Homo nadeli, human evolution take two

[Ludicus]

Definitely not my area of expertise, but I find it interesting. I would like to hear you comments on this. (Sumskilz, are you there?)

Homo naledi and Pleistocene hominin evolution in subequatorial Africa http://dx.doi.org/10.7554/eLife.24234

...and mean that H. naledi possibly lived at the same time, and in the same place, as modern humans. Berger et al. explain that the existence of a relatively primitive species like H. naledi living this recently in southern Africa is at odds with previous thinking about human evolution.

[sumskilz]

Maybe not so primitive...

The overall pattern of these specimens is unique, with a confusing mix of seemingly primitive and derived traits. The species has several anatomical details also known in early species of our genus, such as Homo habilis and early members of Homo erectus. But it has a much smaller brain size than is typical of these species. In this and several aspects of its teeth, H. naledi resembles species that branched from our family tree much earlier in time, such as 3.2-million-year-old Australopithecus afarensis, the species of the famous “Lucy” fossil skeleton...

In evolutionary biology, such a mixture of features is known as an anatomical mosaic. Paleoanthropologists have learned over the past century that human evolution was not a gradual progression from a very apelike ancestor to modern humans. Our small canine teeth and more upright posture evolved very early in our lineage, our pattern of bipedal walking next. At the midpoint of our evolutionary tree, ancestors and relatives went on a spree of evolving larger molar and premolar teeth—a trend that turned around when the first members of our genus, Homo, started hunting and making stone tools. Only then did they develop the kind of social sharing that led to language, which today characterizes people around the world. The brain evolved late, the legs early, and every species in our ancestry has its own mosaic of features from this legacy.

H. naledi’s mosaic seems to conflict with this storyline. Nowhere is that more evident than at its hand, arm, and shoulder. Tracy Kivell of the University of Kent reported on the combination of a wrist and fingertips more humanlike than those of H. habilis, combined with very curved fingers, comparable to those of both the very earliest hominins and to living apes. Elen Feuerriegel of Australia National University showed a shoulder canted upward on the trunk where it would suit a climbing species, and an upper arm twisted in a way unlike other human relatives. Both match well to the thorax anatomy considered by Scott Williams of New York University, with a narrowed upper rib cage. H. naledi appears to have been a climber and a possible toolmaker, although we have not yet found any stone artifacts in the Dinaledi Chamber.

The legs of H. naledi were long and comparatively slender, with some evidence for an elongation of the lower leg, according to Damiano Marchi of the University of Pisa and Christopher Walker of Duke University. However, Caroline VanSickle of the University of Wisconsin–Madison reported that the hips substantially share an anatomical pattern with the much-shorter-statured Lucy skeleton. Zach Throckmorton of Lincoln Memorial University took on the task of building this mixture of features into an overall picture of H. naledi’s gait, noting the evidence for a more humanlike foot.

The overall picture given by the results presented at the April symposium is that H. naledi walked more or less like humans do, seems to have had hands well made for handling and manipulating objects, and had teeth that indicate a high-quality diet—all things that link the species to our genus. Yet, it had a trunk, hips, shoulders, and fingers that contrast with that picture, and it had a brain similar in size to those of some of the earliest branches of the hominin lineage. In many ways H. naledi was adapted like a human, without anything like a human brain...

The Latest on Homo naledi

But wait...

It’s not the size of your brain, it’s how you organise it. The most recently discovered species of early human had a skull only slightly larger than a chimpanzee’s, but its brain looked surprisingly like our own – particularly in an area of the frontal lobe with links to language.

This could back suggestions that these mysterious early humans showed advanced behaviours, such as teamwork and burial, even though we still don’t know exactly when they lived...

It had a peculiar mix of anatomical features, which is part of what makes it hard to tell when the species lived. But what really set tongues wagging was the suggestion by Berger and his colleagues that H. naledi had deliberately disposed of its dead in this deep, dark, difficult-to-reach cave chamber full of remains.

Such an endeavour probably required emotional sophistication, not to mention teamwork, to carry out the task, but H. naledi’s skull was less than half the size of our own. Could its tiny brain have powered such advanced behaviour?

