Colonization Of Eurasia Research Articles

Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice.

Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont's genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting that natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria.

Early Pleistocene stratigraphy, sedimentary environments, and formation contexts at Dmanisi in the Georgian Caucasus

The Early Pleistocene site of Dmanisi is now well known for its large number of fossils of early Homo erectus as well as associated artifacts and faunal remains, recovered mainly in pipe-related geologic features. Testing in the M5 unit 100 m to the west of the main excavations revealed a thick stratigraphy with no evidence of pipes or gullies, indicating that the geologic record at Dmanisi included spatially distinct sedimentary environments that needed further investigation. Here we report the results of a geoarchaeological program to collect data bearing on contexts and formation processes over a large area of the promontory. That work has defined over 40,000 m2 of in situ deposits with artifacts and faunas. Stratum A ashes bury the uppermost Mashavera Basalt, which we have dated to 1.8 Ma in the M5 block. The Stratum A deposits contain stratified occupations that accumulated quickly and offer good potential for recovery of in situ materials. Stratum B1 deposits above the A/B unconformity include all of the pipe and gully facies at Dmanisi, reflecting a brief but very intense phase of geomorphic change. Those deposits contain the majority of faunas and all of the hominin fossils. B1 slope facies offer excellent formation contexts away from the piped area, and all B1 deposits are sealed by Stratum B2 over the whole promontory. Strata B2 to B5 register a return to slope facies, with no further evidence of pipes or gullies. Those deposits also present excellent contexts for recovery of in situ occupations. Overall, Dmanisi's geologic history preserves an exceptional record of the activities and environmental context of occupations during the first colonization of Eurasia.

Ethnicity-specific distribution of <em>TRPM8</em> gene variants in Eurasian populations: signs of selection

The TRPM8 gene encodes the ion channel, which is a cold receptor in afferent neurons of the mammalian somatosensory system. We studied the frequency of haplotype distribution from six SNPs in the TRPM8 gene in Eurasian human populations, including Russians, Kazakhs and Chukchi. Four of the six SNPs are located in exon 7 (rs13004520, rs28901637, rs11562975, rs17868387), rs7593557 is in exon 11. These exons encode parts of the N-terminus, which is necessary for channel functioning in the plasma membrane of neurons. The rs11563071 is in exon 23 encoding part of the C-terminus. The primary difference in population distribution of haplotypes determines the SNP from exon 11 which leads to Ser419Asn substitution in protein. The most pronounced differences in the patterns of diversity and frequencies of haplotypes were observed between Chukchi and Russians. The frequency of major H1 haplotype encompassing the 419Ser gene variant differs in examined populations; 0.738 (Russians), 0.507 (Kazakhs) and 0.337 (Chukchi), p < 0.001. The TRPM8 gene variants encoding 419Asn and carrying the minor alleles of rs28901637 (P249P) and rs11562975 (L250L) in exon 7 are characteristic of Asian populations. The frequency of all 419Asn variants in Chukchi is comparable to that in Africans, however, the minor allele frequencies of rs28901637, rs11562975 in Africans is low. Apparently in the process of human colonization of Eurasia, minor alleles of these SNPs diverged depending on rs7593557 structure in exon 11. We analyzed sequences of five TRPM8 mRNA isoforms extracted by researchers from different tissues. Sequence analysis demonstrates that they are transcribed from major H1 variant of the TRPM8 gene but contain different translation start codons, which are generated by alternative splicing from pro-mRNA.

Archeology: University Textbook and Science (to the 45th Anniversary of the Publication of the Textbook: Martynov A. I. Archeology of the USSR . Moscow, 1973)

