The significance of the discovery of modern humans in Arabia >85kya is that it provides a second spot (other than Israel) were modern humans existed outside Africa long before the alleged 60kya blitz out of the continent. We now have modern humans outside Africa in roughly two locations (Israel and Arabia), and three time slices (~175-85kya) in Misliya, Shkul/Qafzeh, and Al Wusta-1. It is no longer tenable to claim that these modern humans "died out" to make way for the alleged 60kya OoA event.
An important implication of pre-60kya Eurasians not dying out is that in all likelihood mtDNA haplogroup L3 and Y-chromosome haplogroup E originated in Eurasia, not Africa, and represent major Eurasian admixture into Africa.
Out of Africa theory is not dead (yet), but it resembles Rocky Balboa taking punch after punch round after round over the last 10 years or so. Will it make a cinematic last round comeback and prove itself, or will it be dealt a knockout punch in the near future?
Nature Ecology and Evolution (2018)
doi:10.1038/s41559-018-0518-2
Homo sapiens in Arabia by 85,000 years ago
Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130–90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60–50 ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85 ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95–86 ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall.
Link
Showing posts with label Out of Arabia. Show all posts
Showing posts with label Out of Arabia. Show all posts
April 10, 2018
January 26, 2018
Out of Africa: a theory in crisis
The sensational discovery of modern humans in the Levant 177-194 thousand years ago should cause a rethink of the currently held Out-of-Africa orthodoxy.
By Out-of-Africa, I mean here the origin of anatomically modern humans, as opposed to the earlier origin of the genus Homo or the later origin of behaviorally fully modern humans.
Two main pieces of evidence supported the conventional OOA theory:
1. The observation that modern Eurasians possess a subset of the genetic variation of modern Africans.
2. The greater antiquity of AMH humans in the African rather than the Eurasian palaeoanthropological record.
Both these observations are in crisis.
1a. The oldest African fossil AMH is in North Africa (Morocco, Jebel Irhoud); modern genetic variation does not single out this region as a potential source of modern humans. In short, modern genetic variation has nothing to say about where AMH originated.
1b. Eurasians can no longer be seen as a subset of Africans, given that they possess genetic variation from Denisovans, a layer of ancestry earlier than all extant AMH. While it is still true that most Eurasian genetic material is a subset of that of modern Africans, it is also true that the deepest known lineage of humans is the Denisovan-Sima de los huesos, with no evidence for any deeper African lineage. Within humans as a whole, Africans possess a subset of Eurasian genetic variation.
2a. African priority received a boost by 0.1My by the redating of Jebel Irhoud last year. And, non-African AMH received a boost of 0.05My by the Hershkovitz et al. paper yesterday. A very short time ago, Ethiopia boasted the oldest AMH by 0.07My and now it's tied with the Levant and beaten by Morocco. It's a bit silly to argue for temporal priority based on the spotty and ever-shifting palaeoanthropological record.
2b. It is virtually untenable to consider the ~120,000 year old Shkul/Qafzeh hominins as a failed Out-of-Africa, since it now seems that they may have been descendants from the Mislya Cave population of >50,000 or even >100,000 years earlier.
I had previously supported a "two deserts" theory of human origins in which AMH originated in North Africa (Sahara) and then left Africa >100kya as evidenced by the Shkul/Qafzeh hominins and/or the Nubian technocomplex in Arabia. While I am still convinced that AMH originated somewhere in North Africa or the Near East, I am less certain as to where.
Science 26 Jan 2018: Vol. 359, Issue 6374, pp. 456-459 DOI: 10.1126/science.aap8369
The earliest modern humans outside Africa
Israel Hershkovitz et al.
To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.
Link
By Out-of-Africa, I mean here the origin of anatomically modern humans, as opposed to the earlier origin of the genus Homo or the later origin of behaviorally fully modern humans.
Two main pieces of evidence supported the conventional OOA theory:
1. The observation that modern Eurasians possess a subset of the genetic variation of modern Africans.
2. The greater antiquity of AMH humans in the African rather than the Eurasian palaeoanthropological record.
Both these observations are in crisis.
1a. The oldest African fossil AMH is in North Africa (Morocco, Jebel Irhoud); modern genetic variation does not single out this region as a potential source of modern humans. In short, modern genetic variation has nothing to say about where AMH originated.
1b. Eurasians can no longer be seen as a subset of Africans, given that they possess genetic variation from Denisovans, a layer of ancestry earlier than all extant AMH. While it is still true that most Eurasian genetic material is a subset of that of modern Africans, it is also true that the deepest known lineage of humans is the Denisovan-Sima de los huesos, with no evidence for any deeper African lineage. Within humans as a whole, Africans possess a subset of Eurasian genetic variation.
2a. African priority received a boost by 0.1My by the redating of Jebel Irhoud last year. And, non-African AMH received a boost of 0.05My by the Hershkovitz et al. paper yesterday. A very short time ago, Ethiopia boasted the oldest AMH by 0.07My and now it's tied with the Levant and beaten by Morocco. It's a bit silly to argue for temporal priority based on the spotty and ever-shifting palaeoanthropological record.
2b. It is virtually untenable to consider the ~120,000 year old Shkul/Qafzeh hominins as a failed Out-of-Africa, since it now seems that they may have been descendants from the Mislya Cave population of >50,000 or even >100,000 years earlier.
I had previously supported a "two deserts" theory of human origins in which AMH originated in North Africa (Sahara) and then left Africa >100kya as evidenced by the Shkul/Qafzeh hominins and/or the Nubian technocomplex in Arabia. While I am still convinced that AMH originated somewhere in North Africa or the Near East, I am less certain as to where.
Science 26 Jan 2018: Vol. 359, Issue 6374, pp. 456-459 DOI: 10.1126/science.aap8369
The earliest modern humans outside Africa
Israel Hershkovitz et al.
To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.
Link
April 25, 2016
Bursts in human male demography
When the tree is calibrated with a mutation rate estimate of 0.76 × 10-9 mutations per base pair per year9, the time to the most recent common ancestor (TMRCA) of the tree is ~190,000 years, but we consider the implications of alternative mutation rate estimates below. Of the clades resulting from the four deepest branching events, all but one are exclusive to Africa, and the TMRCA of all non-African lineages (that is, the TMRCA of haplogroups DE and CF) is ~76,000 years (Fig. 1, Supplementary Figs. 18 and 19, Supplementary Table 10, and Supplementary Note). We saw a notable increase in the number of lineages outside Africa ~50–55 kya, perhaps reflecting the geographical expansion and differentiation of Eurasian populations as they settled the vast expanse of these continents. Consistent with previous proposals14, a parsimonious interpretation of the phylogeny is that the predominant African haplogroup, haplogroup E, arose outside the continent. This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). Furthermore, the timing of this putative return to Africa—between the emergence of haplogroup E and its differentiation within Africa by 58 kya—is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and nearby regions of Asia 50–80 kya15.I've long argued for the Y-chromosome haplogroup E migration into Africa and it is nice to see this common-sense interpretation finally adopted. Too much focus has been placed on figuring out which routes modern humans took out of Africa, and not at all to figure out how Eurasian males came to overwhelm the African Y-chromosome gene pool so decisively. The Eurasian migration into Africa must have taken place in the ~70-60kya window, constrained by the D/E split and the deepest intra-African E splits. I think that the Out-of-Arabia scenario I outlined in 2012 continues to make a lot of sense. It would be awesome to get data from the first Later Stone Age people from Africa which are probably the best bet to trace this migration from Eurasia into Sub-Saharan Africa.
