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152 results for “Ancient DNA”
Data from: Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary
Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.
Data from: Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus)
The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.
Data from: Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems
Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 A.D. were selected to perform Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st Century samples was clearly different than those of mid-19th Century. This compositional change was correlated to shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in paleolimnological studies to include key microbial community characteristics of great scientific and social interest.
Data from: Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in "oceans" of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km2 of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years, and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528±75 cal yr BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes likely being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.
Data from: Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA
We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentaryDNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM) approach to faunal identification, where DNA from non-diagnostic bone fragments is extracted and sequenced in parallel. However, a large proportion of fishing communities (both past and present) live in tropical regions that have sub-optimal conditions for long-term aDNA preservation. To date, the BBM method has never been applied to fish bones before, or to fossils excavated from an exposed context within a tropical climate. Here, we demonstrate that morphologically indistinct bulk fish bone from the tropics can be identified by sequencing aDNA extracted from 100 to 300 ya archaeological midden material in southwest Madagascar. Despite the biases of the approach, we rapidly obtained family, genus, and species-level assemblage information, and used this to describe a subset of the ichthyofauna exploited by an 18th century fishing community. We identified 23 families of fish, including benthic, pelagic, and coral-dwelling fishes, suggesting a reliance on a variety of marine and brackish habitats. When possible, BBM should be used alongside osteological approaches to address the limitations of both; however, this study highlights how genetic methods can nevertheless be a valuable tool for helping resolve faunal assemblages when morphological identification is hindered by taphonomic processes, lack of adequate comparative collections, and time constraints, and can provide a temporal perspective on fish biodiversity in the context of accelerated exploitation of the marine environment.
Data from: Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds
The Canary Islands were settled in the first millennium AD by colonizers likely originating from North Africa. The settlers developed a farming economy with barley as the main crop. Archaeological evidence suggests the islands then remained isolated until European sea-travellers discovered and colonized them during the 14th and 15th centuries. Here we report a population study of ancient DNA from twenty-one archaeobotanical barley grains from Gran Canaria dating from 1050 to 1440 cal AD. The material showed exceptional DNA preservation and genotyping was carried out for 99 single nucleotide markers. In addition 101 extant landrace accessions from the Canary Islands and the western Mediterranean were genotyped. The archaeological material showed high genetic similarity to extant landraces from the Canary Islands. In contrast, accessions from the Canary Islands were highly differentiated from both Iberian and North African mainland barley. Within the Canary Islands, landraces from the easternmost islands were genetically differentiated from landraces from the western islands, corroborating the presence of pre-Hispanic barley cultivation on Lanzarote. The results demonstrate the potential of population genetic analyses of ancient DNA. They support the hypothesis of an original colonization, possibly from present day Morocco, and subsequent isolation of the islands and reveal a farmer fidelity to the local barley that has lasted for centuries.
Data from: A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability
Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared to the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46–12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping, and in combination reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation of temporal changes in species composition and the determination of indicator species to describe environmental changes. Combining data from all three proxies, reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place in the northern hemisphere during this time, with changes in average annual temperatures of > 22ºC. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene, and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and add to the increasing evidence suggesting large areas of the northern hemisphere remained ecologically stable during the Late Pleistocene.