The paper features the interaction of archaeological science and textbooks on archeology. It successively examines the history of textbooks on archeology in Russia published for higher education institutions of history, from the XIX century to the present. The author stresses the importance of textbooks in the formation and development of archeology as one of the main subjects of university historical education. Archeology and its textbooks play a key role in the reconstruction of important historical events of the three million years of human history, especially in cases when archaeological materials are the only source. Archeology discovered civilizations of the Ancient East, e.g. China, India, Iran, as well as Archaic Greece and ancient Rome. The paper states the significance of the archaeological heritage of Russia. Since 1970s, only two universities in Russia, Lomonosov Moscow State University and Kemerovo State University (Department of Archeology), have been publishing university textbooks on archeology to be used in universities nationwide. The list involves nine publications prepared by Kemerovo State University. These textbooks are unique from the point of view of the content and methodology of the presentation. The article focuses on the interaction of archaeological science and university textbooks. This concerns the explanation of global historical events, e.g. the early colonization of Eurasia, ethnogenesis in the Middle Paleolithic Era, human migration to America in the Upper Paleolithic, the formation of cultural in the early Holocene, revolution of the producing economy in the Paleometallic Era, etc. The author describes the effect of archeological textbooks on the formation of the conceptual foundations of modern archeology as a historical science. The section "One History – Two Sciences" features the shortcomings of modern Russian historical science, in particular, the lack of alternative to the concept of formational explanation of history in school and university textbooks. History is currently being demonstrated exclusively as a social-class development process, which makes it impossible to understand the role of the fundamental foundations of historical development, as well as the role of discoveries, innovations, achievements in the field of material culture and productive economy. As a result, the human achievements of the past, which are indicated in archeology textbooks, do not find proper application in explaining the historical processes in Russia and Eurasia in modern history textbooks.

Acheulean technology and landscape use at Dawadmi, central Arabia

Despite occupying a central geographic position, investigations of hominin populations in the Arabian Peninsula during the Lower Palaeolithic period are rare. The colonization of Eurasia below 55 degrees latitude indicates the success of the genus Homo in the Early and Middle Pleistocene, but the extent to which these hominins were capable of innovative and novel behavioural adaptations to engage with mid-latitude environments is unclear. Here we describe new field investigations at the Saffaqah locality (206–76) near Dawadmi, in central Arabia that aim to establish how hominins adapted to this region. The site is located in the interior of Arabia over 500 km from both the Red Sea and the Gulf, and at the headwaters of two major extinct river systems that were likely used by Acheulean hominins to cross the Peninsula. Saffaqah is one of the largest Acheulean sites in Arabia with nearly a million artefacts estimated to occur on the surface, and it is also the first to yield stratified deposits containing abundant artefacts. It is situated in the unusual setting of a dense and well-preserved landscape of Acheulean localities, with sites and isolated artefacts occurring regularly for tens of kilometres in every direction. We describe both previous and recent excavations at Saffaqah and its large lithic assemblage. We analyse thousands of artefacts from excavated and surface contexts, including giant andesite cores and flakes, smaller cores and retouched artefacts, as well as handaxes and cleavers. Technological assessment of stratified lithics and those from systematic survey, enable the reconstruction of stone tool life histories. The Acheulean hominins at Dawadmi were strong and skilful, with their adaptation evidently successful for some time. However, these biface-makers were also technologically conservative, and used least-effort strategies of resource procurement and tool transport. Ultimately, central Arabia was depopulated, likely in the face of environmental deterioration in the form of increasing aridity.

A historical biogeography of megadiverse Sericini-another story "out of Africa"?

Megadiverse insect groups present special difficulties for biogeographers because poor classification, incomplete knowledge of taxonomy, and many undescribed species can introduce a priori sampling bias to any analysis. The historical biogeography of Sericini, a tribe of melolonthine scarabs comprising about 4000 species, was investigated using the most comprehensive and time-calibrated molecular phylogeny available today. Problems arising through nomenclatural confusion were overcome by extensive sampling (665 species) from all major lineages of the tribe. A West Gondwanan origin of Sericini (c. 112 Ma) was reconstructed using maximum parsimony, maximum-likelihood and model-based ancestral area estimation. Vicariance in the tribe's earliest history separated Neotropical and Old World Sericini, whereas subsequent lower Cretaceous biogeography of the tribe was characterized by repeated migrations out of Africa, resulting in the colonization of Eurasia and Madagascar. North America was colonized from Asia during the Cenozoic and a lineage of "Modern Sericini" reinvaded Africa. Diversification dynamics revealed three independent shifts to increased speciation rates: in African ant-adapted Trochalus, Oriental Tetraserica, and Asian and African Sericina. Southern Africa is proposed as both cradle and refuge of Sericini. This area has retained many old lineages that portray the evolution of the African Sericini fauna as a series of taxon pulses.

Human adaptation and population differentiation in the light of ancient genomes.

The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.

Biology of Culture

The D4500 Dmanisi skull (Georgia) is one of the oldest pieces of evidence of the colonization of Eurasia by humans 1.8 million years ago. Africa long remained central to the evolution and demographics of Hominins. Humans colonized Eurasia only over the last two million years, and finally a species, also originally from Africa, replaced all others and occupied all land areas. It spectacularly modified its environment and extended its hold over the genome of other living forms. Human evolution...

