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The Out of Africa hypothesis and the ancestry of recent humans: Cherchez la femme (et l'homme)
Abstract
The Out of Africa hypothesis (OOAH) has been a mainstay in the discussion of human evolution since its presentation in the 1980's. However, recent advances in palaeontology and molecular genetics have made it possible to examine the hypothesis in a manner that was inconceivable at the time of its proposal. The palaeontological progress relates to early Homo finds in the Caucasus, Denisova finds in the Altai Mountains and Neanderthal finds in a wide range of localities from the Altai Mountains, the Caucasus, the Levant, Asia Minor, southern and Central Europe and the Iberian Peninsula. The Eurasian location of these finds and recognition of the principle of Last common ancestor lend no support to OOAH. The same conclusion is drawn from genomic findings, which (a) have revealed the presence of Denisovan and Neanderthal nuclear DNA, primarily in the genomes of recent Eurasians and (b) have shown genomic introgression from early modern humans into Neanderthals in the Altai Mountains. Similarly, archaeological finds in Sulawesi and the discovery of ≈ 100.000years old human teeth in southern China constitute strong independent challenges to OOAH. The genomic and palaeogenomic results and the new palaeontological and archaeological discoveries suggest (a) that the ancestors of modern humans had their origin in a Eurasian (largely Asian) biogeographic region which may also have extended into NE Africa, and (b) that the founders of basal African lineages became separated, geographically and genetically, in the westernmost part of this region and spread from there to different parts of the African continent.
... The OOAH was addressed previously in two studies [6,7] in which the author maintained on the basis of molecular and palaeontological data that recent humans, Hss, had originated in Eurasia (the Out of Eurasia ypothesis, OOEH) and dispersed from there to other parts of the world including Africa. In the present study the two hypotheses were compared in the light of the identity of the basal divergence of the Hss tree as established in genomic analyses [8,9]. ...
... The tree in Fig. 1 shows the relationship of Hss and Hsn (Hsnn + Hsnd) consistent with the nuDNA monophyly of Hss and Hsn. In the light of this relationship the divergence between Hss and Hsn ≈ 800,000 YBP becomes anchored in Eurasia in accordance with the principle of Last common ancestor and the strict limitation of Hsn to this continent as maintained earlier [6,7] and consistent with the recent Ha results [66,73]. The Hsn branch divides into an Hsnd branch and an Hsnn branch that splits further into SH-Hsnn [18][19][20]62], and the remaining Hsnn [11,14,15], labelled Hsnn*. ...
... The mtDNA introgression from Hss into Hsnn* substantiates the presence of the two lineages in the same area ≈ 300,000 years after the divergence between Hss and Hsn ≈ 800, 000 YBP. With Hsnn strictly limited to Eurasia the coexistence of Hss and Hsnn confirms the restriction of Hss to this continent [6,7]. These phylogenetic, geographic and palaeontological circumstances together with the Fig. 3 Hs mtDNA relationships. ...
Background
The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25–30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo . The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades.
Results
The direction of evolution in the phylogenetic tree of modern humans ( Homo sapiens sapiens , Hss ) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba. The examination identified the African populations as paraphyletic, thereby compromising the OOAH. The finding, which was consistent with the out of Eurasia hypothesis, OOEH, was corroborated by the mtDNA introgression from Hss into Hsnn (Neanderthals) that demonstrated the temporal and physical Eurasian coexistence of the two lineages. The results are consistent with the palaeontologically established presence of H. erectus in Eurasia, a Eurasian divergence between H. sapiens and H. antecessor ≈ 850,000 YBP, an Hs divergence between Hss and Hsn (Neanderthals + Denisovans) ≈ 800,000 YBP, an mtDNA introgression from Hss into Hsnn* ≈ 500,000 YBP and an Eurasian divergence among the ancestors of extant Hss ≈ 250,000 YBP at the exodus of Mbuti/San into Africa.