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
G David Poznik et al.
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
Link
April 10, 2016
Nubian assemblages from the Negev
Nubian assemblages from the Levant are quite important because they provide an intermediate link (along land routes) between those from Africa and Arabia. It's also more difficult now to consider the Arabian finds as a limited event without broader implications about modern human dispersals.
From the paper:
“Diffusion with modifications”: Nubian assemblages in the central Negev highlands of Israel and their implications for Middle Paleolithic inter-regional interactions
Mae Goder-Goldberger, Natalia Gubenko, Erella Hovers
Nubian Levallois cores, now known from sites in eastern Africa, the Nile Valley and Arabia, have been used as a material culture marker for Upper Pleistocene dispersals of hominins out of Africa. The Levantine corridor, being the only land route connecting Africa to Eurasia, has been viewed as a possible dispersal route. We report here on lithic assemblages from the Negev highlands of Israel that contain both Levallois centripetal and Nubian-type cores. Wetter conditions over the Sahara and Negev deserts during MIS 6a–5e provided a generally continuous environmental corridor into the Levant that enabled the dispersal of hominin groups bearing the Nubian variant of prepared core technologies. The Negev assemblages draw renewed attention to the place of the Levant as one of the dispersal routes out of Africa during the Late Pleistocene and could suggest that processes of human dispersals and cultural diffusion resulted in the spread of Nubian technology across eastern Africa, the western Sahara and the Nile Valley, the southern Levant and Arabia.
Link
Mapping the earliest dated sites that contain a Nubian component does not permit an unequivocal identification of a region of origin for the Nubian Technology.Quaternary International doi:10.1016/j.quaint.2016.02.008
“Diffusion with modifications”: Nubian assemblages in the central Negev highlands of Israel and their implications for Middle Paleolithic inter-regional interactions
Mae Goder-Goldberger, Natalia Gubenko, Erella Hovers
Nubian Levallois cores, now known from sites in eastern Africa, the Nile Valley and Arabia, have been used as a material culture marker for Upper Pleistocene dispersals of hominins out of Africa. The Levantine corridor, being the only land route connecting Africa to Eurasia, has been viewed as a possible dispersal route. We report here on lithic assemblages from the Negev highlands of Israel that contain both Levallois centripetal and Nubian-type cores. Wetter conditions over the Sahara and Negev deserts during MIS 6a–5e provided a generally continuous environmental corridor into the Levant that enabled the dispersal of hominin groups bearing the Nubian variant of prepared core technologies. The Negev assemblages draw renewed attention to the place of the Levant as one of the dispersal routes out of Africa during the Late Pleistocene and could suggest that processes of human dispersals and cultural diffusion resulted in the spread of Nubian technology across eastern Africa, the western Sahara and the Nile Valley, the southern Levant and Arabia.
Link
February 17, 2016
Ancestors of Eastern Neandertals admixed with modern humans 100 thousand years ago
If true, this is very hard to reconcile with late (60kya) out of Africa and may be a smoking gun for pre-100kya presence of anatomically modern humans in Eurasia. From the paper:
If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.
Things are bound to get more interesting.
Nature (2016) doi:10.1038/nature16544
Ancient gene flow from early modern humans into Eastern Neanderthals
Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Link
The inferred demographic model confirms and provides quantitative estimates of previously inferred gene flow events among modern and archaic humans2, 3 (Extended Data Fig. 1). These include Neanderthal gene flow into modern humans outside Africa (3.3–5.8%) and gene flow from an unknown archaic hominin into the ancestors of Denisovans (0.0–0.5%). Interestingly, we also detect a signal of gene flow from modern humans into the ancestors of the Altai Neanderthal (1.0–7.1%). The precise source of this gene flow is unclear, but it appears to come from a population that either split from the ancestors of all present-day Africans or from one of the early African lineages, as significant admixture rates are estimated from San as well as Yoruba individuals. This introgression thus occurred in the opposite direction from the previously reported gene flow from Neanderthals to modern humans outside AfricaAnd:
However, it is clear that the source of the gene flow is a population equally related to present-day Africans and non-Africans (Extended Data Fig. 3). We conclude that the introgressing population diverged from other modern human populations before or shortly after the split between the ancestors of San and other Africans (Fig. 3a), which occurred approximately 200,000 years ago11.The implications of this inference (if correct) for modern human origins are potentially monumental as they suggest a Eurasian modern human lineage (only detected in the Altai Neandertal) that diverges from other modern humans as early (if not earlier) than any two African ones.
If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.
Things are bound to get more interesting.
Nature (2016) doi:10.1038/nature16544
Ancient gene flow from early modern humans into Eastern Neanderthals
Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
Link
October 15, 2015
Modern humans in China ~80,000 years ago (?)
Another (?)-worthy paper has just appeared in Nature in the heels of the African ancient genome paper. Time will tell how these worldview-altering discoveries will change the story of Mankind, and a degree of skepticism is warranted. In the view I've held for a few years, modern humans expanded to Arabia before 100 thousand years ago, started leaving it 70 thousand years ago as the ecological situation worsened due to desertification and broke through the "Neandertal barrier" between 70-50 thousand years ago when they developed the skills and technology to overcome them.
The new paper claims that modern humans were in China 80 thousand years ago and came to Europe much later because Neandertal represented a barrier to successful entry to Europe. This begs the question of how they reached China without encountering Neandertals, as Neandertals were also in West Asia where -presumably- they passed through to get to China. A coastal route to south China would explain away this problem, but the coastal migration is usually envisioned much later, at around 60 thousand years ago. On top of that, how did Chinese end up having equal (or more) levels of Neandertals admixture if modern humans first went to China and later moved west and successfully outcompeted the Neandertals. How were they able to do so eventually? (There is no evidence that the kind of advantages associated with behavioral modernity first emerged in East Asia). It's possible that there were 80 thousand year-old modern humans in China (just as there were 100 thousand year-old modern humans in Israel), but that the later East Asians are not descended from them.
One would think that science would present an increasingly reasonable and consistent picture of the past, but it seems that we're a very long way from the point where the dust settles and the puzzle pieces start falling into place.
Nature (2015) doi:10.1038/nature15696
The earliest unequivocally modern humans in southern China
Wu Liu, María Martinón-Torres, Yan-jun Cai, Song Xing, Hao-wen Tong, Shu-wen Pei, Mark Jan Sier, Xiao-hong Wu, R. Lawrence Edwards, Hai Cheng, Yi-yuan Li, Xiong-xin Yang, José María Bermúdez de Castro & Xiu-jie Wu
The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking1, 2, 3, 4. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe5, 6, 7. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.
