Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara.

ABSTRACT: Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.

SUBMITTER: Vai S

PROVIDER: S-EPMC6401177 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara.

Vai Stefania S Sarno Stefania S Lari Martina M Luiselli Donata D Manzi Giorgio G Gallinaro Marina M Mataich Safaa S Hübner Alexander A Modi Alessandra A Pilli Elena E Tafuri Mary Anne MA Caramelli David D di Lernia Savino S

Scientific reports 20190305 1

Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old ind ...[more]

PMID: 30837540

Similar Datasets

Human genomes from the Green Sahara reveal ancestral North African lineage

Project description:Genome-wide ancient DNA data from two 7,000-year-old individuals from Takarkori Rockshelter in Libya, and Archaic admixture capture data from seven 15,000-year-old individuals from Taforalt Cave, Morocco.

| PRJEB84057 | ENA

Rainfall regimes of the Green Sahara.

Project description:During the "Green Sahara" period (11,000 to 5000 years before the present), the Sahara desert received high amounts of rainfall, supporting diverse vegetation, permanent lakes, and human populations. Our knowledge of rainfall rates and the spatiotemporal extent of wet conditions has suffered from a lack of continuous sedimentary records. We present a quantitative reconstruction of western Saharan precipitation derived from leaf wax isotopes in marine sediments. Our data indicate that the Green Sahara extended to 31°N and likely ended abruptly. We find evidence for a prolonged "pause" in Green Sahara conditions 8000 years ago, coincident with a temporary abandonment of occupational sites by Neolithic humans. The rainfall rates inferred from our data are best explained by strong vegetation and dust feedbacks; without these mechanisms, climate models systematically fail to reproduce the Green Sahara. This study suggests that accurate simulations of future climate change in the Sahara and Sahel will require improvements in our ability to simulate vegetation and dust feedbacks.

| S-EPMC5242556 | biostudies-literature

Trapping or tethering stones (TS): A multifunctional device in the Pastoral Neolithic of the Sahara.

Project description:The Pierres de Ben Barour, also known as trapping or tethering stones (TS), are stone artefacts with notches or grooves usually interpreted as hunting devices on the basis of rock art engravings. Though their presence is a peculiar feature of desert landscapes from the Sahara to the Arabian Peninsula, we know little about their age, context and function. Here we present a new approach to the study of these artefacts based on a large dataset (837 items) recorded in the Messak plateau (SW Libya). A statistically-based geoarchaeological survey carried out between 2007 and 2011 in Libya, alongside landscape and intra-site analyses of specific archaeological features (such as rock art, settlement and ceremonial contexts), reveal that these artefacts were used for a prolonged period, probably from the early Holocene. This was followed by a multifunctional use of these devices, particularly during the Pastoral Neolithic phase (ca. 6400-3000 cal BC), with the highest concentrations being found near ceremonial contexts related to cattle burials.

| S-EPMC5784975 | biostudies-literature

Pastoralism may have delayed the end of the green Sahara.

Project description:The climate deterioration after the most recent African humid period (AHP) is a notable past example of desertification. Evidence points to a human population expansion in northern Africa prior to this, associated with the introduction of pastoralism. Here we consider the role, if any, of this population on the subsequent ecological collapse. Using a climate-vegetation model, we estimate the natural length of the most recent AHP. The model indicates that the system was most susceptible to collapse between 7 and 6 ka; at least 500 years before the observed collapse. This suggests that the inclusion of increasing elements of pastoralism was an effective adaptation to the regional environmental changes. Pastoralism also appears to have slowed the deterioration caused by orbitally-driven climate change. This supports the view that modern pastoralism is not only sustainable, but beneficial for the management of the world's dryland environments.

| S-EPMC6167352 | biostudies-literature

The spatiotemporal extent of the Green Sahara during the last glacial period.