Conclusions
The present study showed that Eurasia was not the receiver but the donor in Hss evolution. The findings that Homo left Africa as erectus and returned as sapiens sapiens constitute a change in the understanding of Hs evolution to one that conforms to the extensive Eurasian record of Hs palaeontology and archaeology.
... Therefore, the question arises as to whether the substitution of threonine by a bigger and positively charged amino acid at position 61 possibly occurred by chance (as proposed elsewhere (Enard, 2012)) or whether there were any functional advantages for early humans that are not yet revealed or not yet connected with APOE. Similarly, the corrective R112C substitution may have been a simple adjustment of the deleterious effects of the previous mutation (Enard, 2012) Dating the divergence of humans from primates back to at least 7.5 million years ago and the last common ancestor of Denisovan and anatomically modern humans to 1 million years ago (Arnason, 2016) renders a time window of at least 6 million years for the occurrence of the mutation that gives rise to the T R exchange at position 61. The introduction of the larger positively charged arginine (compared to the former threonine) slightly reduces C-terminal domain stability (Nguyen et al., 2014) and may allosterically impact the interaction of helix 4 of the NT and the CT (Frieden and Garai, 2013). ...
... These fossil evidence argue against the proposed 'Out-of-Africa' theory of single or multiple migration waves of modern humans between 70,000 to 40,000 years ago that spread from Africa to Asia and Europe (Henn et al., 2012, Tassi et al., 2015. More reasonably, it was suggested that a Southern Asian subgroup migrated westwards, entering the Levant, Europe and Africa approximately 50,000 years ago (Arnason, 2016, Liu et al., 2015. Apart from the origin and migration route of modern humans at that time, it seems obvious that certain modern humans must have already carried the ε3 allele, which enabled its geographical distribution. ...
... Taking into account the novel insight regarding modern human existence in East Asia as early as 120,000 years ago (Arnason, 2016, Liu et al., 2015, the evolution and worldwide distribution of the APOE isoforms may be reconsidered. Based on the assumption that modern humans of Asian origin migrated westwards, spreading to the Levant, Africa and Europe, and headed north, entering North and South America, the distribution of the isoforms may be as follows. ...
Apolipoprotein E (APOE) is a member of the vertebrate protein family of exchangeable apolipoproteins that is characterized by amphipathic α-helices encoded by multiple nucleotide tandem repeats. Its equivalent in flying insects − apolipophorin-III − shares structural and functional commonalities with APOE, suggesting the possibility of an evolutionary relationship between the proteins. In contrast to all other known species, human APOE is functionally polymorphic and possesses three major allelic variants (ε4, ε3 and ε2). The present review examines the current knowledge on APOE gene structure, phylogeny and APOE protein topology as well as its human isoforms. The ε4 allele is associated with an increased age-related disease risk but is also the ancestral form. Despite increased mortality in the elderly, ε4 has not become extinct and is the second-most common allele worldwide after ε3. APOE ε4, moreover, shows a non-random geographical distribution, and similarly, the ε2 allele is not homogenously distributed among ethnic populations. This likely suggests the existence of selective forces that are driving the evolution of human APOE isoforms, which may include differential interactions with dietary factors. To that effect, micronutrients such as vitamin D and carotenoids or dietary macronutrient composition are elucidated with respect to APOE evolution.
... Here the evolution of Hss was addressed in the light of the phylogenies of two separate sets of data, viz. the nuclear DNA, nuDNA, tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs [2][3][4], and the mtDNA tree, a non-nuclear tree with maternal inheritance. The findings supported conclusively the results presented in the initial Y-DNA studies [3,4] and the more recent mtDNA findings that have challenged OOAH [1,5,6]. ...
