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A recent FB post from Stuff discussed the rising concerns around the evolution of antibiotic-resistant bacteria. (This is something that Siouxsie Wiles has often written about: here and here, for example; her excellent book on the subject is reviewed here.)

Fairly predictably, it didn't take long for the proponents of essential oils to turn up, soon to be joined by the usual antivax folks and those arguing that an 'alkaline' diet is the best cure-all. (They also believe that drinking lemon juice - an acid - is the best way to achieve thisA. It's not, and alkalosis is not a healthy state of being.) However, someone also commented that we should basically allow natural selection to take its course, by removing the "weak and feeble". It's not the first time I've seen this said, but it annoys me every time.

Firstly, because many diseases don't give a damn whether you're fit & healthy, or not. Smallpox was no respecter of health (or social status), for example; nor was the "Spanish flu"B that caused the pandemic towards the end of World War I. In fact, that particular form of influenza had a more severe effect on the young & the healthy. As this article in the Smithsonian says: 

The 1918 pandemic was unusual in that it killed many healthy 20- to 40-year-olds, including millions of World War I soldiers. In contrast, people who die of the flu [these days] are usually under five years old or over 75.

In the US alone, around 670,000 people died; in New Zealand, the toll was around 8,600. Fiji lost 14% of its population in the space of just 16 days.

This article on the Stanford University site adds further, chilling, information: 

The effect of the influenza epidemic was so severe that the average life span in the US was depressed by 10 years. The influenza virus had a profound virulence, with a mortality rate at 2.5% compared to the previous influenza epidemics, which were less than 0.1%. The death rate for 15 to 34-year-olds of influenza and pneumonia were 20 times higher in 1918 than in previous years. 

In some ways, one of the worst aspects of this pandemic is the way that - in the US at least - truth also became a casualty, with public health officials initially lying about its severity and spread. They were supported in this by newspaper editors, who refused to print letters from doctors that warned of the danger. 

What was it that killed so many healthy young people, in particular? The general consensus seems to be that their deaths were largely due to the impact of their own immune systems, which mounted such a strong response that they severely damaged the patients' lungs (which also made it much easier for secondary bacterial infections, such as pneumonia, to take hold). For these people, "weak & feeble" didn't come into it.

The other reason that attitude annoys me is that it betrays a deep misunderstanding of how natural selection operates. This is because the process isn't future-focused. A population under the influence of natural selection may well become better-adapted to its current environment, but what works now may not work so well if the environment should change.

And some genetic traits of which that original commenter might be dismissive, could turn out to be beneficial. After all, the reason that the sickle-cell allele is retained in many African countries is that it offers some protection against malaria (the same is true for thalassaemia in Mediterranean lands), despite the fact that having two copies of this allele (ie being homozygous for it) confers significant, life-threatening disadvantages. 

Then there's cystic fibrosis (CF) - again, in individuals homozygous for the allele, this disorder is life-threatening. But the allele is relatively common: among newborns in Europe, 1 in 2,500 will have CF. It's hypothesised that this is because an individual with a single copy of the allele (a carrier) may be protected from the worst effects of cholera. This is because cholera results in very large amounts of watery diarrhoea, and the same cell-membrane chloride pumps that are implicated in producing all that watery efflux don't work properly in CF individuals. (There's also a suggestion that the allele may have conferred an advantage to some people early in the development of dairying, when lactase persistence was not widespread.)

I guess I shouldn't really read the comments sections!

 

A In fact, there are an awful lot of totally incorrect claims made for the benefits of drinking lemon juice.

B While it's generally been thought that this pandemic strain originated in China, a second Smithsonian story suggests that it may actually have begun in the US, in Kansas, where the virus may have jumped from pigs (possibly pigs already infected with an avian influenza virus).  

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What follows is loosely based on a workshop I ran at this year's Biolive/ChemEd secondary science teachers' conference. (A most excellent conference, by the way - kudos to those organising & presenting.) I've added a bunch of hotlinked references.