Rapid diversification and dispersal during periods of global warming by plethodontid salamanders.

A phylogeny and timescale derived from analyses of multilocus nuclear DNA sequences for Holarctic genera of plethodontid salamanders reveal them to be an old radiation whose common ancestor diverged from sister taxa in the late Jurassic and underwent rapid diversification during the late Cretaceous. A North American origin of plethodontids was followed by a continental-wide diversification, not necessarily centered only in the Appalachian region. The colonization of Eurasia by plethodontids most likely occurred once, by dispersal during the late Cretaceous. Subsequent diversification in Asia led to the origin of Hydromantes and Karsenia, with the former then dispersing both to Europe and back to North America. Salamanders underwent rapid episodes of diversification and dispersal that coincided with major global warming events during the late Cretaceous and again during the Paleocene-Eocene thermal optimum. The major clades of plethodontids were established during these episodes, contemporaneously with similar phenomena in angiosperms, arthropods, birds, and mammals. Periods of global warming may have promoted diversification and both inter- and transcontinental dispersal in northern hemisphere salamanders by making available terrain that shortened dispersal routes and offered new opportunities for adaptive and vicariant evolution.

Phylogeography of the white‐tailed eagle, a generalist with large dispersal capacity

AbstractAim Late Pleistocene glacial changes had a major impact on many boreal and temperate taxa, and this impact can still be detected in the present‐day phylogeographic structure of these taxa. However, only minor effects are expected in species with generalist habitat requirements and high dispersal capability. One such species is the white‐tailed eagle,Haliaeetus albicilla, and we therefore tested for the expected weak population structure at a continental level in this species. This also allowed us to describe phylogeographic patterns, and to deduce Ice Age refugia and patterns of postglacial recolonization of Eurasia.Location Breeding populations from the easternmost Nearctic (Greenland) and across the Palaearctic (Iceland, continental Europe, central and eastern Asia, and Japan).Methods Sequencing of a 500 base‐pair fragment of the mitochondrial DNA control region in 237 samples from throughout the distribution range.Results Our analysis revealed pronounced phylogeographic structure. Overall, low genetic variability was observed across the entire range. Haplotypes clustered in two distinct haplogroups with a predominantly eastern or western distribution, and extensive overlap in Europe. These two major lineages diverged during the late Pleistocene. The eastern haplogroup showed a pattern of rapid population expansion and colonization of Eurasia around the end of the Pleistocene. The western haplogroup had lower diversity and was absent from the populations in eastern Asia. These results suggest survival during the last glaciation in two refugia, probably located in central and western Eurasia, followed by postglacial population expansion and admixture. Relatively high genetic diversity was observed in northern regions that were ice‐covered during the last glacial maximum. This, and phylogenetic relationships between haplotypes encountered in the north, indicates substantial population expansion at high latitudes. Areas of glacial meltwater runoff and proglacial lakes could have provided suitable habitats for such population growth.Main conclusions This study shows that glacial climate fluctuations had a substantial impact on white‐tailed eagles, both in terms of distribution and demography. These results suggest that even species with large dispersal capabilities and relatively broad habitat requirements were strongly affected by the Pleistocene climatic shifts.

The earliest record of human activity in northern Europe

The colonization of Eurasia by early humans is a key event after their spread out of Africa, but the nature, timing and ecological context of the earliest human occupation of northwest Europe is uncertain and has been the subject of intense debate. The southern Caucasus was occupied about 1.8 million years (Myr) ago, whereas human remains from Atapuerca-TD6, Spain (more than 780 kyr ago) and Ceprano, Italy (about 800 kyr ago) show that early Homo had dispersed to the Mediterranean hinterland before the Brunhes-Matuyama magnetic polarity reversal (780 kyr ago). Until now, the earliest uncontested artefacts from northern Europe were much younger, suggesting that humans were unable to colonize northern latitudes until about 500 kyr ago. Here we report flint artefacts from the Cromer Forest-bed Formation at Pakefield (52 degrees N), Suffolk, UK, from an interglacial sequence yielding a diverse range of plant and animal fossils. Event and lithostratigraphy, palaeomagnetism, amino acid geochronology and biostratigraphy indicate that the artefacts date to the early part of the Brunhes Chron (about 700 kyr ago) and thus represent the earliest unequivocal evidence for human presence north of the Alps.

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

BackgroundRecent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia.ResultsFour new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades.ConclusionsSince the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.