Data from: Ancient DNA from the extinct South American giant glyptodont Doedicurus sp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos
Glyptodonts were giant (some of them up to ~2400 kg), heavily armoured relatives of living armadillos, which became extinct during the Late Pleistocene/early Holocene alongside much of the South American megafauna. Although glyptodonts were an important component of Cenozoic South American faunas, their early evolution and phylogenetic affinities within the order Cingulata (armoured New World placental mammals) remain controversial. In this study, we used hybridization enrichment and high-throughput sequencing to obtain a partial mitochondrial genome from Doedicurus sp., the largest (1.5 m tall, and 4 m long) and one of the last surviving glyptodonts. Our molecular phylogenetic analyses revealed that glyptodonts fall within the diversity of living armadillos. Reanalysis of morphological data using a molecular 'backbone constraint' revealed several morphological characters that supported a close relationship between glyptodonts and the tiny extant fairy armadillos (Chlamyphorinae). This is surprising as these taxa are among the most derived cingulates: glyptodonts were generally large-bodied and heavily armoured, while the fairy armadillos are tiny (~9–17 cm) and adapted for burrowing. Calibration of our phylogeny with the first appearance of glyptodonts in the Eocene resulted in a more precise timeline for xenarthran evolution. The osteological novelties of glyptodonts and their specialization for grazing appear to have evolved rapidly during the Late Eocene to Early Miocene, coincident with global temperature decreases and a shift from wet closed forest towards drier open woodland and grassland across much of South America. This environmental change may have driven the evolution of glyptodonts, culminating in the bizarre giant forms of the Pleistocene.
FIGURE 4. Leiolopisma ceciliae n in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 4. Leiolopisma ceciliae n. sp., material from Grotte au Sable, St-Gilles, La Réunion. Holotype. Dentary (lateral and medial views). Scale in mm.
FIGURE 5. Leiolopisma ceciliae n in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 5. Leiolopisma ceciliae n. sp., material from Grotte au Sable, St-Gilles, La Réunion. Selected paratypes, from individuals of various sizes. Top row: left mandible (lateral view), right maxilla (lateral view), fused left postfrontal and postorbital bone (dorsal view), left quadrate (posterior view). Middle row: right dentary (medial view), posterior left mandible (lateral view). Bottom row: Left humerus, left pelvis (lateral view), sacrum (dorsal view), presacral vertebrae (lateral and ventral views), right femur, tibia. Scale in mm.
FIGURE 6. Leiolopisma ceciliae n in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 6. Leiolopisma ceciliae n. sp., material from Grotte au Sable, St-Gilles, La Réunion. Paratype. Frontal of juvenile animal (ventral and dorsal views, anterior upwards). Scale in mm.
FIGURE 7 in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 7. Variation in number of teeth with size of maxillae (above) and dentary bones (below) in different species of the Mascarene skink genus Leiolopisma. Stars: L. ceciliae n. sp. from La Réunion. Assemblage to left: L. telfairii from Mauritius (triangles: living animals from Round Island, dots: subfossil material from mainland of Mauritius). Assemblage to right: subfossil L. mauritiana from mainland of Mauritius. Some symbols indicate more than one specimen.
FIGURE 2. Nactus soniae n in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 2. Nactus soniae n. sp., material from Grotte au Sable, St-Gilles, La Réunion. c. Paratypes. Left maxilla and right dentary (medial views). Scales in mm.
FIGURE 3. Nactus soniae n in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 3. Nactus soniae n. sp. Scanning electron microscope photograph of holotype frontal bone (dorsal view).
FIGURE 2a, 2b. Nactus soniae n in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 2a, 2b. Nactus soniae n. sp., material from Grotte au Sable, St-Gilles, La Réunion. a. Holotype. Frontal bone (dorsal and ventral views). Scale in mm. b. Paratypes. Left maxilla and right dentary (lateral views). Scales in mm.
FIGURE 1 in A new Nactus gecko (Gekkonidae) and a new Leiolopisma skink (Scincidae) from La Réunion, Indian Ocean, based on recent fossil remains and ancient DNA sequence
FIGURE 1. Phelsuma sp., material from Grotte au Sable, St-Gilles, La Réunion. Above: frontals (dorsal and ventral views). Below: left maxilla (medial view). Scale in mm.