Back when I was in 7th form (or year 13 ie a rather long time ago), the description of human evolution we learned about in bio was essentially a very linear model - and it began with Ramapithecus, dated to around 14 million years ago (mya). Even when I began teaching the subject in secondary school bio classes, the curriculum information still had that linearity: the probable tree went something like Australopithecus africanus → Homo habilis → Homo erectus → Homo sapiens. From memory, the Neandertals were in there as ancestral to our own species, whereas these days they are generally viewed as a sister speciesA

Now, of course, we know that our family tree is much more complex than that, albeit quite heavily pruned in recent geological times, and with a more recent origin for the last common ancestor of hominins and chimpanzees. This knowledge has been informed by both a range of new fossil finds, and ongoing ancient DNA (aDNA) analyses. For example, with the discovery of Homo floresiensis remains (Brown et al, 2004), we had a not-too-distant relative living into our not-so-distant past. And DNA analyses first resulted in the publication of a Neandertal genome (Green et al., 2010), and then in the recognition of interbreeding between Neandertals, sapiens, and another species (the Denisovans), that helped extend our understanding of patterns of migrationB.

Family tree of 4 early human groups

Figure: Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the gene flow between the groups due to interbreeding, From http://news.berkeley.edu/2013/12/18/neanderthal-genome-shows-evidence-of-early-human-interbreeding-inbreeding/  

And the finds keep coming, which makes things difficult for classroom teachers at times. How does it all fit together? How do we accommodate all this in our teaching? [One of the points made by a discussant at the conference was that, while the relevant Achievement Standard talks of 'trends in human evolution', when we look at many of the fossil finds we're seeing a mosaic of features, rather than distinct trends) - but we'll come to that in a minute.]

For example, you might have seen press reports about a fossil ape known as Graecopithecus. Some of the headlines about this really have been rather overblown: "Europe was the birthplace of mankind, not Africa, scientists find", trumpeted the Telegraph in May this year. From that article: 

An international team of researchers say the findings entirely change the beginning of human history and place the last common ancestor of both chimps and humans - the so-called Missing Link - in the Mediterranean region.

Except they didn't. The authors of the actual paper say only that the fossils have "a possible phylogenetic affinity with hominins" (Fuss, Spassov, Begun & Bohme, 2017). But then, that doesn't make such a good headline, does it? Bear in mind, too, that the remains they describe are very fragmentary indeed - a mandible with some permanent teeth, and (possibly) a premolarC - and that they come from two separate geographic locations, Greece and Bulgaria respectively, so the 'reconstruction' that accompanied the story was entirely imaginary. Incidentally, the analysis is new, but the fossils themselves were found quite some time ago - the mandible was unearthed in 1944.

Next up, Homo naledi - those of you who've looked at previous years' scholarship exams will know that this was the focus of a question in last year's paper. This species was first described in 2015, but this year another group of finds were reported by Hawks et al. (2017) that greatly extended our knowledge of its morphology and also its age (Dirks et al. 2017). It turns out that naledi and sapiens may well have been alive during the same time period:

... we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the ... fossils than have previously been hypothesised on their morphology.

That is, these fossils show a startling mix of modern and primitive characteristics. As Ian Sample says, in his excellent article in the Guardian (Sample, 2017), 

Homo naledi stood about 150cm tall fully grown and weighed about 45kg. But it is extraordinary for its mixture of ancient and modern features. It has a small brain and curved fingers that are well-adapted for climbing, but the wrists, hands, legs and feet are more like those found on Neandertals or modern humans. If the dating is accurate, Homo naledi may have emerged in Africa about two million years ago but held on to some of its more ancient features even as modern humans evolved.

In yet another paper on the naledi finds, Berger et al. (2017) comment that

It is now evident that a diversity of hominin lineages existed in this region, with some divergent lineages contributing DNA to living humans and at least H.naledi representing a survivor from the earliest stages of diversification within Homo. The existence of a diverse array of hominins in subequatorial [Africa] comports well with our present knowledge of diversity across other savanna-adapted species, as well as with palaeoclimate and palaeoenvironmental data.

In other words, everything we know about species diversity in this particular environment predicts that our lineage should be similarly diverse; it shouldn't be a surprise. By the way, that Guardian article comes with some excellent illustrations, by the way: images of fossils, and diagrams of the cave in which they were found (which is a great story in itself). 

And then another headline: "Oldest Homo sapiens fossil claim rewrites our species' history". I know the headlines attract reader interest, but we see so many like this, and they really are misleading. What this particular paper has done is extend our understanding of the possible duration of our species' existence, but it doesn't 'rewrite' things: it pushes back our origins, and also suggests that early sapiens either ranged much further than scientists had previously thought, or didn't evolve solely in East Africa. These particular fossils were discovered back in the late 20th century, when they were estimated at around 40,000 years old. The much older dates come from analysis of the sediments they're found in.