Berger and the other members of the H. naledi research team think it could. Using pieces of fossil skull, the group has now produced casts of parts of H. naledi’s small brain. The pattern of ridges and troughs (called gyri and sulci) on the surface of the casts offers hints about the way the brain was organised.

“Some of the casts we are working on are the most extraordinarily preserved I’ve ever seen,” says John Hawks at the University of Wisconsin-Madison. “The detail is just pristine.”

Mystery human species Homo naledi had tiny but advanced brain

The date doesn't actually surprise me, because I was expecting a more recent species in sub-Saharan Africa to be found...

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

But is naledi really that species? Maybe not, depending on time of divergence.

[Ludicus]

Thanks so much for sharing your knowledge, sumskilz

[Cyclops]

How I met your archaic mother? Fabulous stuff guys, very informative.

I have a hard time getting my head around the many variables that shape an individuals morphology, from genetic conditions like Down's Syndrome (I recall the Hobbit debate and the questions as to whether they were a separate species or a specific colony of diseased individuals) to normal variation within a group.

I guess these traps are well understood now, and gone are the days of Neanderthal Man being dismissed as a Cossack casualty of the Napoleonic Wars. I look forward to more finds to clarify this picture. The stuff about archaic introgression reminds me of a recent TV show where a South African researcher discovered really interesting stuff about San and other "Bushman" people, with very ancient Y lineages indeed (she didn't want to say on camera but implied over 200,000 years). Small isolated populations of reasonable size seem to have persisted and maintained an incredible level of genetic diversity in Africa, compared to the (now enormous but initially quite small I guess) exiting populations. This would allow "archaic" groups to coexist proximate with others for the introgression to occur.

[sumskilz]

I have a hard time getting my head around the many variables that shape an individuals morphology, from genetic conditions like Down's Syndrome (I recall the Hobbit debate and the questions as to whether they were a separate species or a specific colony of diseased individuals) to normal variation within a group.

I guess these traps are well understood now, and gone are the days of Neanderthal Man being dismissed as a Cossack casualty of the Napoleonic Wars.

That debate about H. floresiensis is silly when you have nine individuals from over a long span of time and teeth from local likely ancestral individuals. As I remember it, there were some strong public statements made when it was only one individual and still reasonable to be skeptical, but then as more evidence came to light, the skeptics were too ego invested to back down. Which is good for science anyway, but I still think it went on to the point of absurdity. With H. naledi, there have already been fifteen individuals found.

The stuff about archaic introgression reminds me of a recent TV show where a South African researcher discovered really interesting stuff about San and other "Bushman" people, with very ancient Y lineages indeed (she didn't want to say on camera but implied over 200,000 years). Small isolated populations of reasonable size seem to have persisted and maintained an incredible level of genetic diversity in Africa, compared to the (now enormous but initially quite small I guess) exiting populations. This would allow "archaic" groups to coexist proximate with others for the introgression to occur.

The number may be more like 300,000 years if the new mutation rate estimates are more accurate. The best term for Khoi-San people is "basal", as in diverging closest to the base of the tree. Same for the Y lineage mentioned. Professionals shouldn't be using "ancient" because it implies that the population hasn't changed since the divergence. Pygmies are second most basal, but they have a fair amount of admixture from the Bantu expansion:

K=2 separates Pygmy from Bantu:

Spoiler Alert, click show to read: 

Source: Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies

Which means their local ancestors a couple thousand years ago were even smaller. In our species, there is good evidence for convergent evolution of small size in particular environments, so likewise both H. naledi and H. floresiensis could have had larger ancestors.

[Cyclops]

...Professionals shouldn't be using "ancient" because it implies that the population hasn't changed since the divergence. ...

Lucky I'm an amateur then.

Here's the link to the report on Australian TV to Vanessa Haye's work.

http://www.abc.net.au/catalyst/stories/4545616.htm

Just a factoid snippet, sadly she does us the phrase "ancient lineages" (7:28 ff), and she gets all coy when the interviewer asks about how far back the mtDNA lineages go (7.40 or thereabouts), just saying "past 200,000". I think I said Y lineages above, sorry.

She also hints at the political difficulties with this issue: it took backing from Desmond Tutu to get the database up and running, and there's been very little work done on Australian Aborigines.