... The extensive Y-DNA study [4] behind Fig. 3a showed a minimum of five waves of Hss migration from Eurasia into Africa while the more limited mtDNA sampling behind 3b [1] identified a minimum of three migrations with each of these coinciding with the Y-DNA results, consistent with the presence of both males (Y-DNA) and females (mtDNA) in each population migrating into Africa. As apparent a divergence between Mbuti and San prior to their migration into Africa [5] would raise the number of waves into Africa by one, as would also any migration connected to the B + C branch [4] that has been tentatively indicated on the mtDNA tree. ...
Background
The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH.
Results
In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs. The comparison showed full phylogenetic coherence between these two separate sets of data. The results were consistent with potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH at the same time as they lent no support to the OOAH.
Conclusions
The conformity between the mtDNA and Y-DNA phylogenies of Hss is consistent with the understanding that Eurasia was the donor and not the receiver in human evolution. The evolutionary problems related to OOAH became similarly exposed by the mtDNA introgression that took place from Hss into Neanderthals ≈ 500,000 YBP, a circumstance that demonstrated the early coexistence of the two lineages in Eurasia.
Solar energy, which is essential for the origin and evolution of all life forms on Earth, can be objectively recorded as attributes such as climatic ambient temperature (CAT), ultraviolet radiation (UVR), and sunlight duration (SD). These attributes have specific geographical variations and may cause different adaptation traits. However, the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain elusive. Here, we performed a genome-wide adaptation study with respect to CAT, UVR, and SD, using the Human Genome Diversity Project-Centre Etude Polymorphism Humain (HGDP-CEPH) panel data. We singled out CAT as the most important driving force with the most numerous adaptive loci (six SNPs at the genome-wide 1×10⁻⁷ level; 401 at the suggestive 1×10⁻⁵ level). Five of the six genome-wide significant adaptation SNPs were successfully replicated in an independent Chinese population (N = 1395). The corresponding 316 CAT adaptation genes were mostly involved in development and immunity. In addition, 265 (84%) genes were related to at least one genome-wide association study (GWAS) mapped human trait, being significantly enriched in anthropometric loci such as those associated with body mass index (χ²; P < 0.005), immunity, metabolic syndrome, and cancer (χ²; P < 0.05). For these adaptive SNPs, balancing selection was evident in Euro-Asians while purifying selection in Africans. Taken together, our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human populations. It also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.
The substantiality of the Out of Africa hypothesis was addressed in the light of recent genomic analysis of extant humans (Homo sapiens sapiens, Hss) and progress in Neanderthal palaeontology. The examination lent no support to the commonly assumed Out of Africa scenario but favoured instead a Eurasian divergence between Neanderthals and Hss (the Askur/Embla hypothesis) and an Out of Asia/Eurasia hypothesis according to which all other parts of the world were colonized by Hss migrations from Asia. The examination suggested furthermore that the ancestors of extant KhoeSan and Mbuti composed the first Hss dispersal(s) into Africa and that the ancestors of Yoruba made up a later wave into the same continent. The conclusions constitute a change in paradigm for the study of human evolution.
Sulawesi is the largest and oldest island within Wallacea, a vast zone of oceanic islands separating continental Asia from the Pleistocene landmass of Australia and Papua (Sahul). By one million years ago an unknown hominin lineage had colonized Flores immediately to the south, and by about 50 thousand years ago, modern humans (Homo sapiens) had crossed to Sahul. On the basis of position, oceanic currents and biogeographical context, Sulawesi probably played a pivotal part in these dispersals. Uranium-series dating of speleothem deposits associated with rock art in the limestone karst region of Maros in southwest Sulawesi has revealed that humans were living on the island at least 40 thousand years ago (ref. 5). Here we report new excavations at Talepu in the Walanae Basin northeast of Maros, where in situ stone artefacts associated with fossil remains of megafauna (Bubalus sp., Stegodon and Celebochoerus) have been recovered from stratified deposits that accumulated from before 200 thousand years ago until about 100 thousand years ago. Our findings suggest that Sulawesi, like Flores, was host to a long-established population of archaic hominins, the ancestral origins and taxonomic status of which remain elusive.
