Monday, September 26, 2016

Pagani et al., Paragraph 2

Pagani et al
Nature
Published online
(Link)

Paragraph 2:  "The paths taken by AMHs out of Africa (OoA) have been the subject of considerable debate over the past two decades. Fossil and archaeological evidence [13,14], and craniometric studies [15] of African and Asian populations, demonstrate that Homo sapiens was present outside of Africa ~ 120–70 thousand years ago (kya) [11]. However, this colonization has been viewed as a failed expansion OoA [16] since genetic analyses of living populations have been consistent with a single OoA followed by serial founder events [17]."


Pagani et al, Paragraph 2 References:

[13]  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, Aylwyn Scally, Rethinking the dispersal of Homo sapiens out of Africa, Evolutionary Anthropology:  Issues, News, Reviews, 8 July, 2015 (Link)

Abstract:  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.



[14]  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 Bermudez de Castro, Xiu-jie Wu, The earliest unequivocally modern humans in southern China, Nature, Volume: 526, Pages: 696–699, Date published:


 
 
[15]  Hugo Reyes-Centeno, Silvia Ghirotto, Florent Detroit, Dominique Grimaud-Hervé, Guido Barbujani, Katerina Harvati, Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia, PNAS, vol. 111 no. 20 (Link)

Significance:  Current consensus indicates that modern humans originated from an ancestral African population between ∼100–200 ka. The ensuing dispersal pattern is controversial, yet has important implications for the demographic history and genetic/phenotypic structure of extant human populations. We test for the first time to our knowledge the spatiotemporal dimensions of competing out-of-Africa dispersal models, analyzing in parallel genomic and craniometric data. Our results support an initial dispersal into Asia by a southern route beginning as early as ∼130 ka and a later dispersal into northern Eurasia by ∼50 ka. Our findings indicate that African Pleistocene population structure may account for observed plesiomorphic genetic/phenotypic patterns in extant Australians and Melanesians. They point to an earlier out-of-Africa dispersal than previously hypothesized.         
                                                      
Abstract:  Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a “southern route” dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.


[11]  Matt Grove, Henry Lamb, Helen Roberts, Sarah Davies, Mike Marshall, Richard Bates, Hei Huws, Climatic variability, plasticity, and dispersal: A case study from Lake Tana, Ethiopia, Journal of Human Evolution, Volume 87, October 2015, Pages 32–47 (Link)

Abstract:  The numerous dispersal events that have occurred during the prehistory of hominin lineages are the subject of longstanding and increasingly active debate in evolutionary anthropology. As well as research into the dating and geographic extent of such dispersals, there is an increasing focus on the factors that may have been responsible for dispersal. The growing body of detailed regional palaeoclimatic data is invaluable in demonstrating the often close relationship between changes in prehistoric environments and the movements of hominin populations. The scenarios constructed from such data are often overly simplistic, however, concentrating on the dynamics of cyclical contraction and expansion during severe and ameliorated conditions respectively. This contribution proposes a two-stage hypothesis of hominin dispersal in which populations (1) accumulate high levels of climatic tolerance during highly variable climatic phases, and (2) express such heightened tolerance via dispersal in subsequent low-variability phases. Likely dispersal phases are thus proposed to occur during stable climatic phases that immediately follow phases of high climatic variability. Employing high resolution palaeoclimatic data from Lake Tana, Ethiopia, the hypothesis is examined in relation to the early dispersal of Homo sapiens out of East Africa and into the Levant. A dispersal phase is identified in the Lake Tana record between c. 112,550 and c. 96,975 years ago, a date bracket that accords well with the dating evidence for H. sapiens occupation at the sites of Qafzeh and Skhul. Results are discussed in relation to the complex pattern of H. sapiens dispersal out of East Africa, with particular attention paid to the implications of recent genetic chronologies for the origin of non-African modern humans.


[16]  Paul Mellars, Kevin C. Gori, Martin Carr, Pedro A. Soares, Martin B. Richards, Genetic and archaeological perspectives on the initial modern human colonization of southern Asia, PNAS, vol. 110 no. 26 (Link)

Abstract:  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.

[17]  Franck Prugnolle, Andrea Manica, François Balloux, Geography predicts neutral genetic diversity of human populations, Current Biology, Volume 15, Issue 5, pp. 159–R160, 8 March 2005 (Link)

Abstract:  A leading theory for the origin of modern humans, the ‘recent African origin’ (RAO) model [1] , postulates that the ancestors of all modern humans originated in East Africa and that, around 100,000 years ago, some modern humans left the African continent and subsequently colonised the entire world, displacing previously established human species such as Neanderthals in Europe [2,3] . This scenario is supported by the observation that human populations from Africa are genetically the most diverse [2] and that the genetic diversity of non-African populations is negatively correlated with their genetic differentiation towards populations from Africa [3] .

Thursday, September 22, 2016

Some comments on "Genomic analyses inform on migration events during the peopling of Eurasia"

Pagani et al
Nature
Published online
(Link)

"High-coverage whole-genome sequence studies have so far focused on a limited number[1] of geographically restricted populations [2–5], or been targeted at specific diseases, such as cancer[6]. Nevertheless,  the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history[7–9] and refuelled the debate on the mutation rate in humans [10].  Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets.  We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record [11], and admixture between AMHs and Neanderthals predating the main Eurasian expansion [12], our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago."