Link
The new paper claims that modern humans were in China 80 thousand years ago and came to Europe much later because Neandertal represented a barrier to successful entry to Europe. This begs the question of how they reached China without encountering Neandertals, as Neandertals were also in West Asia where -presumably- they passed through to get to China. A coastal route to south China would explain away this problem, but the coastal migration is usually envisioned much later, at around 60 thousand years ago. On top of that, how did Chinese end up having equal (or more) levels of Neandertals admixture if modern humans first went to China and later moved west and successfully outcompeted the Neandertals. How were they able to do so eventually? (There is no evidence that the kind of advantages associated with behavioral modernity first emerged in East Asia). It's possible that there were 80 thousand year-old modern humans in China (just as there were 100 thousand year-old modern humans in Israel), but that the later East Asians are not descended from them.
One would think that science would present an increasingly reasonable and consistent picture of the past, but it seems that we're a very long way from the point where the dust settles and the puzzle pieces start falling into place.
Nature (2015) doi:10.1038/nature15696
The earliest unequivocally modern humans in southern China
Wu Liu, María Martinón-Torres, Yan-jun Cai, Song Xing, Hao-wen Tong, Shu-wen Pei, Mark Jan Sier, Xiao-hong Wu, R. Lawrence Edwards, Hai Cheng, Yi-yuan Li, Xiong-xin Yang, José María Bermúdez de Castro & Xiu-jie Wu
The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking1, 2, 3, 4. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe5, 6, 7. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.
Link
August 13, 2015
Rethinking the dispersal of Homo sapiens out of Africa
An excellent review which -among its other graces- demolishes the view that mtDNA haplogroup L3 provides a terminus post quem of 70 thousand years for the Out-of-Africa expansion, a question I've discussed in this blog before.
I think the evidence is overwhelming at this point that there were modern humans outside Africa before 100,000 years ago. The argument that they were a failed expansion is shoddy and is based, as far as I can tell on things like the age of L3, the assumption that Y-chromosome haplogroup E is native to Africa and not derived from back-to-Africa migrants, the assumption that Out-of-Africa coincided with the Upper Paleolithic cultural efflorescence (disproven by the earlier dating of Neandertal admixture), or the failed hypothesis of a coastal route Out of Africa 60 thousand years ago that seems to be repeated in inverse proportion to the evidence for it. The halving of the human autosomal mutation rate relative to what was inferred before has certainly not helped either.
Rethinking the dispersal of Homo sapiens out of Africa
Huw S. Groucutt, Michael D. Petraglia, Geoff Bailey, Eleanor M. L. Scerri, Ash Parton, Laine Clark-Balzan, Richard P. Jennings, Laura Lewis, James Blinkhorn, Nick A. Drake, Paul S. Breeze, Robyn H. Inglis, Maud H. Devès, Matthew Meredith-Williams, Nicole Boivin, Mark G. Thomas andAylwyn Scally
Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.
Link and here
May 30, 2015
Out of Egypt or Out of Ethiopia?
I am skeptical that once you remove non-African ancestry from Egyptians (even if you were able to do so perfectly), what you are left with is indigenous Northeastern Africans, the direct descendants of people who left Africa tens of thousands of years ago.
For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.
For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.
AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019
Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians
Luca Pagani et al.
The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.
Link
For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.
For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.
AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019
Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians
Luca Pagani et al.
The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.
Link
September 09, 2014
An archaeological scenario for Out of Arabia
Jeffrey Rose and Anthony Marks have a preprint in which he details an archaeological scenario for the emergence of the Emiran (arguably the best candidate for the ur-Upper Paleolithic at the moment) from Arabian progenitors who themselves had Northeast African Nubian Levallois progenitors. I proposed Out of Arabia a few years ago and followed research suggestive of such a trajectory of modern humans in various posts under the Out of Arabia label.
In a nutshell, it seems to me that the 50kya OoAfrica model is wrong, falsified by (i) the dating of Neandertal adixture (which precedes it and could only have happened outside of Africa), (ii) the dating of human mtDNA and NRY trees in numerous papers that show a split that precedes 50kya. This in itself proves that the Upper Paleolithic (which is attested in the post-50kya period and rapidly spreads across Eurasia in a genetic Big Bang of expansion leading to the full disappearance of Neandertals by ~40kya) must have local Eurasian origins rather than being an import from Africa.
If UP is not linked to the Out-of-Africa event, then two questions arise: (i) how did the UP arise in Eurasia, and (ii) when did the Out-of-Africa event take place? The increasing adoption of a "slow mutation rate", the discovery of a potential ~100kya layer of ancestry separating Europeans from East Asians, and, on the archaeology side, the proliferation of evidence against the "coastal migration route" all hint in OoAfrica taking place much earlier than the UP revolution in answer to question (ii). Indeed, one of the few stumbling blocks of a much earlier Out-of-Africa (the date of L3~70kya) may actually be falling, if it turns out that African L3 is nested within Eurasian M+N and not vice versa. The new preprint by Rose snf Marks helps answer question (i) by proposing an archaeological scenario that derives the UP of the Levant from the MP of Arabia.
From the paper:
However, if AMH were also present in Arabia during the MP it is much more difficult to argue for extinction of Eurasian modern humans and later replacement by a "late" Out-of-Africa event: this would imply that both the Levantine and Arabian humans would disappear. Moreover, the genetics no longer requires a late Out-of-Africa event and the UP is no longer plausibly concurrent with the OoAfrica event. In short, a quite simple explanation is that one group of AMH (from Arabia) mixed with another group of AMH (from the Levant) and the UP arose in this population. The latter group (from the Levant) lived in proximity to Neandertals and thus the evidence for Neandertal admixture in non-Africans is easily explained (no need to invoke unattested Neandertals admixing with "coastal route" migrating humans).
"Out of Arabia" and the Middle-Upper Palaeolithic transition in the southern Levant
Jeffrey I. Rose, Anthony E. Marks
Beginning some 50 thousand years ago, a technological transition spread across the Near East and into Eurasia, in the most general terms characterized by a shift from preferential, prepared core reduction systems to the serial production of elongated points via opposed platform cores. The earliest known occurrence of such a technological shift is the Emiran Industry, whose earliest manifestations are found in the southern Levant. The cultural and demographic source(s) of this industry, however, remain unresolved. Looking to archaeogenetic research, the emerging picture indicates a major dispersal of our species out of Africa between 100 and 50 thousand years ago. Ancient DNA evidence points to low levels of admixture between Neanderthal and these pioneering modern human populations, which some suggest occurred in the Near East between 60 and 40 thousand years ago. These propositions underscore the significance of the Emiran and beg a reassessment of its origins. In this paper, we ask whether the Emiran was a local development, a cultural/demographic replacement, or the fusion of indigenous and exogenous lithic traditions. Our analysis considers the techno-typological features of the early Emiran in relation to late Middle Palaeolithic and contemporaneous assemblages from adjacent territories in Northeast Africa and the Arabian Peninsula, in order to identify overlapping cultural features and potential antecedents. Parsimonious with the archaeogenetic scenario of admixture, the Emiran seems to represent a fusion of local southern Levantine Mousterian typological elements with the Afro-Arabian Nubian Levallois reduction strategy. We conclude that the Emiran is primarily rooted in the Early Nubian Complex of the Nile Valley, which spread into the Arabian Peninsula during the Last Interglacial and developed at the interface of these two contextual areas between 100 and 50 thousand years ago.
