary year for palaeoanthropology.

29 September 2017: What ancient hominid left her footprints in Crete?

There is strong evidence that a hominid walked in Crete in the late Miocene, about 5.7 million years ago.

In an article in the 31 August 2017 issue of the Proceedings of the Geologists’ Association, the authors describe the discovery in western Crete of tracks in rock accurately dated to the Messinian age. To quote the abstract, ‘The tracks indicate that the trackmaker lacked claws, and was bipedal, plantigrade, pentadactyl and strongly entaxonic.’

Trachilos footprints Andrzej Boczarowski

Ancient hominid footprints near Trachilos, Crete. Photo: Andrzej Boczarowski

In plain English, the authors are describing footprints impressed in rock that suggest the creature that made them walked on two feet, not four (bipedal), that it walked on its whole foot rather than just on its toes or claws (plantigrade), that it had five digits on each limb (pentadactyl), and that its big toe was bigger than its other toes (entaxonic).

In short, a footprint that resembles those that are left behind by hominins – the family of humans that includes you and me.

The paper caused a small storm in palaeoanthrapological circles for two reasons. First, there is little direct evidence anywhere of bipedalism before the Pliocene (the epoch immediately following the Miocene, starting around five million years ago), and second, there was no evidence of bipedalism outside of Africa before the Pliocene.

If the tracks discovered in Crete have been accurately dated, and the evidence seems strong on this point, then several intriguing possibilities present themselves.

First, that bipedalism, as palaeoanthrapological orthodoxy has it, evolved in Africa in a species that subsequently migrated to Eurasia (or possibly one of that species’ close descendants made the journey) much earlier than first believed.

Second, that bipedalism in our family may have evolved in Eurasia and not Africa.

Third, that bipedalism evolved more than once in our family. This would make it an extraordinary example of convergent evolution.

At this point, without completely discounting it, the first possibility seems the most unlikely, simply because there is no evidence – fossil or footprint – to support it. However, if this turns out to be the correct answer, a prime candidate would have to be Orrorin tugenensis, the oldest hominid for which we have strong evidence for bipedalism. Orrorin lived in Kenya in the late Miocene, so the dates fit.

The second possibility has been championed by scientists who think it may have been left by Graecopithecus freybergi, a hominin known by one mandible and a few teeth discovered in Greece. Although we do not know if Graecopithecus was bipedal, a recent paper proposed that its dental morphology suggests it is the oldest hominin and that therefore humans first appeared in Eurasia and not Africa.

Graecopithecus_tooth

Teeth from Graecopithecus freybergi

While this claim has been controversial, if Graecopithecus was the first hominin then it was almost certainly bipedal and may well have left impressions of its footprints in Crete. However, generally speaking dentition follows diet. Our teeth can evolve quickly to take advantage of new resources in food, so it is possible that despite its human-like teeth Graecopithecus was a hominid (a member of the family that include great apes as well as humans) but not specifically a member of the tribe Hominini. If this is the case, then Graecopithecus is only our distant cousin rather than an ancestor.

This leads to the third possibility, that bipedalism evolved more than once in the hominid clade. If this is the case, then there is one other strong Eurasian candidate for the owner of those footprints left behind in Miocene Crete, and some scientists think this candidate may have been bipedal.

Oreopithecus bambolii is known from 9-7-million-year-old fossils discovered in Italy from the 1870s. The best and most complete fossil was found in lignite, earning it the name of the Abominable Coalman.

For a long time the position of Oreopithecus in the hominid record has been controversial, most disagreement revolving around whether it is part of the ape or the human family.

Oreopithecus

Oreopithecus bambolii – the ‘Abominable Coalman’

Work done on Oreopithecus in the 1990s controversially proposed it was bipedal, although with a curiously positioned big toe that meant its foot may have acted almost like a tripod. This suggests it could walk on two feet, but probably not at any great pace.

A recent survey of the hominid’s spine, however, has led some scientists to think Oreopithecus was not fully bipedal. Furthermore, the footprints in Crete do indicate a more conventionally shaped foot.

The tracks were discovered in Crete, and dated to the Messinian age when the sea level of the Mediterranean was probably similar to now. Graecopithecus somehow would have had to make it across the equivalent of the Aegean Sea to reach Crete, and Oreopithecus across the Ionian and Aegean seas. Orrorin would have had to make it all the way from Africa. Of course, many animals throughout history have crossed seas and even oceans to reach isolated islands, including members of the hominid clade (Homo erectus to Java and Homo floresiensis to Flores, for example), but to date there is no fossil evidence of either Graecopithecus or Oreopithecus having lived – let alone walked – on Crete.

(This blog entry is based on an idea proposed by Colin Groves, Emeritus Professor of Bioanthropology at the Australian National University.)

15 July 2017: New dates for Homo naledi and (surprise!) new dates for H. sapiens

I originally intended to write about how recent dates discovered for Homo naledi meant that it and H. sapiens, our own species, had only the narrowest window in time to cross paths, but recent finds in Morocco have put paid to that. The announcements of the two sets of dates occurred within days of each other, and demonstrate just how quickly our knowledge of early human evolution is itself evolving.

