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opencc-zeroJun 2022View details →

Ancient sedimentary plant DNA dataset from Batagay (B17), Yakutia

Here we provide a dataset on genetic plant diversity retrieved from permafrost sedimentary ancient DNA (sedaDNA) of the Batagay megaslump, Yakutia. Our dataset encompasses sedaDNA sequence data of 10 sediment samples. We used a PCR-based metabarcoding approach combined with Next-Generation Sequencing to assess the past, local vegetation compositional changes around the megaslump. As a plant specific metabarcode we applied the established chloroplastidal P6 loop trnL marker for plant diversity assessment. PCR products were sequenced on one Illumina sequencing HiSeq 2500 run.

opencc-zeroOct 2022View details →

Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period

Aim: Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene. Location: Europe Taxon: Common vole (Microtus arvalis) Methods: We generated a dataset comprised of a 4.2-kb-long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated. Results: We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than previous estimates. We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM), even at high latitudes. Main conclusions: The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas climate deterioration during the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.

Supplementary material 4 from: Slater G, Scheel D, Kolokotronis S, Potter C, Rotstein D, Tsangaras K, Greenwood A, Helgen K (2014) Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. ZooKeys 409: 1-33. https://doi.org/10.3897/zookeys.409.6244

Fifty percent majority-rule consensus tree based on 1000 bootstrap pseudoreplicates generated using the maximum parsimony phylogenetic optimality criterion.: Explanation note: Values at nodes indicate the proportion of bootstrap trees (>50%) for which a particular bipartition was recovered.

Supplementary material 2 from: Slater G, Scheel D, Kolokotronis S, Potter C, Rotstein D, Tsangaras K, Greenwood A, Helgen K (2014) Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. ZooKeys 409: 1-33. https://doi.org/10.3897/zookeys.409.6244

Alignment of Neomonachus tropicalis cytb with extant monk seal cytb sequences.: Explanation note: The extinct Caribbean monk seal sequence was used as a reference. Dots indicate identity to the reference. Differences are shown as the base change relative to the reference. Numbering starts from the first base of the ATG start codon.

Supplementary material 1 from: Slater G, Scheel D, Kolokotronis S, Potter C, Rotstein D, Tsangaras K, Greenwood A, Helgen K (2014) Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. ZooKeys 409: 1-33. https://doi.org/10.3897/zookeys.409.6244

Amplicons covering cytb in this study.: Explanation note: Sequence of the cytb gene and the resulting PCR amplicons with length in number of base pairs (bp). Asterisks indicate that the sequence extends over the 3' or 5' border of the target sequence.

Supplementary material 3 from: Slater G, Scheel D, Kolokotronis S, Potter C, Rotstein D, Tsangaras K, Greenwood A, Helgen K (2014) Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. ZooKeys 409: 1-33. https://doi.org/10.3897/zookeys.409.6244

Alignment of three Neomonachus tropicalis D-loop hypervariable region sequences (from USNM 100358, 102527, and 102534).: Explanation note: The Neomonachus schauinslandi sequence was used as a reference. Dots indicate identity to the reference. Differences are shown as the base change relative to the reference. Numbering starts at the first base after the primer closest to the 5' end. The X symbols indicate the break between the two amplicons that are approximately 200 bp apart. Sequences were generated from consensus sequences of 3–5 individual PCR product clones. Several products were cloned and sequenced from more than one amplicon to confirm that the differences observed were not DNA damage related or due to sequencing errors.

opencc-by-4.0May 2024View details →

Ancient mitochondrial DNA

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opencc-zeroJul 2024View details →

Data from: Far away from home? Ancient DNA shows presence of bicoloured shrew (Crocidura leucodon) in Bronze Age Denmark

An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archaeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6X coverage). Phylogenetic analyses determined this specimen as a bicoloured shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archaeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.

opencc-zeroDec 2013View details →

Data from: Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.

opencc-zeroDec 2013View details →

Data from: Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys

Background: The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced.Results: Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. Conclusions: This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.