Link
In a nutshell, it seems to me that the 50kya OoAfrica model is wrong, falsified by (i) the dating of Neandertal adixture (which precedes it and could only have happened outside of Africa), (ii) the dating of human mtDNA and NRY trees in numerous papers that show a split that precedes 50kya. This in itself proves that the Upper Paleolithic (which is attested in the post-50kya period and rapidly spreads across Eurasia in a genetic Big Bang of expansion leading to the full disappearance of Neandertals by ~40kya) must have local Eurasian origins rather than being an import from Africa.
If UP is not linked to the Out-of-Africa event, then two questions arise: (i) how did the UP arise in Eurasia, and (ii) when did the Out-of-Africa event take place? The increasing adoption of a "slow mutation rate", the discovery of a potential ~100kya layer of ancestry separating Europeans from East Asians, and, on the archaeology side, the proliferation of evidence against the "coastal migration route" all hint in OoAfrica taking place much earlier than the UP revolution in answer to question (ii). Indeed, one of the few stumbling blocks of a much earlier Out-of-Africa (the date of L3~70kya) may actually be falling, if it turns out that African L3 is nested within Eurasian M+N and not vice versa. The new preprint by Rose snf Marks helps answer question (i) by proposing an archaeological scenario that derives the UP of the Levant from the MP of Arabia.
From the paper:
In sum, the tool assemblages of the early Emiran include a combination of both classic UP tool types and MP Levallois points; it cannot be accurately characterized as fully UP, rather, an amalgamation of MP and UP forms. Viewed solely within a Levantine context, the technological and typological patterning of the early Emiran might suggest it derived from local innovation without significant external demographic input.
...
So, with no clear cut antecedents in the Levant, do the three Emiran technological traits that have no deep Levantine ancestry (i.e., bidirectional core preparation, the use of cresting, and the presence of lateral modification on Levallois points), have demonstrable origins elsewhere? Conversely, do those deeply rooted Levantine characteristics of the Emiran (i.e., elongated Levallois point production and UP tool manufacture) have comparable analogues in adjacent areas?
...
Given these technological and typological considerations, we find no direct relationship between any northeast African MIS 5 industry and the early Emiran. The African data do suggest that the Emiran preferential bidirectional Levallois point production strategy ultimately arose in northeast Africa during late MIS 6. This reduction strategy became increasingly widespread during MIS 5, where it spread as far south as the Ethiopian Rift and east into the Arabian Peninsula. This wide distribution suggests extensive cultural contact, either direct or indirect, along the Nile Valley and across the Red Sea during the Last Interglacial, when climatic conditions were optimal.
...
By MIS 5.3 (~ 100 ka), perhaps, even as early as the Last Interglacial, the African Nubian Complex was widespread in Arabia, from the Yemeni Hadramawt to the eastern edge of the Nejd Plateau in southern Oman. Additional manifestations of this technocomplex have been found in the Rub' al Khali, central Saudi Arabia, and the Al Jawf basin of northern Saudi Arabia, less than 300 km southeast of ‘Ain Difla. Given the Nilotic origin of the Nubian Complex, its presence in Arabia may be firmly understood as a huntergatherer range expansion out of northeast Africa.
...
The techno-typological patterns we have observed point to an origin of the Emiran that was neither wholly rooted in the Levant nor the result of a complete demographic replacement from groups expanding out of Africa; rather, the Emiran combines elements of the Nubian Levallois system with typological elements from the southern Levantine Mousterian. This scenario envisions a zone stretching across the interface of northwestern Arabia and the southern Levant, where the territories of Levantine and Arabian huntergatherer populations overlapped during MIS 5. Bilateral exchange over time resulted in the incorporation of an Afro-Arabian core reduction strategy with a Levantine toolmaking tradition that extends back to the Early Mousterian.
...
African Nubian Complex toolmakers, at least, were modern humans. AMH specimens have been documented in North Africa from 150 ka onward (Smith et al., 2007; Hublin and McPherron, 2012), while no other species has yet been found there. An AMH child burial was excavated from an extraction pit associated with Activity Phase III at Taramsa Hill 1 (Vermeersch et al., 1998; Van Peer et al., 2010), with a terminus post quem of ca. 70 ka. Given the technological similarity of the Classic Dhofar Nubian and the Late Nubian Complex of the Middle Nile Valley in Egypt, as well as the fact that there is no evidence for prior MP human occupation in southern Oman, it is reasonable to associate the distribution of Nubian Complex sites with a population of AMHs spread across northeast Africa and the Arabian Peninsula. The presence of Nubian Levallois technology in southern Arabia and the Horn of Africa (Clark, 1954; Kurashina, 1978; Clark, 1988; Beyin, 2013), as well as northern Arabia and in the Red Sea hills of Egypt, suggests that early human groups traveled to and from Africa via both the Arabian and Levantine Corridors.It is unfortunate that Arabia is so poor (to wholly deficient?) in ancient human remains from this critical period. Nonetheless, it makes sense that if modern humans were present in Northeast Africa in association with Nubian Complex tools, they would be the ones who carried them to Arabia. The presence of AMH in the Levant (associated with Mousterian tools) was often dismissed until recently as the Out-of-Africa that failed, partly because the Shkul/Qafzeh hominins were the only pre-UP modern humans in Eurasia (making their extinction plausible) and partly because of the widespread view that Out-of-Africa happened ~70-50kya (which by definition would imply that the Mount Carmel hominins weren't the Out-of-Africa.
However, if AMH were also present in Arabia during the MP it is much more difficult to argue for extinction of Eurasian modern humans and later replacement by a "late" Out-of-Africa event: this would imply that both the Levantine and Arabian humans would disappear. Moreover, the genetics no longer requires a late Out-of-Africa event and the UP is no longer plausibly concurrent with the OoAfrica event. In short, a quite simple explanation is that one group of AMH (from Arabia) mixed with another group of AMH (from the Levant) and the UP arose in this population. The latter group (from the Levant) lived in proximity to Neandertals and thus the evidence for Neandertal admixture in non-Africans is easily explained (no need to invoke unattested Neandertals admixing with "coastal route" migrating humans).