My comments: 

Sounds good to me.  I would add that it is pretty backward to think that there is no "Eurasian" ancestry in Africans.  And if there is "Eurasian" ancestry in Africans, due to obvious high mobility of hominins backward and forwards across and between continents for hundreds of thousands of years, (and most large mammals for that matter) then most of these calculations regarding the degree of archaic and modern admixture in the hominin past are grossly under-estimated (since the degree of admixture in non-Africans has been inferred against Africans, and assumes that Africans [incorrectly] have no Neanderthal or Denisovan admixture.)  Furthermore, the time estimates of population splits would be different if we started to include the idea of high mobility and "soft" splits between hominin populations and continents.

Unfortunately, we rarely see sophisticated models accounting for bidirectional gene flow, high mobility, and other possible confounding phenomena.   The models reflect the same "just so" human origin genetic story, with ever so minor a variation, and are carefully crafted so as not to too directly tread on the toes of a small number of prominent and entrenched paleoanthropologists and human origin geneticists.

At least this paper managed to state the obvious that AMH was present in Eurasia earlier than 75,000 years ago (given those "80,000 year old" Daoxian AMH teeth).

:)

Yes, I'm smiling, but only because I don't work professionally in any field related to the cloying, over specialized, highly politicized and narrow field of human origin genetics.

Tuesday, September 20, 2016

Evolution of middle-late Pleistocene human cranio-facial form: A 3-D approach

Katerina Harvati, Jean-Jacque Hublin, Philipp Gunz
Journal of Human Evolution
59(5):445-64
November 2010
(Link)

Abstract


The classification and phylogenetic relationships of the middle Pleistocene human fossil record remains one of the most intractable problems in paleoanthropology. Several authors have noted broad resemblances between European and African fossils from this period, suggesting a single taxon ancestral to both modern humans and Neanderthals. Others point out 'incipient' Neanderthal features in the morphology of the European sample and have argued for their inclusion in the Neanderthal lineage exclusively, following a model of accretionary evolution of Neanderthals. We approach these questions using geometric morphometric methods which allow the intuitive visualization and quantification of features previously described qualitatively. We apply these techniques to evaluate proposed cranio-facial 'incipient' facial, vault, and basicranial traits in a middle-late Pleistocene European hominin sample when compared to a sample of the same time depth from Africa. Some of the features examined followed the predictions of the accretion model and relate the middle Pleistocene European material to the later Neanderthals. However, although our analysis showed a clear separation between Neanderthals and early/recent modern humans and morphological proximity between European specimens from OIS 7 to 3, it also shows that the European hominins from the first half of the middle Pleistocene still shared most of their cranio-facial architecture with their African contemporaries.

Monday, September 19, 2016

The earliest occupation of Europe: the Balkans

Andreas Darlas
Analecta Praehistorica Leidensia
1995
(Link) pdf

The absence of knowledge of prehistoric man in the Balkans is aciually due to the lack of prehistoric research within this area. Information on the Palaeolithic of the Balkan countries started to become available only in recent years. Data concerning the Lower Palaeolithic are very scarce and sites known from this period are not numerous. The only excavated sites which date to the earlier parts of the Middle Pleistocene are the caves of Yarimburgaz (Turkey), Petralona (Greece), Gajtan (Albania) and Sandalja (Croatia).

Saturday, September 3, 2016

Revisiting Kokkinopilos: Middle Pleistocene radiometric dates for stratified archaeological remains in Greece










Vangelis Tourloukis, Panagiotis Karkanas, Jakob Wallinga
Journal of Archaeological Science
March 2015
(Link)

Abstract

The red-bed site of Kokkinopilos is an emblematic and yet also most enigmatic open-air Palaeolithic site in Greece, stimulating controversy ever since its discovery in 1962. While early research raised claims for stratigraphically in situ artifacts, later scholars considered the material reworked and of low archaeological value, a theory that was soon to be challenged again by the discovery of in situ lithics, including handaxes. Here we present results of a latest and long-term research that includes geoarchaeological assessments, geomorphological mapping and luminescence dating. We show that the site preserves an overall undisturbed sedimentary sequence related to an ephemeral lake, marked by palaeosols and stratigraphic units with Palaeolithic material that is geologically in situ and hence datable. Our study resolves the issues that have been the source of controversy: the depositional environment, stratigraphic integrity, chronological placement and archaeological potential of the site. Moreover, the minimum ages obtained through luminescence dating demonstrate that the lithic component with bifacial specimens considerably pre-dates the last interglacial and therefore comprises the earliest stratigraphically defined and radiometrically-assessed archaeological material in Greece. Kokkinopilos has served as a reference site for the interpretation of all other red-bed sites in north-west Greece, therefore our results have significantly wider implications: by analogy to Kokkinopilos, the open-air sites of Epirus should not anymore be considered ‘by default’ as inscrutable palimpsests with limited archaeological potential; rather, these sites can be excavated and chronologically constrained. This realization opens up new prospects for future research in Epirus, an area that is the most prolific in Palaeolithic remains in Greece.