Supplementary Data - Haplotype-based inference of recent effective population size in modern and ancient DNA samples
<p>This repository contains the simulated data analyzed in our manuscript titled "Haplotype-based Inference of Recent Effective Population Size in Modern and Ancient DNA Samples".The data is split into 7 datasets. </p><p><strong>- demographies.tar.gz</strong>: the simulated demographic models.<br><strong>- modern_data.tar.gz:</strong> simulated SNP-araray data. The genotypes were simulated under 4 demographic histories (see demographies.tar.gz) for 256 samples and under 10 different random seeds (Replicate 1-10). Additionally, Replicates 11 and 12 include simulations at larger sample sizes. Note that the results at lower sample sizes can be obtained by keeping the first N samples of the simulated files.<br><strong>- true_ibd.tar.gz :</strong> This dataset contains the IBD segments from the simulated modern_data (ground truth from ARGON simulator).<br><strong>- ancient_data.tar.gz</strong> dataset contains simulated aDNA data. The dataset contains data simulated at different coverages (MISSING_$M, where $M = exp(-coverage)), sample sizes, demographic models, and random seeds. Split into three parts. See below for instructions on how to reconstruct the dataset. <br><strong>- structure.tar.gz</strong> and<strong> admixture.tar.gz :</strong> contain the data simulated under more complex demographic histories involving 2 isolated populations (structure) or a single population undergoing a recent admixture event (admixtuer.tar.gz). The manuscript provides more details about the demographic histories.<br>- <strong>imputed.tar.gz</strong> dataset contains simulated imputed aDNA data. Each region was simulated independently. Each folder corresponds to a chromosome arm and contains:<br> - data.anc_array.npy: list of the SNPs included in the analysis (simulating a 1240k array)<br> - data.glimpse.vcf.gz: phased ancient population data as phased by GLIMPSE v1<br> - data.glimpse.vcf.gz.csi: index for the above VCF file<br> - data.imputed.vcf.gz: imputed ancient population data (unphased, including dosages and genotype posteriors)<br> - data.imputed.vcf.gz.csi: index file for the above VCF<br> - data.map.gz: genetic map for GLIMPSE (tab-separated format: pos chr cM)<br> - data.ref.tsv.gz: file used for calculating genotype likelihoods with BCFtools mpileup command to use as input for GLIMPSE (format: chromosome position ref_allele,alt_allele)<br> - data.ref.tsv.gz.tbi: index for the above file<br> - data.ref.vcf.gz: simulated sequencing data from the reference panel<br> - data.ref.vcf.gz.csi: index file for the above VCF<br> - data.target_ground_truth.vcf.gz: simulated sequencing data for the ancient population (ground truth)<br> - datalist.txt: list of genotype likelihood files for each target individual (to be used for merging into a single file)<br> - data.temp.map.gz: genetic map for data creation with msprime simulator (format: chr position rate(cM/Mb) cM)<br> - data.tree -> msprime simulator output containing all samples, both reference panel samples and ancient population samples<br> - data.vcf.gz: VCF containing ground truth sequencing data, phased genotypes for reference panel samples and for ancient population samples<br> - dataref.fa.fai: index for reference fasta file used during reads creation</p><p> </p><p>Note that some of the datasets have been split into multiple parts, for example admixed.tar.gz has been split into three different parts admixed.tar.gz-part-aa, admixed.tar.gz-part-ab, and admixed.tar.gz-part-ac<br>You can get the data by typing:</p><p>cat admixed.tar.gz.part-* > admixed.tar.gz</p><p><br> </p>
Sedimentary ancient DNA (sedaDNA) from Tramacastilla Lake (Central Pyrenees, Spain)
<p>Here is the data used in Julián-Posada et al., 2024 for sedaDNA analysis in a Pyrenean lacustrine sequence (Tramacastilla lake, 1682 m a.s.l.)</p>
Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA
<p>The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains (Mathieson et al., 2015; Narasimhan et al., 2019) or sediments (Vernot et al., 2021; Wang et al., 2021; Zavala et al., 2021) in single studies. Yet demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here we explore the possibility of improving the economics of sample preparation via multiplex capture, i.e. the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible for small genomic targets, such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the re-amplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination. </p>
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