"Out of Arabia" and the Middle-Upper Palaeolithic transition in the southern Levant
Jeffrey I. Rose, Anthony E. Marks
Beginning some 50 thousand years ago, a technological transition spread across the Near East and into Eurasia, in the most general terms characterized by a shift from preferential, prepared core reduction systems to the serial production of elongated points via opposed platform cores. The earliest known occurrence of such a technological shift is the Emiran Industry, whose earliest manifestations are found in the southern Levant. The cultural and demographic source(s) of this industry, however, remain unresolved. Looking to archaeogenetic research, the emerging picture indicates a major dispersal of our species out of Africa between 100 and 50 thousand years ago. Ancient DNA evidence points to low levels of admixture between Neanderthal and these pioneering modern human populations, which some suggest occurred in the Near East between 60 and 40 thousand years ago. These propositions underscore the significance of the Emiran and beg a reassessment of its origins. In this paper, we ask whether the Emiran was a local development, a cultural/demographic replacement, or the fusion of indigenous and exogenous lithic traditions. Our analysis considers the techno-typological features of the early Emiran in relation to late Middle Palaeolithic and contemporaneous assemblages from adjacent territories in Northeast Africa and the Arabian Peninsula, in order to identify overlapping cultural features and potential antecedents. Parsimonious with the archaeogenetic scenario of admixture, the Emiran seems to represent a fusion of local southern Levantine Mousterian typological elements with the Afro-Arabian Nubian Levallois reduction strategy. We conclude that the Emiran is primarily rooted in the Early Nubian Complex of the Nile Valley, which spread into the Arabian Peninsula during the Last Interglacial and developed at the interface of these two contextual areas between 100 and 50 thousand years ago.
Link
August 09, 2014
New estimates of human mtDNA node dates and substitution rates (Rieux et al. 2014)
This is a quite useful paper as it compares different methods of obtaining mutation rate estimates, either using "archaeological calibration" based on known migration events or ancient mtDNA genomes (with known archaeological dates). The authors write:
It should be fairly easy to pick out the common ancestor of Eurasian mtDNA (the common ancestor of M+N). I am reasonably sure that the two African red dots to the right of event "8" in the figure are African L3's, and this would place them within the Eurasian variation, and in particular as a relative of Eurasian M.
A similar observation could be found in Supplementary Figure 14 of the Lippold et al. (2014) preprint, with African L3 lineages clearly related to Eurasian M (and nested within the Eurasian phylogeny).
In any case, I don't see any evidence at all from this phylogeny that the date of L3 corresponds to an Out-of-Africa event. Unfortunately I couldn't see an estimate for the split of L3 from the rest of the phylogeny; my eyeball estimate from the figure is that it's about 20ky earlier. Hopefully, someone sooner or later will deal with the question of L3 phylogeny, because the "conventional wisdom" that Eurasian M, N are nested within African L3 variation does not appear to be quite right.
Mol Biol Evol (2014) doi: 10.1093/molbev/msu222
Improved calibration of the human mitochondrial clock using ancient genomes
Adrien Rieux et al.
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g. the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g. first entry into the Americas). The recent availability of ancient mtDNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analysed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive dataset of 350 ancient and modern human complete mtDNA genomes, among which 146 were generated for the purpose of this study, and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same dataset, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.
Link
Our estimate of 143 Kya [112-180 95% HPD] for the TMRCA of all modern human mtDNA is slightly younger but highly consistent with the 157 Kya [120-197 95% HPD] value obtained by Fu et al. (2013b). We stimate the coalescence of the L3 haplogroup (the lineage from which all non-African mtDNA haplogroups descend), often used to date the “out-of-Africa” event, to 72 Kya [54-93 95%HPD], a value also onsistent with Fu et al. (2013b) estimation of 78 Kya [62-95 95%HPD]. This estimation rather places a conservative upper bound of 93 kya for the time of the last major gene exchange between non-African nd sub-Saharan African populations. As pointed out by Fu et al. (2013b), it is important to recognize that this divergence time may merely represent the most recent gene exchanges between the ancestors f non-Africans and the most closely related sub-Saharan Africans and thus may reflect only the most recent population split in a long, drawn-out process of population separation (Scally and Durbin 2012).The 72kya date would agree quite well with my postulated Out-of-Arabia event circa 70 thousand years ago.
It should be fairly easy to pick out the common ancestor of Eurasian mtDNA (the common ancestor of M+N). I am reasonably sure that the two African red dots to the right of event "8" in the figure are African L3's, and this would place them within the Eurasian variation, and in particular as a relative of Eurasian M.
A similar observation could be found in Supplementary Figure 14 of the Lippold et al. (2014) preprint, with African L3 lineages clearly related to Eurasian M (and nested within the Eurasian phylogeny).
In any case, I don't see any evidence at all from this phylogeny that the date of L3 corresponds to an Out-of-Africa event. Unfortunately I couldn't see an estimate for the split of L3 from the rest of the phylogeny; my eyeball estimate from the figure is that it's about 20ky earlier. Hopefully, someone sooner or later will deal with the question of L3 phylogeny, because the "conventional wisdom" that Eurasian M, N are nested within African L3 variation does not appear to be quite right.
Mol Biol Evol (2014) doi: 10.1093/molbev/msu222
Improved calibration of the human mitochondrial clock using ancient genomes
Adrien Rieux et al.
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g. the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g. first entry into the Americas). The recent availability of ancient mtDNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analysed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive dataset of 350 ancient and modern human complete mtDNA genomes, among which 146 were generated for the purpose of this study, and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same dataset, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.
Link
May 04, 2014
Genealogical vs. Evolutionary Y-STR mutation rate
Long-time readers will remember my Y-STR series which was inspired by my desire to figure out why some papers used the directly observed mutation rate for Y-STRs while others used a 3-times slower "evolutionary" one. My conclusion was that the evolutionary rate was misapplied because its theoretical justification hinged on an assumption of constant population size that was wrong for modern humans and even modest amounts of growth led to a mutation rate that was closer to the genealogical one.
My enthusiasm for Y-STR based dating waned in 2011 when Busby et al. (2011) published a study which showed the effect of microsatellite choice on TMRCA estimates due to the fact that Y-STRs don't follow the the unconstrained strict symmetrical stepwise model (i.e., increase by +/- 1 steps per mutational event with equal probability). This meant that various published age estimates depended on the cocktail of slow/fast Y-STRs used as well as the age of the target node in the phylogeny (because deviations from linearity were more egregious for older nodes). Additionally, at that time it was clear that whole Y chromosome sequencing was around the corner and so the issue would soon be resolved by a new technology.
A new preprint presents an interesting coda to this long-standing controversy and basically agrees that the genealogical rate is better than the evolutionary one in the sense that it produces age estimates that are closer to those from resequencing. The evolutionary rate is good only for the very deep split in the tree which is not surprising since this is the domain where deviations from linearity plague the genealogical rate so a slower rate will do better.
One comment to the authors is that the generation length of 25 years is not applicable to modern humans, but rather a male generation length of 31-32 years has been estimated across different cultures. The authors estimate the "super-Eurasian" CT clade at 56.26kya (using sequence data) which would correspond to ~71 thousand years if we apply a 31.5/25 multiplier. This would bring it closer to the age estimate for Eurasian M+N mtDNA which has been estimated without an assumption of generation length using ancient DNA. (There is of course no a priori reason that the two should match, but the dates seem to match with the drying up of the Sahara-Arabia zone c. 70kya. As I've argued before, the population contraction that must have accompanied such a traumatic event would be a good opportunity for drift to shed genetic lineages and leave the CT/M+N pair as the inheritors of Eurasia).
bioRxiv doi: 10.1101/004705
Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates
Chuan-Chao Wang, Li Hui
We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R. In addition, genealogical rates lead to more plausible time estimates for Neolithic coalescent sublineages compared with sequence-based dating.
