Abstract Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa 1–4 . Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations 3,5 . Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.
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Archaeological Recovery of Late Pleistocene Hair and Environmental DNA from Interior Alaska
Ancient hair and remnant plant DNA are important environmental proxies that preserve for millennia in specific archaeological contexts. However, recovery has been rare from late Pleistocene sites and more may be found if deliberately sought. Once discovered, singular hair fragments are not easily identified to taxa through comparative analyses and environmental DNA (eDNA) extraction can be difficult depending on preservation or contamination. In this paper, we present our methods for the combined recovery of ancient hair specimens and eDNA from sediments to improve our understanding of late Pleistocene environments from the Holzman site along Shaw Creek in interior Alaska. The approach serves as a useful case study for learning more about local environmental changes.
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- Award ID(s):
- 1850949
- NSF-PAR ID:
- 10323602
- Date Published:
- Journal Name:
- Environmental Archaeology
- ISSN:
- 1461-4103
- Page Range / eLocation ID:
- 1 to 16
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)The primary objectives of International Ocean Discovery Program (IODP) Expedition 367/368 to the northern South China Sea (SCS) margin were to (1) examine its history of continental breakup and (2) compare it with other nonvolcanic or magma-poor rifted margins with the broader goal of testing models for continental breakup. A secondary objective was to further our understanding of the paleoceanographic and environmental development of the SCS and southeast Asia during the Cenozoic. Four primary sites were selected for the overall program: one in the outer margin high (OMH) and three seaward of the OMH on distinct, margin-parallel basement ridges. These three ridges are informally labeled A, B, and C and are located in the continent–ocean transition (COT) zone ranging from the OMH to the interpreted steady-state oceanic crust (Ridge C) of the SCS. The main scientific objectives include the following: Determining the nature of the basement in crustal units across the COT of the SCS that are critical to constrain style of rifting, Constraining the time interval from initial crustal extension and plate rupture to the initial generation of igneous ocean crust, Constraining vertical crustal movements during breakup, and Examining the nature of igneous activity from rifting to seafloor spreading. In addition, the sediment cores from the drill sites targeting primarily tectonic and basement objectives will provide information on the Cenozoic regional environmental development of the Southeast Asia margin. Site U1499 on Ridge A and Site U1500 on Ridge B were drilled during Expedition 367. Expedition 368 was planned to drill at two primary sites (U1501 and U1503) at the OMH and Ridge C, respectively, but based on drilling results from Expedition 367, Expedition 368 chose to insert an alternate site on Ridge A (Site U1502). In addition, Expedition 368 added two more sites on the OMH (Sites U1504 and U1505). Expedition 367/368 completed operations at six of the seven sites (U1499–U1502, U1504, and U1505). Site U1503, however, was not completed beyond casing without coring to 990 m because of mechanical problems with the drilling equipment that prevented the expedition, after 25 May 2017, from operating with a drill string longer than 3400 m. New alternate Site U1504, proposed during Expedition 367, met this condition. Original Site U1505 also met the operational constraints of the 3400 m drill string (total) and was an alternate site for the already-drilled Site U1501. At Site U1499, we cored to 1081.8 m in 22.1 days with 52% recovery and then logged downhole data from 655 to 1020 m. In 31 days at Site U1500, we penetrated to 1529 m, cored a total of 1012.8 m with 37% recovery, and collected log data from 842 to 1133 m. At Site U1501, we cored to 697.1 m in 9.4 days with 78.5% recovery. We also drilled ahead for 433.5 m in Hole U1501D and then logged downhole data from 78.3 to 399.3 m. In 19.3 days at Site U1502, we penetrated 1679.0 m in Holes U1502A (758 m) and U1502B (921 m), set 723.7 m of casing and cored a total of 576.3 m with 53.5% recovery, and collected downhole log data from 785.3 to 875.3 m and seismic data through the 10¾ inch casing. At Site U1503, we penetrated 995.1 m and set 991.5 m of 10¾ inch casing, but no cores were taken because of a mechanical problem with the drawworks. At Site U1504, we took 40 rotary core barrel (RCB) cores over two holes. The cored interval between both holes was 277.3 m with 26.8% recovery. An 88.2 m interval