However, it's worth noting (& is reported in the story at the above link) that not everyone agrees with this analysis. 

Palaeontologist Jeffrey Schwartz, at the University of Pittsburgh, Pennsylvania, says the new finds are important - but he is not convinced that they should be considered H.sapiens. Too many different-looking fossils have been lumped together under the species, he thinks, complicating efforts to interpret new fossils and to come up with scenarios on how, when and where our species emerged. 

"Homo sapiens, despite being so well known, was a species without a past until now," says Maria Martinon-Torres, a palaeoanthropologist at University College London, noting the scarcity of fossils linked to human origins in Africa. But the lack of features that, she says, define our species - such as a prominent chin and forehead - convince htere that the Jebel Irhoud remains should not be considered H.sapiens.

I think there are some great 'teachable moments' here, in incorporating this new information into classroom teaching. The first relates to the nature of science - it isn't fixed, and new data may lead to changes in our understanding. (This both makes science a constant adventure, and also contributes to some public mistrust around science - 'how can we trust those scientists when they keep changing their story?'.) The second is that evolution's not a linear, directional process, and the hominin family tree demonstrates this rather well. And the third is that evolution may result in a mosaic of features, as we see with naledi. 

I'll finish off with a great quote from the discussion thread for a blog post by Steve Novella:

What evolutionary theory predicted was that humans must have evolved from something, and morphologically the great apes are closest to us. So, we should find species that fill in the morphological space between humans and great apes. Further, they should occur in a geological and temporal pattern that makes sense evolutionarily. Finally, when we date the last common ancestor by genetic analysis and fossil analysis, they should roughly fit. 

All of these predictions are true. Evolutionary theory was fantastically successful in that regard - we are finding a whole host of hominid species that are part-way between apes and humans. 

 

A As you might imagine, we had an interesting discussion around what 'species' even means in this context. A rigid application of the biological species concept would preclude neanderthalensis and sapiens being sister species, after all, given the increasing evidence of interbreeding between the two. Of course, further back in the fossil record (beyond the point where useable DNA can be retrieved), we have to rely on morphological characteristics only - an approach that's fraught with difficulties. There's this example in the pachycephalosaur dinosaurs, for example. And the NZ moa - once aDNA techniques made the analysis possible, scientists found that what we thought were something like 22 different species were 11 strongly sexually dimorphic species (large female, small male). 

B From Green et al. (2010): "We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other." 

C As a total aside, back in 1922 there was a flurry of excitement when Henry Fairfield Osborn used a single tooth to posit the existence of "Nebraska Man", supposedly a 10-million-year-old human ancestor, as a means of showing that human evolution was a thing (and that it had happened in the US). He was wrong.  

 

LR Berger, J Hawks, PHGM Dirks, M Elliott, & EM Roberts (2017) Homo naledi and Pleistocene hominin evolution in subequatorial Africa. eLife 6: e24234. DOI: 10.7554/eLife.24234

P Brown, T Sutikna, MJ Morwood, RP Soejone, Jatmiko, E Wayhu Saptomo & Rokus Awe Due (2004) A new small-bodied homin from the Late Pleistocene of Flores, Indonesia. Nature 431: 1055-1061. DOI: 10.1038/nature02999

PHGM Dirks, EM Roberts, H Hilbert-Wolf, JD Kramers, J Hawks, A Dosseto, M Duval, M Elliott, M Evans et al. (2017) The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa. eLife e24231. DOI 10.7554/eLife.24231

J Fuss, N Spassov, DR Begun & M Bohme (2017) Potential hominin affinities of Graecopithecus from the Late Miocene of Europe. PLoS ONE 12(5): e0177127. DOI: 10.1371/journal.pone.0177127

RE Green, J Krause, AW Briggs, T Maricic, U Stenzel, et al. (2010) A draft sequence of the Neandertal Genome. Science 328(5979): 710-722, DOI: 10.1126/science.1188021

J Hawks, M Elliott, P Schmid, SE Churchill, DJ de Ruiter, EM Roberts, H Hilbert-Wolf, HM Garvin, SA Williams et al. (2017) New fossil remains of Homo naledi from the Lesedi Chamber, South Africa. eLife 6: 324232, DOI 10.7554/eLife.24232

I Sample (2017) New haul of Homo naledibones sheds surprising light on human evolution. https://www.theguardian.com/science/2017/may/09/new-haul-of-homo-naledi-bones-sheds-surprising-light-on-human-evolutionThe Guardian

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I'm currently supervising a graduate student who's writing a review of the literature on tool use in wild chimpanzees. This has become a most enjoyable interaction: it's a topic I've been interested in for quite a while now, so the supervision role is an excuse to extend my own knowledge, and it's great helping the student to enhance their own skills in relation to academic research and writing. 