opencc-zeroDec 2015View details →

Data from: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

opencc-zeroDec 2016View details →

Data from: HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA

Over the last decade, protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been widely developed. Their use is however limited to DNA of relatively high molecular weight. During the last year, several methods exploiting hybridization capture using probes based on RAD-sequencing loci have circumvented this limitation and opened avenues to the study of samples characterized by degraded DNA, such as historical specimens. Here, we present a major update to those methods, namely Hybridization capture from RAD-derived probes obtained from a reduced eXome template (hyRAD-X), a technique applying RAD-sequencing to messenger RNA from one or few fresh specimens to elaborate bench-top produced probes, i.e., a reduced representation of the exome, further used to capture homologous DNA from a samples set. In contrast to previous hybridization-capture methods, the reference catalog on which reads are aligned does not rely on de novo assembly of anonymous RAD-sequencing loci, but on an assembled transcriptome obtained from RNAseq data, thus increasing the accuracy of loci definition and Single-Nucleotide-Polmorphisms (SNP) call, and targeting, specifically, expressed genes. Finally, the capture step of hyRAD-X relies on RNA probes, increasing stringency of hybridization, making it well suited for low-content DNA samples. As a proof of concept, we applied hyRAD-X to subfossil needles from the coniferous tree Abies alba, collected in lake sediments (Origlio, Switzerland) and dating back from 7200-5800 years before present (BP). More specifically we investigated genetic variation before, during, and after an anthropogenic perturbation that caused an abrupt decrease in Abies alba population size, 6500-6200 years BP. HyRAD-X produced a matrix encompassing 524 exome-derived SNPs. Despite a lower observed heterozygosity was observed during the 6.500-6.200 years BP time slice, genetic composition was nearly identical before and after the perturbation, indicating that re-expansion of the population after the decline was driven by autochthonous specimens. To the best of our knowledge, this is the first time a population genomic study incorporating ancient DNA samples of tree subfossils is conducted at a moderate cost using reproducible exome-reduced complexity.

opennotspecifiedApr 2013View details →

FIGURE 5 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)

FIGURE 5. Molecular phylogeny of Orestias complexes including 'fresh' species and morphotype ("morpho") representatives, and type specimens. Maximum clade credibility tree for rhodopsin sequences. Values at branch nodes refer to highest posterior probability of occurrence for clades (> 0.95); within parenthesis are shown posterior values when removing type specimens from the analysis. Scale bar below tree indicates sequence divergence. Type specimens are highlighted with an asterisk. See Table 2 for specimen acronyms.

opennotspecifiedApr 2013View details →

FIGURE 2 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)

FIGURE 2. Gel electrophoresis displaying extracted DNA (a) and amplified PCR fragments (b) in two historical samples of O. mulleri (MNHN 1981-1428#4 and #13). In a, columns 1–2: extracted DNA for specimen #4 (aliquots a and b); columns 3–4: extracted DNA for specimen #13 (aliquot a and b); column 5: negative DNA extraction control; M: molecular weight marker (100 bp ladder). In b, PCR amplification products for control region and rhodopsin are left and right to the molecular weight marker, respectively. Columns 1–2: specimen #4 (aliquots a and b); columns 3–4: specimen #13 (aliquots a and b); column 5: negative PCR control; column 6: positive PCR control. M: molecular weight marker (100 bp ladder).

opennotspecifiedApr 2013View details →

FIGURE 3 in Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)

FIGURE 3. Example of type specimens treated by incubation in GuSCN bath. Left/right sides: specimens before/after DNA extraction procedure. Damage scale (see Material and Methods): A and B = 1, C = 2 and D = 3. Scale bar represents 2 cm.

Figure 6 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)

Figure 6. Lateral view of posterior braincase of Marmosops (Sciophanes) pinheiroi (A, AMNH 267345) and Marmosops (Marmosops) noctivagus (B, MUSM 13288) illustrating diagnostic subgeneric morphologies of the squamosal (green) and petrosal (yellow). Abbreviations: als, alisphenoid; exo, exoccipital; lspc, lateral surface of pars canalicularis (of petrosal); par, parietal; pet, petrosal; sps, sulcus for the prootic sinus (of petrosal); sq, squamosal; srza, squamosal root of zygomatic arch; ssf, subsquamosal foramen.

Figure 5 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)

Figure 5. Phylogeny of Marmosops obtained by Bayesian analysis of a concatenated-gene [cytochrome b + breast cancer activating 1 (CYTB + BRCA1)] data set. Terminals are putative species recovered by general mixed Yule coalescent model analyses of CYTB plus Marmosops juninensis (uniquely represented by a BRCA1 sequence). Filled semicircles at internal nodes indicate high support (posterior probability ≥ 0.95, bootstrap ≥ 75%). Abbreviations: BI, Bayesian inference; ML, maximum likelihood.

Figure 3 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)

Figure 3. Collection localities for sequenced specimens of Atlantic Forest species included in subgenus II of Marmosops. Progressively darker shading indicates the following elevations: pale grey ≥ 500 m, medium grey ≥ 1000 m, and dark grey ≥ 2000 m.

Figure 2 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)

Figure 2. Collection localities for sequenced specimens of subgenus I of Marmosops. Progressively darker shading indicates the following elevations: pale grey ≥ 500 m, medium grey ≥ 1000 m, dark grey ≥ 2000 m, and darkest grey ≥ 3000 m.

Figure 1 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)

Figure 1. Collection localities for sequenced specimens of subgenus II of Marmosops. Progressively darker shading indicates the following elevations: pale grey ≥ 500 m, medium grey ≥ 1000 m, dark grey ≥ 2000 m, and darkest grey ≥ 3000 m.