Project description:The Sahara Desert, one of today's most inhospitable environments, has known periods of enhanced precipitation that supported pre-historic humans. However, the Green Sahara timing and moisture sources are not well known due to limited paleoclimate information. Here, we present a multi-proxy (δ18O, δ13C, Δ17O, and trace elements) speleothem-based climate record from Northwest (NW) Africa. Our data document two Green Sahara periods during Marine Isotope Stage (MIS) 5a and the Early to Mid-Holocene. Consistency with paleoclimate records across North Africa highlights the east-west geographical extent of the Green Sahara, whereas millennial-scale North Atlantic cooling (Heinrich) events consistently resulted in drier conditions. We demonstrate that an increase in westerly-originating winter precipitation during MIS5a resulted in favorable environmental conditions. The comparison of paleoclimate data with local archaeological sequences highlights the abrupt climate deterioration and the decline in human density in NW Africa during the MIS5-4 transition, which suggests climate-forced dispersals of populations, with possible implications for pathways into Eurasia.

| S-EPMC10320408 | biostudies-literature

Modeling the contrasting Neolithic male lineage expansions in Europe and Africa.

Project description:BACKGROUND:Patterns of genetic variation in a population carry information about the prehistory of the population, and for the human Y chromosome an especially informative phylogenetic tree has previously been constructed from fully-sequenced chromosomes. This revealed contrasting bifurcating and starlike phylogenies for the major lineages associated with the Neolithic expansions in sub-Saharan Africa and Western Europe, respectively. RESULTS:We used coalescent simulations to investigate the range of demographic models most likely to produce the phylogenetic structures observed in Africa and Europe, assessing the starting and ending genetic effective population sizes, duration of the expansion, and time when expansion ended. The best-fitting models in Africa and Europe are very different. In Africa, the expansion took about 12 thousand years, ending very recently; it started from approximately 40 men and numbers expanded approximately 50-fold. In Europe, the expansion was much more rapid, taking only a few generations and occurring as soon as the major R1b lineage entered Europe; it started from just one to three men, whose numbers expanded more than a thousandfold. CONCLUSIONS:Although highly simplified, the demographic model we have used captures key elements of the differences between the male Neolithic expansions in Africa and Europe, and is consistent with archaeological findings.

| S-EPMC4177147 | biostudies-literature

Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae.

Project description:Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.

| S-EPMC6821328 | biostudies-literature

Complete mitochondrial genomes reveal neolithic expansion into Europe.

Project description:The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.

| S-EPMC3302788 | biostudies-literature

End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia.

Project description:Between 5 and 4 thousand years ago, crippling megadroughts led to the disruption of ancient civilizations across parts of Africa and Asia, yet the extent of these climate extremes in mainland Southeast Asia (MSEA) has never been defined. This is despite archeological evidence showing a shift in human settlement patterns across the region during this period. We report evidence from stalagmite climate records indicating a major decrease of monsoon rainfall in MSEA during the mid- to late Holocene, coincident with African monsoon failure during the end of the Green Sahara. Through a set of modeling experiments, we show that reduced vegetation and increased dust loads during the Green Sahara termination shifted the Walker circulation eastward and cooled the Indian Ocean, causing a reduction in monsoon rainfall in MSEA. Our results indicate that vegetation-dust climate feedbacks from Sahara drying may have been the catalyst for societal shifts in MSEA via ocean-atmospheric teleconnections.

| S-EPMC7442841 | biostudies-literature

Paleolithic and neolithic lineages in the European mitochondrial gene pool.

Project description:Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individuals from Europe and the Middle East distinguishes five major lineage groups with different internal diversities and divergence times. Consideration of the diversities and geographic distribution of these groups within Europe and the Middle East leads to the conclusion that ancestors of the great majority of modern, extant lineages entered Europe during the Upper Paleolithic. A further set of lineages arrived from the Middle East much later, and their age and geographic distribution within Europe correlates well with archaeological evidence for two culturally and geographically distinct Neolithic colonization events that are associated with the spread of agriculture. It follows from this interpretation that the major extant lineages throughout Europe predate the Neolithic expansion and that the spread of agriculture was a substantially indigenous development accompanied by only a relatively minor component of contemporary Middle Eastern agriculturalists. There is no evidence of any surviving Neanderthal lineages among modern Europeans.

| S-EPMC1915109 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data