Anyway, a couple of days ago I came across a new paper (Boesch et al., 2016) on an intriguing aspect of chimpanzee behaviour, and my student and I had a stimulating discussion about it at our regular weekly meeting this morning. (There's a general summary of the findings and the project which generated them here.) I'd previously heard of (& shared with her) what appeared to be an isolated incident of 'fishing' by an orangoutan, but this new paper documents wild common chimpanzees, Pan troglodytes, using a new technique to obtain freshwater algae. (Of interest in the orangoutan example were the claims that the image of the animal in action were faked, claims discussed here and dismissed as false.)

It seems that it's unusual for primates to eat aquatic plants, although they may eat fish and invertebrates when available. Both bonobos (Pan paniscus) and gorillas eat plants growing in swampy areas. Common chimpanzees do the same, but have also been reported eating algae - something that's really unusual in animals apart from marine species. And it's highly unusual in chimps too: 

despite decades of chimpanzee research, there are only a few observations of algae harvesting, suggesting that this behavior is indeed rare

and in most of these observations the chimps used their hands, rather than tools, to scoop algae from the water. It's possible, of course, that the local ecology of other well-studied chimpanzee groups just don't favour consumption of aquatic algae. But this behaviour could also be due to cultural evolution in a few small social groups.

So, Boesch and his team set up a research station at Bakoun, in Guinea (not far south of the equator), as part of a continent-wide attempt to 

contribute to a fuller understanding of the extent of chimpanzee behavioral variation and flexibility

in order to help get a handle on the actual level of behavioural diversity in wild chimps, and to answer questions around the relative effects of ecological diversity and cultural evolution on differences in behaviour shown by different groups of animals.

The chimps in the study area at Bakoun hadn't been studied before, and to minimise the potential impacts of interaction with humans, all observations were made using 'remote video camera traps', triggered to begin recording on detecting movement. These cameras were set up at sites where there was other evidence of chimp activity, such as remains of tools. Obviously they captured much more than chimpanzee activity, but of the 1,473 video clips that showed chimps, 486 (from 11 different sites), showed the animals 'fishing' for algae (Spirogyra sp.). Most of these events happened during the dry season, when water levels were lower, peaking in the 'hot dry' season when chimps returned repeatedly to the same sites over several days. 


The chimpanzees were observed to fish for algae at sites where the algae occurred in large accumulations at the bottom of the river bed.We rarely observed free floating, surface algae being targeted... [and we] observed all age and sex classes perform and succeed in fishing for algae from deep ponds or river shores.

Interestingly, the researchers found that every single animal used a tool to collect algae, even those only 2 or 3 years old - and they tended to use the same hand each time they fished. They fished by holding one end of a long stick, reaching it down to the bottom of the water, and then twirling the stick so that strings of algae were wound onto it. They then withdrew the stick and pulled the algae off with their lips. And, when algae fishing, the chimps usually avoided getting wet as much as possible. 

To see how successful this was as a food-gathering strategy, two of the research team used a discarded chimp tool - they managed to collect 400g of Spirogyra in just 10 minutes. Since individual chimps were seen fishing for an hour at a time, algae fishing could make quite a contribution to their seasonal diet:

chimpanzees may be fulfilling substantial dietary requirements [for protein, carbohydrates, and lipids, plus antioxidants and minerals] by ingesting large amounts of Spirogyra algae during the dry season

And just what were these tools? Mostly woody branches, modified by stripping off smaller branches and fraying one of both ends; some of these branches were up to 4m long, allowing access to algae that was otherwise unreachable in deeper parts of the river. In around 20% of events chimps arrived at their fishing sites already prepared ie bringing tools with them.