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 lacking. 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 Europe. 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.
Neandertal Shadows in Us
Non-African modern humans carry a remnant of Neandertal DNA from interbreeding events that have been postulated to have occurred as humans migrated out of Africa. While the total amount of Neandertal sequence is estimated to be less than 3% of the modern genome, the specific retained sequences vary among individuals. Analyzing the genomes of more than 600 Europeans and East Asians, Vernot and Akey (p. 1017 , published online 29 January) identified Neandertal sequences within modern humans that taken together span approximately 20% of the Neandertal genome. Some Neandertal-derived sequences appear to be under positive selection in humans, including several genes associated with skin phenotypes.
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
The site of Dmanisi, Georgia, has yielded an impressive sample of hominid cranial and postcranial remains, documenting the
presence of Homo outside Africa around 1.8 million years ago. Here we report on a new cranium from Dmanisi (D4500) that, together with its
mandible (D2600), represents the world's first completely preserved adult hominid skull from the early Pleistocene. D4500/D2600
combines a small braincase (546 cubic centimeters) with a large prognathic face and exhibits close morphological affinities
with the earliest known Homo fossils from Africa. The Dmanisi sample, which now comprises five crania, provides direct evidence for wide morphological
variation within and among early Homo paleodemes. This implies the existence of a single evolving lineage of early Homo, with phylogeographic continuity across continents.
Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.
We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a
Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity
indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen
on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day
human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern
humans since their divergence from Denisovans.
Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome--a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.
It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
The early Pleistocene colonization of temperate Eurasia by Homo erectus was not only a significant biogeographic event but also a major evolutionary threshold. Dmanisi's rich collection of hominin fossils, revealing a population that was small-brained with both primitive and derived skeletal traits, has been dated to the earliest Upper Matuyama chron (ca. 1.77 Ma). Here we present archaeological and geologic evidence that push back Dmanisi's first occupations to shortly after 1.85 Ma and document repeated use of the site over the last half of the Olduvai subchron, 1.85-1.78 Ma. These discoveries show that the southern Caucasus was occupied repeatedly before Dmanisi's hominin fossil assemblage accumulated, strengthening the probability that this was part of a core area for the colonization of Eurasia. The secure age for Dmanisi's first occupations reveals that Eurasia was probably occupied before Homo erectus appears in the East African fossil record.
The Acheulian presence in the Dead Sea Rift and its environs is characterized by the discontinuity of its cultural manifestations. Nevertheless, the long stratigraphic sequences of the Acheulian Technocomplex provide a unique opportunity for synergetic examination along a temporal trajectory. Hominin cognitive and cultural behaviour are studied at Gesher Benot Ya'aqov through analyses of lithic, palaeontological and palaeobotanical assemblages, as well as the Early-Middle Pleistocene environment, ecology and climate. The study attempts to reconstruct reduction sequences of some major artefact groups at the site, which include raw material acquisition, production, technology, typology, usage and discard. Experimental archaeology illustrates artefact mobility on the palaeo-landscape. Strategies of biomass-exploitation are studied in detail, with other aspects yielding additional information on hominin subsistence and adaptive responses to their environment. The cultural marker of fire and the spatial association of selected categories of finds are integrated in the general synthesis, allowing reconstruction of the cultural and cognitive realm of Acheulian hominins. The synthesis attempts to reassess the abilities, social structure, subsistence and adaptability to the changing environment of hominins in the Levantine Corridor.
Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before
disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides
from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts
of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans,
including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic
variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow
from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined, the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans.
Variations in small game hunting along the northern and eastern rims of the Mediterranean Sea and results from predator-prey
simulation modeling indicate that human population densities increased abruptly during the late Middle Paleolithic and again
during the Upper and Epi-Paleolithic periods. The demographic pulses are evidenced by increasing reliance on agile, fast-reproducing
partridges, hares, and rabbits at the expense of slow-reproducing but easily caught tortoises and marine shellfish and, concurrently,
climate-independent size diminution in tortoises and shellfish. The results indicate that human populations of the early Middle
Paleolithic were exceptionally small and highly dispersed.