[sumskilz]

Just a factoid snippet, sadly she does us the phrase "ancient lineages" (7:28 ff), and she gets all coy when the interviewer asks about how far back the mtDNA lineages go (7.40 or thereabouts), just saying "past 200,000". I think I said Y lineages above, sorry.

They also have Y-haplogroup A which is the most basal, so it sounded reasonable as well, but actually the most basal Y is believed to be younger. What she says about the distinctiveness of the Khoi from the San could give the wrong impression. Autosomally they form a clade with each other to the exclusion of other human populations. The issue with uniparental markers (that she's basing her observation on) is that it's not unusual for them to go extinct in a particular population or region.

Mitochondrial DNA was extracted from H. heidelbergensis in Spain. Now you'd assume that it would be ancestral to European Neanderthal mtDNA, but so far there is no evidence for that. It is however ancestral to mtDNA lineages in East Asian Denisovans.

Autosomal DNA from naledi could really clear some things up, but so far they've failed at even extracting mtDNA.

[Copperknickers II]

Interesting that modern humans were coexisting with other hominid species. Obviously this is well known in Europe and Asia but had it been encountered before in Africa at this time? It seems that for most of the past 250,000 years the world resembled Lord of the Rings, with various different types of 'person' interacting with each other both violently and peacefully. One wonders what the relationship was between the diminutive homo naledi and homo sapiens: the relations between the Bantu and the Pygmies after all are not hugely good, they Pygmies were effectively enslaved. Perhaps homo naledi were the helots of ancient Africa?

[Magister Militum Flavius Aetius]

Or Morlocks and Eloi.

[sumskilz]

Interesting that modern humans were coexisting with other hominid species. Obviously this is well known in Europe and Asia but had it been encountered before in Africa at this time?

This is the first clear fossil evidence. There was the aforementioned indirect evidence of archaic introgression, particularly in pygmies. There is also the issue that we have modern human lineages that, based on mutation rate estimates, diverged from each other earlier than modern humans are believed to have evolved from H. heidelbergensis, which suggests that anatomically modern humans may have lived in Africa at the same time as some humans who were morphologically more similar to earlier heidelbergensis. That's more of a gray area regarding speciation though, rather than a clear example of two species living side by side.

Some consider H. sapiens idaltu (dated 160,000 and 154,000 years ago) to be a different species rather than a sub-species:



Morphologically, they are intermediate between the African H. heidelbergensis​ and the oldest relatively complete anatomically modern humans we've found - in modern Israel dated (by various methods) to ~95,000 years ago.



Earlier than that, the only H. sapiens fossils have are from Kenya dated to ~196,000 years ago, but you can see why one might be skeptical about drawing too many morphological conclusions:

[Copperknickers II]

Incidentally I'm surprised nobody posted about this:

https://www.newscientist.com/article...pe-not-africa/

It seems our understanding of human evolution has been undergoing some major changes in the past 10 years, so many textbooks are going to have to be rewritten.

[sumskilz]

Incidentally I'm surprised nobody posted about this:

https://www.newscientist.com/article...pe-not-africa/

It seems our understanding of human evolution has been undergoing some major changes in the past 10 years, so many textbooks are going to have to be rewritten.

It's in the wrong sub-forum. You know, assuming these guys were preliterate.

[Phier]

I was recently at the Field Museum in Chicago. They have a very nice big permanent exhibit on Evolution, starting from the start as best we know it, and you walk through various Eras and such with fossils, explaining it.

Well I get to the Neanderthal and it says this...

http://imgur.com/a/Wx1um

So my genetic test showing I have almost 4% Neanderthal DNA....

[sumskilz]

I was recently at the Field Museum in Chicago. They have a very nice big permanent exhibit on Evolution, starting from the start as best we know it, and you walk through various Eras and such with fossils, explaining it.

Well I get to the Neanderthal and it says this...

http://imgur.com/a/Wx1um

So my genetic test showing I have almost 4% Neanderthal DNA....

You'd think seven years would have been enough time to change the sign, but I think it's more than that because I see this sort of thing in writing all the time by people who should, and probably do, know better. Introgression is ancestry, but the problem is the word "our" in the most inclusive sense.