Link
My enthusiasm for Y-STR based dating waned in 2011 when Busby et al. (2011) published a study which showed the effect of microsatellite choice on TMRCA estimates due to the fact that Y-STRs don't follow the the unconstrained strict symmetrical stepwise model (i.e., increase by +/- 1 steps per mutational event with equal probability). This meant that various published age estimates depended on the cocktail of slow/fast Y-STRs used as well as the age of the target node in the phylogeny (because deviations from linearity were more egregious for older nodes). Additionally, at that time it was clear that whole Y chromosome sequencing was around the corner and so the issue would soon be resolved by a new technology.
One comment to the authors is that the generation length of 25 years is not applicable to modern humans, but rather a male generation length of 31-32 years has been estimated across different cultures. The authors estimate the "super-Eurasian" CT clade at 56.26kya (using sequence data) which would correspond to ~71 thousand years if we apply a 31.5/25 multiplier. This would bring it closer to the age estimate for Eurasian M+N mtDNA which has been estimated without an assumption of generation length using ancient DNA. (There is of course no a priori reason that the two should match, but the dates seem to match with the drying up of the Sahara-Arabia zone c. 70kya. As I've argued before, the population contraction that must have accompanied such a traumatic event would be a good opportunity for drift to shed genetic lineages and leave the CT/M+N pair as the inheritors of Eurasia).
bioRxiv doi: 10.1101/004705
Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates
Chuan-Chao Wang, Li Hui
We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R. In addition, genealogical rates lead to more plausible time estimates for Neolithic coalescent sublineages compared with sequence-based dating.
Link
March 09, 2014
Green Arabia 2014 conference
The program of an upcoming conference that will take in about a month. I don't see abstracts but the list of talks seems interesting and hopefully there will be a twitter stream by attendees in April.
December 15, 2013
Arabian origin of the Upper Paleolithic in the Levant
This is a very useful review of research on the origin of the Upper Paleolithic (Emiran) in the Levant, arguing against a recent (c. 50kya ) African origin and in favor of an Arabian one. The argument is mainly archaeological, although it is informed by genetic evidence. From the chapter:
A century of research into the origins of the Upper Palaeolithic in the Levant
Anthony E. Marks and Jeffrey I. Rose
Link
After a century of research, the origins of the Levantine UP still remain an enigma. At this point, at least one thing is clear: the Emiran has no African progenitor. As such, there is a disconnect between the archaeological database and the Replacement paradigm, which necessitates that the earliest Levantine Upper Paleolithic must have come fully developed from northeast Africa. The Replacement model should have been a parsimonious prism through which to view the transition from the MP to the UP in the Levant. It was not.The recent acceptance of: (i) a slower autosomal mutation rate, and (ii) evidence for interbreeding with Neandertals largely predating the c. 50kya mark, and (iii) coalescence of Eurasian mtDNA haplogroup N well before that time, have all but killed, in my opinion the idea of a 50kya spread of modern humans from Africa. Modern humans must have lived in Eurasia much earlier than that time, and what remains is to figure out how much earlier.
A century of research into the origins of the Upper Palaeolithic in the Levant
Anthony E. Marks and Jeffrey I. Rose
Link
July 25, 2013
Middle Paleolithic and Neolithic occupations around Mundafan palaeolake (Crassard et al. 2013)
Survey in the Mundafan palaeolake basin revealed, for the first time, Middle Palaeolithic occupations. Recovery of Middle Palaeolithic assemblages corresponds with recent environmental and geoarchaeological studies that indicate at least three lacustrine wet phases in MIS 5 [23]. The main diagnostic lithic technology observed is the preferential Levallois reduction method, which is also present at the Jubbah palaeolake during MIS 5 (JQ-1, JSM-1 and JKF-1 sites: [21], [22]) and at the Jebel Faya rock shelter at the transition between MIS 6–5e (Assemblage C: [6]). This technology is absent in MIS 3 in southwest Yemen (SD1, SD2 and AS1 sites: [8], [9]). Earlier dating for preferential Levallois in Arabia, in MIS 7, is possible, but still insufficiently represented owing to small sample size at the Jubbah palaeolake (JQ-1: [22]). Other preferential Levallois methods have been observed in Dhofar, including in the Nubian Complex, dated to at least ca. 106 ka [7], in Hadramawt and the southern fringe of the Rub’ al-Khali, Oman [10], and in central Saudi Arabia at Al-Kharj [75]. Nubian Complex technology has not yet been identified at Mundafan. We associate the Levallois component in Mundafan with the wet pluvials of MIS 5, most probably during the wetter events of MIS 5e (ca. 125 ka), MIS 5c (ca. 100 ka) and MIS 5a (80 ka), when conditions were more favorable for hominin dispersals. The Middle Palaeolithic evidence thus provides empirical support for Rosenberg and colleagues assertion [23] that the dispersal of hominins into the Rub’ al-Khali occurred during ameliorated periods, and perhaps supports their claim for the expansion of Homo sapiens into this marginal environment.PLoS ONE 8(7): e69665. doi:10.1371/journal.pone.0069665
Middle Palaeolithic and Neolithic Occupations around Mundafan Palaeolake, Saudi Arabia: Implications for Climate Change and Human Dispersals
Rémy Crassard et al.
The Arabian Peninsula is a key region for understanding climate change and human occupation history in a marginal environment. The Mundafan palaeolake is situated in southern Saudi Arabia, in the Rub’ al-Khali (the ‘Empty Quarter’), the world’s largest sand desert. Here we report the first discoveries of Middle Palaeolithic and Neolithic archaeological sites in association with the palaeolake. We associate the human occupations with new geochronological data, and suggest the archaeological sites date to the wet periods of Marine Isotope Stage 5 and the Early Holocene. The archaeological sites indicate that humans repeatedly penetrated the ameliorated environments of the Rub’ al-Khali. The sites probably represent short-term occupations, with the Neolithic sites focused on hunting, as indicated by points and weaponry. Middle Palaeolithic assemblages at Mundafan support a lacustrine adaptive focus in Arabia. Provenancing of obsidian artifacts indicates that Neolithic groups at Mundafan had a wide wandering range, with transport of artifacts from distant sources.