Multiregional evolution is a model to account for the pattern of human evolution in the Pleistocene. The underlying hypothesis is that a worldwide network of genic exchanges, between evolving human populations that continually divide and reticulate, provides a frame of population interconnections that allows both species-wide evolutionary change and local distinctions and differentiation. "Multiregional" does not mean independent multiple origins, ancient divergence of modern populations, simultaneous appearance of adaptive characters in different regions, or parallel evolution. A valid understanding of multiregional evolution would go a long way toward reducing the modern human origins controversy.
The search for the earliest fossil evidence of the human lineage has been concentrated in East Africa. Here we report the discovery of six hominid specimens from Chad, central Africa, 2,500 km from the East African Rift Valley. The fossils include a nearly complete cranium and fragmentary lower jaws. The associated fauna suggest the fossils are between 6 and 7 million years old. The fossils display a unique mosaic of primitive and derived characters, and constitute a new genus and species of hominid. The distance from the Rift Valley, and the great antiquity of the fossils, suggest that the earliest members of the hominid clade were more widely distributed than has been thought, and that the divergence between the human and chimpanzee lineages was earlier than indicated by most molecular studies.
Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies. Both ML (maximum likelihood) and Bayesian analyses identified four basal monophyletic groups, Afroplacentalia (=Afrotheria: Hyracoidea, Proboscidea, Sirenia, Tenrecidea, Tubulidentata, Macroscelidea, Chrysochloridea), Xenarthra, Archontoglires (Primates, Dermoptera, Scandentia, Lagomorpha, Rodentia) and Laurasiaplacentalia (Lipotyphla, Chiroptera, Pholidota, Carnivora, Perissodactyla, Artiodactyla, Cetacea). All analyses joined Archontoglires and Laurasiaplacentalia on a common branch (Boreoplacentalia), but the relationship between Afroplacentalia, Xenarthra and Boreoplacentalia was not conclusively resolved. The phylogenomic hypothesis with a sister group relationship between Notoplacentalia (Afroplacentalia/Xenarthra) and Boreoplacentalia served as the basis for estimating the times of placental divergences using paleontologically well-supported mammalian calibration points. These estimates placed the basal placental divergence between Boreoplacentalia and Notoplacentalia at approximately 102 MYA (million years ago). The current estimates of ordinal placental divergences are congruent with recent estimates based on nuclear data, but inconsistent with paleontological notions that have placed the origin of essentially all placental orders within an interval of 5-10 MY in the early Tertiary. Among less deep divergences the estimates placed the split between Gorilla and Pan/Homo at approximately 11.5 MYA and that between Pan and Homo at approximately 8 MYA. As a consequence of these estimates, which are in accord with recent progress in primate paleontology, the earliest divergences among recent humans become placed approximately 270,000 years ago, i.e. approximately 100,000 years earlier than the traditional age of "Mitochondrial Eve". Comparison between the two new mt genomes of Hylomys suillus (short-tailed gymnure) patently demonstrates the inconsistency that may exist between taxonomic designations and molecular difference, as the distance between these two supposedly conspecific genomes exceeds that of the three elephantid genera Elephas, Mammuthus and Loxodonta. In accordance with the progressive use of the term Placentalia for extant orders and extinct taxa falling within this group we forward new proposals for the names of some superordinal clades of placental mammals.
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.