was drilled in Hole U1504B. At Site U1505, we cored 668.0 m with 101.1% recovery. Logging data was collected from 80.1 to 341.2 m. Operations at this site covered 6.1 days. Except for Sites U1503 and U1505, all sites were drilled to acoustic basement. A total of 6.65 days were lost due to mechanical breakdown or waiting on spare supplies for repair of drilling equipment, but drilling options were severely limited from 25 May to the end of the expedition by the defective drawworks limiting deployment of drill string longer than 3400 m. At Site U1499, coring ~200 m into the interpreted acoustic basement sampled sedimentary rocks, possibly including early Miocene chalks underlain by Oligocene polymict breccias and poorly cemented gravels of unknown age comprising sandstone pebbles and cobbles. Preliminary structural and lithologic analysis suggests that the gravels might be early to late synrift sediment. At Site U1500, the main seismic reflector corresponds to the top of a basalt sequence at ~1379.1 m. We cored 149.90 m into this volcanic package and recovered 114.92 m (77%) of sparsely to moderately plagioclase-phyric basalt comprising numerous lava flows, including pillow lavas with glass, chilled margins, altered veins, hyaloclastites, and minor sediment. Preliminary geochemical analyses indicate that the basalt is tholeiitic. Sampling of the Pleistocene to lower Miocene sedimentary section at Sites U1499 and U1500 was not continuous for two reasons. First, there was extremely poor recovery in substantial intervals interpreted to be poorly lithified sands, possibly turbidites. Second, we chose to drill down without coring in some sections at Site U1500 to ensure sufficient time to achieve this site’s high-priority deep drilling objectives. The upper Miocene basin sequence, which consists of interbedded claystone, siltstone, and sandstone can be correlated between the two sites by seismic stratigraphic mapping and biostratigraphy. At Site U1501 on the OMH, coring ~45 m into the acoustic basement sampled prerift(?) deposits comprising sandstone to conglomerate of presumed Mesozoic age. These deposits are overlain by siliciclastic synrift sediments of Eocene to Oligocene age followed by primarily carbonaceous postrift sediments of early Miocene to Pleistocene age. Site U1502 on Ridge A was cased to 723.7 m. No coring was attempted shallower than 380 m to save operational time and because of low expectations for core recovery in the upper Plio–Pleistocene sequence. At this site, we recovered 180 m of hydrothermally altered brecciated basalts comprising sheet and pillow lavas below deep-marine sediments of Oligocene to late Miocene age. At Site U1503 on Ridge C, 991.5 m of casing was installed in preparation for the planned deep drilling to ~1800 m. No coring was performed due to mechanical failures, and the site was abandoned without further activity except for installation of a reentry cone. Coring at Site U1504 on the OMH, located ~45 km east of Site U1501, recovered mostly foliated, greenschist facies metamorphic rocks below late Eocene(?) carbonate rocks (partly reef debris) and early Miocene to Pleistocene sediments. At Site U1505, we cored to 480.15 m through Pleistocene to late Oligocene mainly carbonaceous ooze followed at depth by early Oligocene siliciclastic sediments. Efforts were made at every drill site to correlate the core with the seismic data and seismic stratigraphic unconformities interpreted in the Eocene to Plio–Pleistocene sedimentary sequence prior to drilling. The predrilling interpretation of ages of these unconformities was in general confirmed by drilling results, although some nontrivial corrections can be expected from detailed postexpedition work on integrating seismic stratigraphic interpretations with detailed bio- and lithostratigraphy. As a result of the limited length of drill string that could be deployed during the later part of Expedition 368, the secondary expedition objectives addressing the environmental history of the SCS and Southeast Asia received more focus than originally planned, allowing Site U1505 (alternate to Site U1501) to be included. Despite this change in focus, Expedition 367/368 provided solid evidence for a process of breakup that included vigorous synrift magmatism as opposed to the often-favored interpretation of the SCS margin as a magma-starved margin or a margin possibly overprinted at a much later stage by plume-related magmatism. In this broader perspective, Expedition 367/368 accomplished a fundamental objective of the two-expedition science program.more » « less
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Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost.
Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including
Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost.Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.