Link
Nubian complex site from central Arabia (Crassard & Hilbert 2013)
The palaeoclimatic record of Arabia indicates that three distinct wet phases occurred during MIS 5 [109]. The first of these wet phases occurred between 130 and 125 kya (MIS 5e) and precedes the presence of Nubian technology in Arabia. The two following wet phases, positioned around 100 kya (MIS 5c) and between 80 to 75 kya (MIS 5a) may be viewed as possible windows for the Nubian expansion into and across Arabia (Figure 11).PLoS ONE 8(7): e69221. doi:10.1371/journal.pone.0069221
A Nubian Complex Site from Central Arabia: Implications for Levallois Taxonomy and Human Dispersals during the Upper Pleistocene
Rémy Crassard, Yamandú Hieronymus Hilbert
Archaeological survey undertaken in central Saudi Arabia has revealed 29 surface sites attributed to the Arabian Middle Paleolithic based on the presence of Levallois blank production methods. Technological analyses on cores retrieved from Al-Kharj 22 have revealed specific reduction modalities used to produce flakes with predetermined shapes. The identified modalities, which are anchored within the greater Levallois concept of core convexity preparation and exploitation, correspond with those utilized during the Middle Stone Age Nubian Complex of northeast Africa and southern Arabia. The discovery of Nubian technology at the Al-Kharj 22 site represents the first appearance of this blank production method in central Arabia. Here we demonstrate how a rigorous use of technological and taxonomic analysis may enable intra-regional comparisons across the Arabian Peninsula. The discovery of Al-Kharj 22 increases the complexity of the Arabian Middle Paleolithic archaeological record and suggests new dynamics of population movements between the southern and central regions of the Peninsula. This study also addresses the dichotomy within Nubian core typology (Types 1 and 2), which was originally defined for African assemblages.
Link
July 12, 2013
A Middle Paleolithic link between North Africa and the Thar desert
And, one more piece of evidence against the idea that early modern humans in Eurasia died out and were replaced wholesale circa 50-60 thousand years ago from a fresh OoA impulse. It would have been possible to suppose such a thing if the evidence for MP African influence was minor or geographically localized, but much more difficult when it extends over a wide region.
Of course, the attribution of the Katoati assemblages to modern humans is done indirectly by linking them to MSA sites of the Sahara, but the proliferation of real archaeological sites (see map) that can be linked to OoA makes it difficult to adopt the idea of an archaeologically invisible late OoA that (somehow) replaced all previous inhabitants.
Quaternary Science Reviews Available online 5 July 2013
Middle Palaeolithic occupation in the Thar Desert during the Upper Pleistocene: the signature of a modern human exit out of Africa?
James Blinkhorn et al.
The Thar Desert marks the transition from the Saharo-Arabian deserts to the Oriental biogeographical zone and is therefore an important location in understanding hominin occupation and dispersal during the Upper Pleistocene. Here, we report the discovery of stratified Middle Palaeolithic assemblages at Katoati in the north-eastern Thar Desert, dating to Marine Isotope Stages (MIS) 5 and the MIS 4–3 boundary, during periods of enhanced humidity. Hominins procured cobbles from gravels at the site as evidenced by early stages of stone tool reduction, with a component of more formalised point production. The MIS 5c assemblages at Katoati represent the earliest securely dated Middle Palaeolithic occupation of South Asia. Distinctive artefacts identified in both MIS 5 and MIS 4–3 boundary horizons match technological entities observed in Middle Palaeolithic assemblages in South Asia, Arabia and Middle Stone Age sites in the Sahara. The evidence from Katoati is consistent with arguments for the dispersal of Homo sapiens populations from Africa across southern Asia using Middle Palaeolithic technologies.
Link
June 11, 2013
~60-50 thousand coastal migration to Asia from Africa affirmed
My own opinions on this matter have been repeated ad nauseam in this blog, so I will only briefly touch on a couple of points in this new article.
Contrary to the authors' claim that: "The size of the mtDNA database is very substantial: currently there are almost 13,000 complete non-African mtDNA genomes available, not one of which is pre-L3." there are plenty of pre-L3 mtDNA in Eurasia. Some (or indeed most?) of these might represent more recent African admixture, and one could argue why they believe that to be the case, but no one has ever studied pre-L3 Eurasian mtDNA to conclude that none of it had an ancient presence in Eurasia. The native non-existence of pre-L3 in Eurasia is a viewpoint, not a fact.
Second, the authors present the following table:
Note, however, that they have chosen to date the common ancestor of all African sublineages (to ~70.2ky using ML method), but they have not done the same for the common ancestor of all non-African sublineages (i.e., M+N). A recent study estimates M+N to be 77KBP and L3 to be 78.3KBP, with other possibilities depending on method and portion of the molecule examined.
At present, I see no good reason to think that haplogroup L3 originated either in Africa or Eurasia; one could argue for an African origin, but temporal priority for African L3 is not established. The only thing that seems to be established is that there are "more" L3 subclades in Africa, which is phylogenetically meaningless until the bifurcating structure of the L3 subtree is resolved. And, we should also not forget that the Toba eruption did not cause a volcanic winter in Africa, nor was Africa affected by the drying up of the Sahara-Arabia belt c. 70kya, both of which may have suppressed Eurasian mtDNA variation within L3, irrespective of its ultimate origins. And, as I've argued before, both Toba and the post-70kya ecological crisis are excellent candidates for a Eurasian bottleneck caused by pre-existing populations surviving in refugia such as this.
Finally, the authors dismiss the possibility of an overestimated autosomal mutation rate and its implications for human history: "Recent reestimates of the autosomal mutation rate from whole-genome pedigree data suggest a European–Asian split time of 40–80 ka, although they do not, as has been suggested, lend any support to a dispersal fromAfrica before 80 ka (36) (Genetics)."
Actually, the most recent estimate might be consistent with a ~96ky split of Africans from non-Africans, and the mutation rate issue is material to the timing of the African/non-African split. It's not clear where the needle will settle when the issue is resolved, but there's plenty of room for both pre- and post-Toba Out-of-Africa as things stand.
PNAS doi: 10.1073/pnas.1306043110
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia
Paul Mellars et al.
It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.
Link
Contrary to the authors' claim that: "The size of the mtDNA database is very substantial: currently there are almost 13,000 complete non-African mtDNA genomes available, not one of which is pre-L3." there are plenty of pre-L3 mtDNA in Eurasia. Some (or indeed most?) of these might represent more recent African admixture, and one could argue why they believe that to be the case, but no one has ever studied pre-L3 Eurasian mtDNA to conclude that none of it had an ancient presence in Eurasia. The native non-existence of pre-L3 in Eurasia is a viewpoint, not a fact.
Second, the authors present the following table:
Note, however, that they have chosen to date the common ancestor of all African sublineages (to ~70.2ky using ML method), but they have not done the same for the common ancestor of all non-African sublineages (i.e., M+N). A recent study estimates M+N to be 77KBP and L3 to be 78.3KBP, with other possibilities depending on method and portion of the molecule examined.
At present, I see no good reason to think that haplogroup L3 originated either in Africa or Eurasia; one could argue for an African origin, but temporal priority for African L3 is not established. The only thing that seems to be established is that there are "more" L3 subclades in Africa, which is phylogenetically meaningless until the bifurcating structure of the L3 subtree is resolved. And, we should also not forget that the Toba eruption did not cause a volcanic winter in Africa, nor was Africa affected by the drying up of the Sahara-Arabia belt c. 70kya, both of which may have suppressed Eurasian mtDNA variation within L3, irrespective of its ultimate origins. And, as I've argued before, both Toba and the post-70kya ecological crisis are excellent candidates for a Eurasian bottleneck caused by pre-existing populations surviving in refugia such as this.