Soils are known to be products of environmental factors such as climate, vegetation, topographic setting, parent material, and time for formation, so that paleosols, or fossil soils, can potentially reveal changing environments of the past. Evidence from paleosols for past climate and vegetation in East Africa does not support traditional narratives of human evolution during a single transition from primeval forest to dry climate and open grassland. Instead, paleosols indicate climatic oscillations between wet and dry, and alternating expansion of woodland and grassland, since at least 18 Ma (million years ago). Acquisition of dry grassland adaptations such as thick enamel by 18 Ma, adducted hallux by 14 Ma, and cursorial legs by 1.8 Ma, alternated with woodland adaptations such as short stiffback by 16Ma, erect stance by 6 Ma, and flat face by 3.5 Ma. Our ancestors survived profoundly changing climate and vegetation, with some adaptations lasting only to the next environmental shift, but others proving to be of lasting value.
Remains of an early hominid have been recovered from four localities in
the Lukeino Formation, Tugen Hills, Kenya, in sediments aged ca 6 Ma. 13
fossils are known, belonging to at least five individuals. The femora
indicate that the Lukeino hominid was a biped when on the ground, whilst
its humerus and manual phalanx show that it possessed some arboreal
adaptations. The upper central incisor is large and robust, the upper
canine is large for a hominid and retains a narrow and shallow anterior
groove, the lower fourth premolar is ape-like, with offset roots and
oblique crown, and the molars are relatively small, with thick enamel. A
new genus and species is erected for the remains.
Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.
Human evolution may be usefully considered as part of the evolution of the larger mammalian fauna of the Tertiary and Quaternary
periods. When viewed in this way, the dispersion of the hominins, and the questions of timings and directions, can be examined
in the context of movements in other mammalian groups without being treated as special case with a unique set of causes. Earliest
migrations by Primates into Africa during the Oligocene and Miocene were accompanied by numerous other taxa that were capable
of crossing the closing gap between continents. While the later evolution of the Hominidae may well have taken place in Africa,
the dispersion patterns of the dryopithecine apes during the early Middle Miocene into Eurasia and then back into Africa toward
the Late Miocene suggest a rather wider ancestry for humans and the living African apes. Earliest movements across the Gibraltar
Straits during the Pliocene and Pleistocene can be ruled out for any terrestrial mammals, and while a Late Pliocene dispersal
across the opening Bab-el-Mandeb region of the southern Red Sea may have been possible, such a route appears an unlikely choice
for a Pleistocene gateway leaving only the Levantine route across Sinai as a plausible way out of or into Africa.
Being based solely on neontological data, all «unique parent» evolutionary hypotheses, of which «Mitochondrial Eve» is one,
fall into the category ofscala naturae. Mathematical treatment of neontological data bases, using cladistic approaches does not confer the status of scientific
hypotheses onto such scenarios. Apart from these fundamental problems, such hypotheses are flawed on a number of other bases,
including the fact that there is a proportion of parental contribution to mitochondrial lineages, despite widely publicised
statements that mithocondrial DNA in mammals is «strictly» maternally inherited. Other weaknesses of «unique mother» hypotheses
on that their proponents endeavour to describe the evolution of diploid organisms on the basis of variability in extant haploid
organelles, the evolution of which is delinked from that of the diploid organism. A further difficulty is that it is not possible
to reconstruct interspecific relationships on the basis of intraspecific variability. There is a general ignorance among proponents
of «unique mother» hypotheses regarding the distribution of biological variability on the surface of the globe, a fact which
renders the molecular clock inaccurate, and which upsets the simplistic proposal that molecular diversity equates with time.
«Unique mother» scenarios are also invalidated by the presence of shared chromosome and other polymorphisms in african great
apes and humans at similar percentages in the different lineages, a fact which indicates that these evolving populations did
not experience «bottlenecks». These and other difficulties effectively refute the «Mitochondrial Eve» hypothesis, which in
any case much resembles creationism of a special kind, in which the offspring of a breeding pair are visualised as belonging
to a species different from its parents. Such extreme examples of the punctuational mode of evolution are highly likely to
be incorrect.