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null (Ed.)International Ocean Discovery Program Expedition 368 is the second of two consecutive cruises that form the South China Sea Rifted Margin program. Expeditions 367 and 368 share the common key objectives of testing scientific hypotheses of breakup of the northern South China Sea (SCS) margin and comparing its rifting style and history to other nonvolcanic or magma-poor rifted margins. Four primary sites were selected for the overall program: one in the outer margin high (OMH) and three seaward of the OMH on distinct, margin-parallel basement ridges. These three ridges are informally labeled A, B, and C. They are located within the continent–ocean transition (COT) zone ranging from the OMH to the interpreted steady-state oceanic crust (Ridge C) of the SCS. The main scientific objectives include 1. Determining the nature of the basement within crustal units across the COT of the SCS that are critical to constrain style of rifting, 2. Constraining the time interval from initial crustal extension and plate rupture to the initial generation of igneous ocean crust, 3. Constraining vertical crustal movements during breakup, and 4. Examining the nature of igneous activity from rifting to seafloor spreading. In addition, the sediment cores from the drill sites targeting primarily tectonic and basement objectives will provide information on the Cenozoic regional environmental development of the Southeast Asia margin. Expedition 368 was planned to drill at two primary sites (U1501 and U1503) at the OMH and Ridge C, respectively. However, based on drilling results from Expedition 367, Expedition 368 chose to insert an alternate site on Ridge A (Site U1502). In total, the expedition completed operations at four sites (U1501, U1502, U1504, and U1505). Site U1503, however, was not completed beyond casing to 990 m because of mechanical problems with the drilling equipment that limited the expedition from 25 May 2017 to the end of the expedition to operate with a drill string not longer than 3400 m. New alternate Site U1504 proposed during Expedition 367 met this condition. Site U1505 also met the operational constraints of the 3400 m drill string (total) and was an alternate site for the already drilled Site U1501. At Site U1501, we cored to 697.1 m in 9.4 days, with 78.5% recovery. We also drilled ahead for 433.5 m in Hole U1501D and then logged downhole data from 78.3 to 399.3 m. In 19.3 days at Site U1502, we penetrated 1679.0 m, set 723.7 m of casing and cored a total of 576.3 m with 53.5% recovery, and collected downhole log data from 785.3 to 875.3 m and seismic data through the 10¾ inch casing. At Site U1503, we penetrated 995.1 m, setting 991.5 m of 10¾ inch casing, but no cores were taken. At Site U1504, we took 40 rotary core barrel (RCB) cores over two holes. The cored interval between both holes was 277.3 m with 26.8% recovery. An 88.2 m interval was drilled in Hole U1504B. At Site U1505, we cored 668.0 m with 101.1% recovery. Logging data was collected from 80.1 to 341.2 m. Operations at this site covered 6.1 days. Except for Site U1505, we drilled to acoustic basement, which prior to the expedition, except for Site U1501, had been interpreted to be crystalline basement. A total of 6.65 days were lost due to mechanical breakdown or waiting on spare supplies for repair of drilling equipment. At Site U1501 on the OMH, coring ~45 m into the acoustic basement sampled highly lithified sandstone to conglomerate of presumed Mesozoic age overlain by siliciclastic Eocene pre- to synrift sediments of Oligocene age and topped by primarily carbonaceous postrift sediments of early Miocene to Pleistocene age. Site U1502 on Ridge A was cased to 723.7 m. At this site, we recovered 180 m of hydrothermally altered brecciated basalts comprising sheet and pillow lavas below deep-marine sediments of Oligocene to late Miocene age. Coring was not performed within the upper 380 m (~Pliocene–Pleistocene) at Site U1502. At Site U1503 on Ridge C, 991.5 m of casing was installed in preparation for the planned deep drilling to ~1800 m, but no coring was performed due to mechanical failures, and the site was abandoned without further activity. Coring at Site U1504 on the OMH ~45 km east of Site U1501 recovered metamorphic schist to gneiss (greenschist facies) below late Eocene (?) carbonate rocks (partly reef debris) and early Miocene to Pleistocene sediments. At Site U1505, we cored to 480.15 m through Pleistocene to late Oligocene mainly carbonaceous ooze followed at depth by early Oligocene to late Eocene siliciclastic sediments. Efforts were made at every drill site to correlate the core with the seismic data and seismic stratigraphic unconformities interpreted within the Eocene to Plio–Pleistocene sedimentary sequence prior to drilling. The predrilling interpretation of ages of these unconformities was in general confirmed by drilling results. As a result of the constraints on the length of drill string that could be deployed during the later part of Expedition 368, the secondary expedition objectives addressing the environmental history of the SCS and Southeast Asia received more focus than planned because these sites are located in shallower water depths and required less penetration depth. This forced change in emphasis, however, was without fatal consequences for the primary tectonic objectives. The two expeditions together provided solid evidence for a process of breakup that included vigorous synrift magmatism as opposed to the often-favored interpretation of the SCS margin as a magma-starved margin.more » « less