As I commented to my student, research like that described by Boesch and his colleagues goes well beyond simply documenting the activities of our close cousins. This is because, while it's likely our own hominin ancestors used a variety of plant-based tools, these aren't the sort of thing that's likely to be found by palaeontologists, and so 

research on primates can illuminate the potential repertoire of tool use behaviors that may reasonably be assumed to have been present in our last common ancestor (Boesch et al. 2016).

For example:

we suggest that in Bakoun, tool use permits a more efficient access to a rarely available but highly preferred resource, such as algae, that permits chimpanzees to flourish in an environment otherwise more limited in food and water. It is therefore probable that our last common ancestor would have similarly made and used tools to also engage in rudimentary fishing, to collect and consume rich aquatic fauna, and perhaps flora too (ibid.).

And

This [research] demonstrates the flexibility in [chimpanzee] technical skills and how this helps them to obtain access to valuable resources in a drier habitat and new context. Such technological skills have been suggested to be present in our human ancestors when they invaded drier, savanna habitat during the course of human evolution (ibid.).

C.Boesch, A.K.Kalan, A.Agbor, M.Arandjelovic, P.Dieguez, V.Lapeyre, and H.S.Kuhl (2016) Chimpanzees routinely fish for algae with tools during the dry season in Bakoun, Guinea. American Journal of Primatology 78(12), published on-line 3 November 2016. DOI: 10.1002/ajp.22613

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I've just come across a most excellent article by the Genetic Literacy Project. In it, Nicholas Staropoli notes that a proportion of the human genome actually has viral origins.

This might sound a bit strange - after all, we tend to think of viruses as our enemies (smallpox, measles, and the human papilloma virus come to mind). But, as Staropoli notes, there are a lot of what are called 'endogenous retroviruses' (ERVs) - or their remains - tucked away in our genome. (An ERV has the ability to write its own genes into the host's DNA.) And he links to a study that draws this conclusion: 

We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes.

Carl Zimmer writes about one such example in his blog The Loom: it seems that a gene that's crucial in the development of the placenta (that intimate connection between a foetus and its mother) is viral in origin. In fact, one gene encoding the protein syncytin is found in primates - but carnivores have a quite different form of the gene, while rabbits have a different form again, and mice yet another!

This is a very complex evolutionary story indeed. And so you could do much worse than read the two articles, by Staropolis and Zimmer, in their entirety. 

 

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Demodex mites are tiny little creatures that live in mammals' hair follicles. I first heard about them years ago, when I watched a documentary with my science class back at PN Girls' High. It was about animals that are parasitic on humans, and after the segment on eyelash mites, I don't know about the girls but I felt itchy for days!

For eyelash mites live where the name suggests, in the follicles of our eyelashes. (There are 2 species: Demodex folliculorum and D. brevis.) The common name gives an idea of just how small they are: adult length is 0.3 to 0.4 mm. They spend a lot of time inside the eyelash follicles, snacking on the sebum and dead cells (or maybe the bacteria) that accumulate there. But at night... at night, they come out and wander across our faces as we sleep, achieving a speed of 10cm/hr or more. Which doesn't sound much, but when you remember how small they are, that's quite an achievement. Presumably that's also when they mate, which they do where an eyelash follicle opens to the skin's surface. 

I was surprised to discover that these mites lack an anus. This sounds somewhat problematic, but the eyelash mites have survived, with their human hosts, for at least tens of thousands of years, so they obviously cope somehow. And when they die, their little bodies degrade and release their contents. On your face. Or in the follicles where they spent most of their lives.

Though demodex mites are tiny, there are an awful lot of them. There may be only one or two per hair follicle (they don't restrict themselves to the eyelashes), but an individual human has around 5,000,000 hairs on their body (Thoemmes et al., 2014), so that's an awful lot of available places for a mite to set up home in.

Thoemmes & her co-workers were interested in the genetic diversity of these mites. They predicted there'd be geographically-distinct lineages, because the tiny animals are very closely associated with their hosts and don't seem to be particularly mobile between hosts. However,

if Demodex lack strong geographic structure, it suggests the movement of mites among humans must occur very frequently (perhaps even with social greeting rituals) and across large geographic distances.

To test this hypothesis, the team examined adults (from a single North American population) visually, but also tested skin scrapings for the presence of mite DNA. The results showed that despite being able to see mites on only 23% of their sample population, 16S rDNA sequencing indicated that 100% of those sampled actually had mites present. The latter matched other research showing that 100% of dead bodies tested positive for the presence of Demodex.