Homo_naledi_holotype_specimen_(DH1)

Holotype specimen of H. naledi (Photo: Lee Roger Berger research team)

The new information for H. naledi appeared in three papers published in eLife (here, here and here) in May 2017, and provided more detail about when this newly discovered species walked the Earth, as well as announcing the discovery of a second area – the Lesedi Chamber in the Rising Star cave system about 50 km northwest of Johannesburg in South Africa – containing yet more H. naledi remains.

(For more on the first discovery, see in an earlier blog the interview I did with Elen Feuerriegel, one of the ‘underground astronauts’ involved in the recovery of the H. naledi remains in the Dinaledi Chamber).

Morphologically, the new species contained features that positioned it somewhere between the Australopithecines and the early members of our own genus, Homo; this would place it somewhere around two million years old. Confusingly, however, the bones found in the Dinaledi Chamber were still made up of hydroxylapatite, a form of calcium that takes up around 70% of the weight of human bones. Normally, fossilization results in the hydroxylapatite being replaced by minerals like silica. This suggested a more recent existence for H. naledi.

And the bones spoke true. The new papers give dates for the remains that placed it between 335,000 and 236,000 years old. Since the conservative dates for our own species up to May were 190,000 years ago, or 260,000 if you count the Florisbad skull as belonging to our own species instead of another such as H. heidelbergensis, it seemed unlikely, if remotely possible, that our ancestors crossed path with H. naledi.

But then came the second announcement.

A paper published in Nature in June 2017 revealed that H. sapiens remains discovered at a cave called Jebel Irhoud in Morocco, approximately 100km west of Marrakesh, and retrieved largely during the 1960s, have now been dated to extend as far back as 300,000 years, pushing it way beyond Florisbad and well within reach of H. naledi.

Jebel_Irhoud_1._Homo_Sapiens

Irhoud 1(Photo: Ryan Somma)

The skulls among these finds are not shaped like modern human skulls; the remains were originally classified as belonging to a sort of African Neanderthal. But the faces are flat, like our own, without the prominent inflated brow ridge of Neanderthal.

Where exactly they lie in the long line of human evolution is not known for certain, but their location and their age suggest strongly that they are archaic H. sapiens and not some other species.

While this does not change the overall pattern of human evolution as currently understood, it does dramatically extend the time that our species has existed, and strengthens the argument that the cradle of modern humanity was indeed Africa.

08 May 2917: Update on Homo floresiensis

Since my last blog on Homo floresiensis almost a year ago, two new discoveries have pushed back the origin of the species to at least 700,000 years ago and clarified its line of descent.

The original remains were found in Liang Bua cave on the Indonesian island of Flores in 2004. A short hominin that stood about a metre high, almost inevitably the new species was dubbed the ‘Hobbit’.

H. floresiensis

Homo floresiensis almost certainly not descended from …

There was initial controversy in some corners about whether the remains represented a new species or diseased specimens of Homo sapiens. Mounting evidence that it was indeed a new species climaxed with the announcement in June 2016 that fossils found in the So’a Basin of central Flores in 2014 possess characteristics that are morphologically similar to those found in Liang Bua fossils.

At 700,000 years old, these new fossils are the most ancient hominin remains yet found in Flores, and strongly suggest the ancestors of H. floresiensis first reached the island long before anatomically modern humans had evolved in Africa.

The main debate subsequently shifted to whether or not H. floresiensis was descended from Homo erectus – whose fossils were first discovered in Java – or some other early hominin.

H. erectus

Home erectus, but possibly from …

If descended from H. erectus, the Hobbit was an excellent example of ‘island dwarfism’, where populations of larger animals restricted in geographical range – usually islands – decrease in size over time. (Ironically, smaller animals in the same situation, lacking predators, tend to increase in size.)

A new paper published in the Journal of Human Evolution in April this year, however, presents strong evidence that H. floresiensis most likely descended from an earlier hominin. In the words of the authors, the results of their research indicates it is ‘a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa … ’

H. habilis

Homo habilis.

Using Bayesian phylogenetic methods and ‘parsimony’, the authors conclude that H. floresiensis is sister either to H. habilis alone or to a clade consisting of other hominin species including H. erectus and H. sapiens. However, they point out that a close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be ruled out.

These findings are important for two reasons.

First, they should finally put paid to any theory that the Hobbits are simply pathological specimens of our own species.

Second, it suggests that our hominin ancestors were migrating from their African homeland long before Home ergaster – the probable ancestor of H. erectus and sister species – decided to emigrate to pastures new some two million years ago.

Wanderlust, it seems, is an essential part of our genetic makeup.

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.

16 May 2016: New dates for the ‘Hobbit’

Homo floresiensis

Photo: Ryan Somma

Updating my blog celebrating the 10th anniversary of the discovery of Homo floresiensis, better known as the ‘Hobbit’, a letter in Nature has revised the most recent dates for the remains from 12,000 years back to 60,000 years. The sediment layers in the cave of Liang Bua on the Indonesian island of Flores, where the remains were discovered, had not been laid evenly, leading to an initial miscalculation.

Stone artefacts attributed to H. floresiensis are dated more recently, to 50,000 years ago.

The biggest implication of the new dates is that it is now less likely that the ‘Hobbit’ coexisted at the same time as H. sapiens on Flores. Although it cannot be ruled out, the earliest dates for human occupation at Flores is 50,000 years, leaving a very narrow window of opportunity.