Discoveries of fossil Homo outside Africa predating 1.0 Ma have generated much discussion about hominin dispersal routes. However, tool-using bipeds were only one element of the inter-continental mammalian dispersals that occurred during the climatic changes of the Pliocene and Pleistocene. This paper will place hominin movements in the context of those of the wider mammalian fauna, which includes carnivores, bovids and non-human primates. The distribution of these different taxa suggests that species moved individually when the environmental conditions were right for them, rather than in multi-species waves of dispersal, and allows evaluation of the contextual evidence for the newly emerging ‘Out of Asia’ paradigm as well as the established ‘Out of Africa’ model.
Western Eurasia yielded a rich Middle (MP) and Late Pleistocene (LP) fossil record documenting the evolution of the Neandertals that can be analyzed in light of recently acquired paleogenetical data, an abundance of archeological evidence, and a well-known environmental context. Their origin likely relates to an episode of recolonization of Western Eurasia by hominins of African origin carrying the Acheulean technology into Europe around 600 ka. An enhancement of both glacial and interglacial phases may have played a crucial role in this event, as well as in the subsequent evolutionary history of the Western Eurasian populations. In addition to climatic adaptations and an increase in encephalization, genetic drift seems to have played a major role in their evolution. To date, a clear speciation event is not documented, and the most likely scenario for the fixation of Neandertal characteristics seems to be an accretion of features along the second half of the MP. Although a separation time for the African and Eurasian populations is difficult to determine, it certainly predates OIS 11 as phenotypic Neandertal features are documented as far back as and possibly before this time. It is proposed to use the term "Homo rhodesiensis" to designate the large-brained hominins ancestral to H. sapiens in Africa and at the root of the Neandertals in Europe, and to use the term "Homo neanderthalensis" to designate all of the specimens carrying derived metrical or non-metrical features used in the definition of the LP Neandertals.
Mitochondrial DNAs from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly.
Relationships among and within baleen and toothed whales were examined using the complete sequence of the mitochondrial cytochrome b gene. Based on parsimony analyses of conservative nucleotide substitutions, five primary evolutionary lineages of extant cetaceans were identified, one represented by baleen whales (Mysticeti) and four represented by odontocetes (toothed whales). Based on the most comprehensive representation of taxa, both cetaceans and artiodactyls, the most parsimonious relationship among the five lineages is (Mysticeti, Odontoceti (Platanistoidea (Physeteroidea (Ziphioidea (Delphinida))))). This relationship, however, is labile and sensitive to ingroup representation and the choice of outgroup. The short nodes among the five cetacean lineages suggest that the divergence among these lineages occurred over a narrow time period, a finding consistent with the limited fossil evidence that indicates a major cetacean radiation 30-34 Mya. The level of divergence among the five cetacean lineages, and that seen between cetaceans and artiodactyls, suggests that cetaceans and artiodactyls had a common ancestor approximately 60 Mya.
Although the sister-group relationship between Cetacea and Artiodactyla is widely accepted, the actual artiodactyl group which is closest to Cetacea has not been conclusively identified. In the present study, we have sequenced the complete mitochondrial genome of the hippopotamus, Hippopotamus amphibius, and included it in phylogenetic analyses together with 15 other placental mammals. These analyses separated the hippopotamus from the other suiform included, the pig, and identified the hippopotamus as the artiodactyl sister group of the cetaceans, thereby making both. Artiodactyla and the suborder. Suiformes paraphyletic. The divergence between the hippopotamid and cetacean lineages was calculated using this molecular data and was estimated at ca. 54 Ma BP.
The Acheulean site of Gesher Benot Ya'aqov in the Dead Sea Rift of Israel documents hominin movements and technological development on a corridor between Africa and Eurasia. New age data place the site at 780,000 years ago (oxygen isotope stage 19), considerably older than previous estimates. The archaeological data from the site portray strong affinities with African stone tool traditions. The findings also reflect adroit technical skills and in-depth planning abilities, more advanced and complex than those of earlier archaeological occurrences in the Levant.