Figure 2 from Thoemmes et al. (2014): Maximum likelihood (ML) phylogeny of mites based on 18S rDNA sequences.

While the results of their phylogenetic analysis of the mite DNA are based on samples from only 29 people, they're interesting nonetheless. It appears from that analysis that the 2 species, D.folliculorum & D.brevis, probably colonised humans at different times. Because D.brevis' DNA indicates that their nearest living relatives are mites living on dogs, then the researchers suggest that we acquired this species from our doggy friends, perhaps as recently as 11,000 years ago but possibly as many as 40,000 years ago. There does appear to be some regional variation (based on a comparison of the US data with earlier sequencing results from Chinese populations), but there's also quite a bit of variation within populations, due perhaps to individual humans picking up different mites on different occasions as individual humans came into close physical contact.

And after reading all this & watching a few videos, I feel itchy again!

Thoemmes MS, Fergus DJ, Urban J, Trautwein M, Dunn RR (2014) Ubiquity and Diversity of Human-Associated Demodex Mites. PLoS ONE 9(8): e106265. doi:10.1371/journal.pone.0106265

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Well, probably not1, in the sense that most would place on the term 'tummy bug' (where a close proximity to the toilet is a Good Thing), but it turns out that he did have some rather interesting intestinal bacteria.

Ötzi is perhaps better known as the 'Iceman', who died around 5,300 years ago in the Otztai Alps of the Italian Tyrol. (He's the subject of a fascinating web page & I have to say, I'd love to visit the museum, maybe when we next visit family in Europe.) His body, clothing, and equipment are exceptionally well-preserved & are yielding a great deal of information on life in Neolithic Europe - including, as described in the latest issue of Science, the nature of his microbiome. (You'll find the full paper here, but there's also an open-access summary here. I do have a gripe about the use of the term 'tummy bug' in the latter, though!)

In their just-published paper, Maixner's research team reports on their finding of a strain of Helicobacter pylori in Ötzi's stomach contents (he'd apparently eaten a full meal not long before he died). I've written about H.pylori before: while it's been found to be associated with development of gastritis, stomach ulcers, & sometimes cancer in a small proportion of those carrying it2, there's also evidence that it has a protective effect against other disorders, including acid reflux and oesophageal cancer. And it's been with us for a long time:

Predominant intrafamilial transmission of H. pylori and the long-term association with humans has resulted in a phylogeographic distribution pattern of H. pylori that is shared with its host. This observation suggests that the pathogen not only accompanied modern humans out of Africa, but that it has also been associated with its host for at least 100,000 years. Thus, the bacterium has been used as a marker for tracing complex demographic events in human prehistory.

Most modern Europeans carry one particular strain of this bacterium, which is believed to have originated via recombination of two earlier strains. However, the origins of these strains have been uncertain, & the researchers hoped that Ötzi's gut microbes might throw some light on this. The Iceman himself was born and lived in Southern Europe, and DNA comparisons link him to early European farmers. However, the strain of H.pylori found in his gut is most closely related to a haplotype now found in central and southern Asia, and not to those of Europe and Africa.

The detection of an hpAsia2 strain in the Iceman’s stomach is rather surprising because despite intensive sampling, only three hpAsia2 strains have ever been detected in modern Europeans. Stomachs of modern Europeans are predominantly colonized by recombinant hpEurope strains.

Maixner suggests that the Iceman's ancestors must have brought this Asian strain of H.pylori with them when they migrated to Europe. Well after Ötzi died, later immigrants from Africa brought their own strain of the bacterium, and subsequent recombination produced the modern European strain of this microbe. This is evidence for rapid evolution of H.pylori in Europe as waves of human migrants moved into and across the continent.

The researchers also noted that Ötzi's version of the bacterium represents a strain that's associated with stomach inflammation in modern humans - and that protein biomarkers expressed in his gut indicate that he had an inflammatory response to the infection. This may or may not have manifested in actual disease - his stomach lining was not sufficiently well-preserved to let them draw any conclusions on this.