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null (Ed.)The Amundsen Sea sector of Antarctica has long been considered the most vulnerable part of the West Antarctic Ice Sheet (WAIS) because of the great water depth at the grounding line and the absence of substantial ice shelves. Glaciers in this configuration are thought to be susceptible to rapid or runaway retreat. Ice flowing into the Amundsen Sea Embayment is undergoing the most rapid changes of any sector of the Antarctic Ice Sheet outside the Antarctic Peninsula, including changes caused by substantial grounding-line retreat over recent decades, as observed from satellite data. Recent models suggest that a threshold leading to the collapse of WAIS in this sector may have been already crossed and that much of the ice sheet could be lost even under relatively moderate greenhouse gas emission scenarios. Drill cores from the Amundsen Sea provide tests of several key questions about controls on ice sheet stability. The cores offer a direct record of glacial history offshore from a drainage basin that receives ice exclusively from the WAIS, which allows clear comparisons between the WAIS history and low-latitude climate records. Today, warm Circumpolar Deep Water (CDW) is impinging onto the Amundsen Sea shelf and causing melting of the underside of the WAIS in most places. Reconstructions of past CDW intrusions can assess the ties between warm water upwelling and large-scale changes in past grounding-line positions. Carrying out these reconstructions offshore from the drainage basin that currently has the most substantial negative mass balance of ice anywhere in Antarctica is thus of prime interest to future predictions. The scientific objectives for this expedition are built on hypotheses about WAIS dynamics and related paleoenvironmental and paleoclimatic conditions. The main objectives are 1. To test the hypothesis that WAIS collapses occurred during the Neogene and Quaternary and, if so, when and under which environmental conditions; 2. To obtain ice-proximal records of ice sheet dynamics in the Amundsen Sea that correlate with global records of ice-volume changes and proxy records for atmospheric and ocean temperatures; 3. To study the stability of a marine-based WAIS margin and how warm deep-water incursions control its position on the shelf; 4. To find evidence for earliest major grounded WAIS advances onto the middle and outer shelf; 5. To test the hypothesis that the first major WAIS growth was related to the uplift of the Marie Byrd Land dome. International Ocean Discovery Program (IODP) Expedition 379 completed two very successful drill sites on the continental rise of the Amundsen Sea. Site U1532 is located on a large sediment drift, now called Resolution Drift, and penetrated to 794 m with 90% recovery. We collected almost-continuous cores from the Pleistocene through the Pliocene and into the late Miocene. At Site U1533, we drilled 383 m (70% recovery) into the more condensed sequence at the lower flank of the same sediment drift. The cores of both sites contain unique records that will enable study of the cyclicity of ice sheet advance and retreat processes as well as bottom-water circulation and water mass changes. In particular, Site U1532 revealed a sequence of Pliocene sediments with an excellent paleomagnetic record for high-resolution climate change studies of the previously sparsely sampled Pacific sector of the West Antarctic margin. Despite the drilling success at these sites, the overall expedition experienced three unexpected difficulties that affected many of the scientific objectives: 1. The extensive sea ice on the continental shelf prevented us from drilling any of the proposed shelf sites. 2. The drill sites on the continental rise were in the path of numerous icebergs of various sizes that frequently forced us to pause drilling or leave the hole entirely as they approached the ship. The overall downtime caused by approaching icebergs was 50% of our time spent on site. 3. An unfortunate injury to a member of the ship's crew cut the expedition short by one week. Recovery of core on the continental rise at Sites U1532 and U1533 cannot be used to precisely indicate the position of ice or retreat of the ice sheet on the shelf. However, these sediments contained in the cores offer a range of clues about past WAIS extent and retreat. At Sites U1532 and U1533, coarse-grained sediments interpreted to be ice-rafted debris (IRD) were identified throughout all recovered time periods. A dominant feature of the cores is recorded by lithofacies cyclicity, which is interpreted to represent relatively warmer periods variably characterized by higher microfossil abundance, greater bioturbation, and higher counts of IRD alternating with colder periods characterized by dominantly gray laminated terrigenous muds. Initial comparison of these cycles to published records from the region suggests that the units interpreted as records of warmer time intervals in the core tie to interglacial periods and the units interpreted as deposits of colder periods tie to glacial periods. The cores from the two drill sites recovered sediments of purely terrigenous origin intercalated or mixed with pelagic or hemipelagic deposits. In particular, Site U1533, which is located near a deep-sea channel originating from the continental slope, contains graded sands and gravel transported downslope from the shelf to the abyssal plain. The channel is likely the path of such sediments transported downslope by turbidity currents or other sediment-gravity flows. The association of lithologic facies at both sites predominantly reflects the interplay of downslope and contouritic sediment supply with occasional input of more pelagic sediment. Despite the lack of cores from the shelf, our records from the continental rise reveal the timing of glacial advances across the shelf and thus the existence of a continent-wide ice sheet in West Antarctica at least during longer time periods since the late Miocene. Cores from both sites contain abundant coarse-grained sediments and clasts of plutonic origin transported either by downslope processes or by ice rafting. If detailed provenance studies confirm our preliminary assessment that the origin of these samples is from the plutonic bedrock of Marie Byrd Land, their thermochronological record will potentially reveal timing and rates of denudation and erosion linked to crustal uplift. The chronostratigraphy of both sites enables the generation of a seismic sequence stratigraphy not only for the Amundsen Sea rise but also for the western Amundsen Sea along the Marie Byrd Land margin through a connecting network of seismic lines.more » « less
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- https://doi.org/10.1080/14614103.2022.2031836