Finally, the authors dismiss the possibility of an overestimated autosomal mutation rate and its implications for human history: "Recent reestimates of the autosomal mutation rate from whole-genome pedigree data suggest a European–Asian split time of 40–80 ka, although they do not, as has been suggested, lend any support to a dispersal fromAfrica before 80 ka (36) (Genetics)."
Actually, the most recent estimate might be consistent with a ~96ky split of Africans from non-Africans, and the mutation rate issue is material to the timing of the African/non-African split. It's not clear where the needle will settle when the issue is resolved, but there's plenty of room for both pre- and post-Toba Out-of-Africa as things stand.
PNAS doi: 10.1073/pnas.1306043110
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia
Paul Mellars et al.
It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.
Link
May 10, 2013
Lakes in SE Arabia ~60 thousand years ago
From the current archaeological evidence, it seems that after MIS 5, the different lithic traditions within Arabia develop along separate trajectories, with no indication of additional input from Africa. Recent genetic evidence (Fernandes et al., 2012) also indicates that the relict distribution of minor haplogroups N1, N2 and X, reflects an ancient ancestry of these groups within the Arabian Peninsula which, the authors conclude, then spread from the Gulf region toward the Near East and Europe between 55 and 24 ka. The potential occurrence of increased humidity within the Arabian interior during MIS 3 would, therefore, have been instrumental in determining the success and trajectory of the autochthonous development of early human communities within the region at this time. Although Rosenberg et al. (2012) may be correct in their description of Arabia between ca. 75 and 10.5 ka as a natural barrier for human dispersal, it is possible that indigenous inhabitants may have persisted in environmental refugia around Arabia, such as the Gulf Oasis (e.g. Rose, 2010). The occurrence of a pluvial phase during the early stages of MIS 3, therefore, may have facilitated a range expansion of early humans previously contained within such refugia. To address these important issues, we present a multiproxy record of an early MIS 3 wet phase from a palaeolake sequence within the continental interior of SE Arabia.Quaternary International Available online 22 February 2013
An early MIS 3 pluvial phase in Southeast Arabia: Climatic and archaeological implications
Ash Parton et al.
Climatic changes in Arabia are of critical importance to our understanding of both monsoon variability and the dispersal of anatomically modern humans (AMH) out of Africa. The timing of dispersal is associated with the occurrence of pluvial periods during Marine Isotope Stage (MIS) 5 (ca. 130–74 ka), after which arid conditions between ca. 74 and 10.5 ka are thought to have restricted further migration and range expansion within the Arabian interior. Whilst a number of records indicate that this phase of aridity was punctuated by an increase in monsoon strength during MIS 3, uncertainties regarding the precision of terrestrial records and suitability of marine archives as records of precipitation, mean that the occurrence of this pluvial remains debated. Here we present evidence from a series of relict lake deposits within southeastern Arabia, which formed at the onset of MIS 3 (ca. 61–58 ka). At this time, the incursion of monsoon rainfall into the Arabian interior activated a network of channels associated with an alluvial fan system along the western flanks of the Hajar Mountains, leading to lake formation. Multiproxy evidence indicates that precipitation increases intermittently recharged fluvial systems within the region, leading to lake expansion in distal fan zones. Conversely, decreased precipitation led to reduced channel flow, lake contraction and a shift to saline conditions. These findings are in contrast to the many other palaeoclimatic records from Arabia, which suggest that during MIS 3, the latitudinal position of the monsoon was substantially further south and did not penetrate the peninsula. Additionally, the occurrence of increased rainfall at this time challenges the notion that the climate of Arabia following MIS 5 was too harsh to permit the further range expansion of indigenous communities.
Link
January 25, 2013
The case for earlier Out-of-Africa (Boivin et al. 2013)
From the paper:
Another under-appreciated issue is the anomalous nature of the genetic evidence for a rapid spread of modern humans from Africa to Asia. Echoing the fossil date anomaly, the mtDNA branch lengths for sampled populations are longest for those which are farthest east, in Near Oceania, and shortest in the Asian areas that would have been encountered first (Merriwether et al., 2005; Oppenheimer, 2009). The real problem, however, is that the variation in branch lengths suggests that a single genotype engaged in the expansion actually existed for 30 ka, which does not support a rapid expansion. The anomaly can be explained by what we call an an ‘M buffer’ effect (see Supplementary material A) which implies that the branch ages we observe are considerable underestimates of the time of arrival of the genotype to these areas. Such anomalously long-lived genotypes have been directly observed through ancient DNA in species such as the Iberian lynx (Dalen et al., 2011).and:
We have focused here on the possibility that the modern human exit recorded by fossil evidence in the Levant in MIS 5 does not represent a failed dispersal, and that in fact our species was not only in the Levant but also the Arabian peninsula during this marine isotope stage, and spread to India before the Toba eruption at 74 ka (Petraglia et al., 2007). Another valid hypothesis we do not explore here is that H. sapiens was able to leave Africa in MIS 6 via a grassland corridor (Frumkin et al., 2011; see also Scally and Durbin, 2012). Yet another is that our species dispersed out of Africa shortly after its first appearance c. 195 ka, in MIS 7 (Dennell and Roebroeks, 2005: 1102). One other possibility is that there were several, separate dispersals of our species out of Africa (Dennell and Petraglia, 2012). At the same time, we acknowledge that major demographic changes occurred in MIS 4 and MIS 3, perhaps explaining the relatively young mtDNA coalescence age in living populations. The increasing evidence for complexity as well as the clear patterns of bias for all records, whether archaeological, fossil or genetic, suggests the need for an open mind to multiple scenarios for Out of Africa, as well as for more rather than less complex models of H. sapiens dispersal across Eurasia.Quaternary International doi:10.1016/j.quaint.2013.01.008
Human Dispersal Across Diverse Environments of Asia during the Upper Pleistocene
Nicole Boivin et al.
The initial out of Africa dispersal of H. sapiens, which saw anatomically modern humans reach the Levant in Marine Isotope Stage 5, is generally regarded as a ‘failed dispersal’. Fossil, archaeological and genetic findings are seen to converge around a consensus view that a single population of H. sapiens exited Africa sometime around 60 thousand years ago (ka), and rapidly reached Australia by following a coastal dispersal corridor. We challenge the notion that current evidence supports this straightforward model. We argue that the fossil and archaeological records are too incomplete, the coastal route too problematic, and recent genomic evidence too incompatible for researchers not to remain fully open to other hypotheses. We specifically explore the possibility of a sustained exit by anatomically modern humans, drawing in particular upon palaeoenvironmental data across southern Asia to demonstrate its feasibility. Current archaeological, genetic and fossil data are not incompatible with the model presented, and appear to increasingly favour a more complex out of Africa scenario involving multiple exits, varying terrestrial routes, a sub-divided African source population, slower progress to Australia, and a degree of interbreeding with archaic varieties of Homo.
Link
December 27, 2012
Zoogeographic map of the world
Science DOI: 10.1126/science.1228282
An Update of Wallace's Zoogeographic Regions of the World
Ben G. Holt et al.
Modern attempts to produce biogeographic maps focus on the distribution of species and are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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