 

1  Which is a real pity, as I was so going to steal my friend Grant's suggested phrase, "the Tyrolean trots", for my title :( 

 It's "found in approximately half the world’s human population, but fewer than 10% of carriers develop disease that manifests as stomach ulcers or gastric carcinoma" (Maixner, Krause-Kyora, Turaev, Hoopmann et al., 2016)

F.Maixner, B.Krause-Kyora, D.Turaev, A.Herbig, M.R.Hoopmann, J.L.Hallows, U.Kusebauch, E.Vigi, P.Malfertheiner, F.Megraud, N.O'Sullivan, G.Cipollini, V.Coia, M.Samadelli, L.Engstrand, B.Linz, R.L.Moritz, R.Grimm, J.Krause, A.Nebel, Y.Moodley, T.Rattei, & A.Zink (2016) The 5300-year-old Helicobacter pylori genome of the Iceman. Science 351 (6269):162-165 . DOI: 10.1126/science.aad2545

 
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Why is it that practically every time there's a new discovery relating to the evolution of our own species, there is a headline saying that this finding 'could rewrite human history'?

Because, bingo! At least one newspaper report1, of a paper published last week in Nature, carried the header: "Homo erectus engraving could re-write human history, and might show art began 300,000 years earlier than we knew." 

Now, the story's really interesting & surely didn't need the overblown headline, even if one of the research team was reported as using the phrase. Certainly the work of a large team of researchers (Joordens et al, 2014) has pushed back the dates for human use of symbols, to around 0.5 million years ago (on the basis of 40Ar/39Ar and luminescence dating), which is far older than the carvings and paintings of Cro-Magnons, and perhaps Neandertals - but doesn't necessitate a total rewrite of our history. And if their attribution of the finds to erectus is correct, then it extends our understanding of cognition in this species. (In fact, headlines like that fall right into the hands of creationists.)

This is a nice piece of detective work, & it also shows how serendipitous some discoveries can be: one of the team, Stephen Munro, noticed the marked mussel shell in photos he'd previously taken of specimens in a museum collection in Leiden, and that sparked a thorough investigation of the provenance and age of the shells. It turns out that the shell assemblage was originally collected at Trinil in Indonesia - the same location, and in fact the same strata (the 'main bone layer') as that of the 'type' specimen for H.erectus, collected in 1891 by Eugene Dubois. This led the team to the conclusion that this marked shell, and what looks like intentional damage to other shells, were the work of Homo erectus.

So what can we tell from these results? Well, it looks as if erectus enjoyed a good feed of seafood from time to time. The evidence for this lies in shells with holes in them - holes that lie over the position of the adductor muscle that holds the shell closed. Around 1/3 of the shells from this particular site had these holes, & overall the shell assembly contained "only large adult-sized specimens (about 80-120mm in length), while under normal conditions mussel populations contain all size classes" (Joordens et al, 2014): this strongly suggests that the molluscs were deliberately collected.

As for the holes themselves - the research team ruled out the possibility of damage by non-human predators, but noted that comparable holes were made in gastropod shells by pre-Hispanic modern humans living in the Caribbean. They went on to experiment on modern mussels and found that someone could use a tool such as a shark's tooth to drill a hole in the animal's shell over the adductor muscle; piercing the adductor caused the bivalve's shell to open. This speaks both to erectus' ability to conceive of and use rather smaller tools than we usually associate with them, and to their knowledge of shellfish anatomy. (You'd certainly find molluscs opened this way much easier to eat than if you had to bash them with a rock!) Another shell appears to have been retouched using a flaker, presumably for use as a scraper or other tool. 

The team then looked at the geometric lines found on the outer surface of one shell & determined that they were highly unlikely to be due to the shell knocking around with other shells & stones, but were probably produced using a shark's tooth or something similar. The lines were most likely laid down while the shell was fresh & so covered with the coloured periostracum common to mussels, "which would have produced a striking pattern of white lines on a dark 'canvas' " (ibid.) The lines are quite deep, would have required a fair bit of force and also good manual control to make, and Joordens & her colleagues concluded that "a single individual made the whole pattern in a single session with the same tool" (ibid.).

So, we've got evidence of what may be the earliest known use of a shell as a tool; evidence of Homo erectus including seafood in their diet; and evidence of someone consciously & deliberately scoring lines in a fresh mussel shell. But was it 'art'? And does it really necessitate the rewriting of our entire evolutionary history?

 

1 I'm not sure why the Independent reporter correctly identified the engraved lines as being on a shell & then went on to talk about them being on 'a rock'. Poor subbing?

