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Consensify
(2020)
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
Consensify
(2020)
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.
Masafuera Rayadito (Aphrastura masafuerae; Furnariidae) is a Critically Endangered species endemic to Alejandro Selkirk Island (Juan Fernandez Archipelago, Chile). Categorized as probably extinct in 1980, later estimates, ranging from 140 (in 2002) to 500 individuals (in 2006-2007), showed a fluctuating population size of the species. The grazing of goats and cattle has increased habitat loss for the species. Other threats are lack of nesting sites, introduced species such as feral cats and rats (Rattus rattus and R. norvegicus), and increased populations of natural predators like the Masafuera Hawk. In order to increase the availability of nesting sites, 81 nest boxes were installed in different habitats in 2006, with evidence of use during subsequent breeding seasons. Despite conservation concerns, however, no genetic studies are yet available for this furnariid. This study reports for the first time the levels of genetic divergence of the species, based on nucleotide sequences of the mitochondrial DNA (cytochrome oxidase subunit 1 gene; COI). Aphrastura masafuerae is closely related to a widespread species of furnariid distributed mainly in Chile on the mainland, the Thorn-tailed Rayadito (A. spinicauda). The Masafuera Rayadito diverged from its mainland sister species probably during the Pleistocene 0.57 +/- 0.19 Myr ago. Consistent with mitochondrial and nuclear molecular clocks, the estimated time of the split between A. masafuerae and A. spinicauda is in perfect agreement with the geological origin of the Juan Fernandez Archipelago, which is of volcanic origin. In order to assess genetic variability within the population of this fragile bird, further studies using a multi-locus genetic approach at the population level are necessary.
Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
The origin of ambling horses
(2016)
Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called ‘gaited’ horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th–11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date.
Arch filament systems occur in active sunspot groups, where a fibril structure connects areas of opposite magnetic polarity, in contrast to active region filaments that follow the polarity inversion line. We used the GREGOR Infrared Spectrograph (GRIS) to obtain the full Stokes vector in the spectral lines SiI lambda 1082.7 nm, He I lambda 1083.0 nm, and Ca I lambda 1083.9 nm. We focus on the near-infrared calcium line to investigate the photospheric magnetic field and velocities, and use the line core intensities and velocities of the helium line to study the chromospheric plasma. The individual fibrils of the arch filament system connect the sunspot with patches of magnetic polarity opposite to that of the spot. These patches do not necessarily coincide with pores, where the magnetic field is strongest. Instead, areas are preferred not far from the polarity inversion line. These areas exhibit photospheric downflows of moderate velocity, but significantly higher downflows of up to 30 km s(-1) in the chromospheric helium line. Our findings can be explained with new emerging flux where the matter flows downward along the field lines of rising flux tubes, in agreement with earlier results. (C) 2016 WILEY-VCH Verlag GmbH& Co. KGaA, Weinheim
Aims. We study small-scale brightenings in Ca II 8542 angstrom line-core images to determine their nature and effect on localized heating and mass transfer in active regions. Methods. High-resolution two-dimensional spectroscopic observations of a solar active region in the near-infrared Ca II 8542 angstrom line were acquired with the GREGOR Fabry-Perot Interferometer attached to the 1.5-m GREGOR telescope. Inversions of the spectra were carried out using the NICOLE code to infer temperatures and line-of-sight (LOS) velocities. Response functions of the Ca II line were computed for temperature and LOS velocity variations. Filtergrams of the Atmospheric Imaging Assembly (AIA) and magnetograms of the Helioseismic and Magnetic Imager (HMI) were coaligned to match the ground-based observations and to follow the Ca II brightenings along all available layers of the atmosphere. Results. We identified three brightenings of sizes up to 2 ' x 2 ' that appeared in the Ca II 8542 angstrom line-core images. Their lifetimes were at least 1.5 min. We found evidence that the brightenings belonged to the footpoints of a microflare (MF). The properties of the observed brightenings disqualified the scenarios of Ellerman bombs or Interface Region Imaging Spectrograph (IRIS) bombs. However, this MF shared some common properties with flaring active-region fibrils or flaring arch filaments (FAFs): (1) FAFs and MFs are both apparent in chromospheric and coronal layers according to the AIA channels; and (2) both show flaring arches with lifetimes of about 3.0-3.5 min and lengths of similar to 20 ' next to the brightenings. The inversions revealed heating by 600 K at the footpoint location in the ambient chromosphere during the impulsive phase. Connecting the footpoints, a dark filamentary structure appeared in the Ca II line-core images. Before the start of the MF, the spectra of this structure already indicated average blueshifts, meaning upward motions of the plasma along the LOS. During the impulsive phase, these velocities increased up to -2.2 km s(-1). The structure did not disappear during the observations. Downflows dominated at the footpoints. However, in the upper photosphere, slight upflows occurred during the impulsive phase. Hence, bidirectional flows are present in the footpoints of the MF.