 

J.C.A.Joordens, F.d'Errico, R.P.Wesselingh, S.Munro, J.de Vos, J.Wallinga, C.Ankjaergaard, T.Reimann, J.R.Wijbrans, K.F.Kuiper, H.J.Mucher, H.Coqueugniot, V.Prie, I.Joosten, B.van Os, A.S.Schulp, M.Panuel, V.van der Haas, W.Lustenhouwer, J.J.G.Reijmer & W.Roebroeks (2014) Homo erectus at Trinil on Java used shells for tool production and engraving. Nature  doi: 10.1038/nature13962, published on-line 3 December 2014

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The 'paleo' diet story on Campbell Live tonight spurred me to finish my review of one of the most entertaining popular books on genetics that I have read for some time. Entertaining, and informative, in equal measure. I wonder what author Marlene Zuk would have made of the TV story.

book cover

Marlene Zuk (2013) Paleofantasy: what evolution really tells us about sex,diet, and how we live.  Norton (New York)

ISBN 978-0-393-34792-0 (paperback)

For in that story we heard gems like this: "It's a commitment to eating food that is unadulterated, eating food in its most natural state." Paleo proponents (says the TV story) believe our most natural diet is that of our Palaeolithic cavemen ancestors. Somehow I doubt our 'cavemen' ancestors were eating avocados, beetroot, bacon or kale. (There's also an air of chemophobia, with one proponent of paleo eating stating that their diet contains "[n]othing nasty and nothing you can't pronounce" - which reminded me of the series of posters by Australian teacher James Kennedy, showing the list of chemical compounds found in natural food items: blueberries, anyone?).

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I saw this story in the newspaper yesterday, & again today on one of the science feeds

Researchers in the US have studied the skulls of ancient human ancestors and concluded that fist-fighting may have played a role in shaping the male face.

You can read the paper itself here (Carrier & Morgan, 2014). I'm sorry, but to me it reads like a just-so story. Just because modern humans take a swing at each other from time to time, doesn't mean that this was the case for earlier hominins. The authors of the paper argue that the facial features of robust australopithecines are the result of natural selection acting through bare-fist fighting. However, they don't offer any actual evidence that this might have happened: nothing on whether paranthropine skulls show the sort of facial damage that you might expect if fighting in this way was sufficiently widespread to act as a selective force. And similarly, no real discussion of whether Paranthropus could form a fist capable of doing such damage. (The paper on Australopithecus sediba to which they refer actually describes sediba's hand as a mosaic of features.) In other words, they're making a sweeping assumption - that paranthropines routinely beat the heck out of each other - to support the a priori assumption that our own facial evolution was shaped by this.

There's also the question of whether modern human faces show much evidence of having evolved in this way; they actually seem quite prone to damage. Noses & cheekbones are rather susceptible to damage, and the bones of the cranium - thinner than those of Paranthropus - are dangerously easy to break. At the same time, according to the authors' speculative view, our hands are particularly well adapted to deliver blunt-force trauma.

This quote from the paper (emphasis mine) says it for me; we really are dealing with conjecture & imagination: 

Starting with the hand of an arboreal great ape ancestor, it is possible to imagine a number of evolutionary transformations that would have resulted in a club-like structure adapted for fighting.

Rudyard Kipling might have appreciated it - a point also made by Brian Switek in his excellent commentary over at National Geographic.

Carrier, D. & Morgan, M. (2014) Protective buttressing of the hominin face. Biological Reviews doi: 10/1111/brv.12112

 

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In posting an item about the 'pig-ape hybridisation' suggestion for human origins, the Daily Mail is a) coming rather late to the story (a slow day in the newsroom, perhaps?) and b) showing more regard for sensationalism than for good investigative journalism.

The story's one I've posted about before (& I've reposted my original piece below). Seeing it again really makes me think that the originator of this particular idea is trying to have it both ways. If our morphology is as similar as he claims to that of pigs, and different from chimps, then the differences should show up in our genes. Yet they don't; genetically we are much closer to chimps than to swine. He claims that this can be explained by repeated back-crossing with early humans - which is effectively no more than special pleading (& conveniently ignores the issue of significant differences in chromosome number between the two taxa). 

 

The internet is a wondrous place: a source of information, of amusement, and - alarmingly often - of material that elicits a combination of 'say what?' and <head-desk>. And a hat-tip to PZ Myers for this particular example...

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Blog For Darwin Swan girl - portrait of the author as a young scientist

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