Ayinuer Aximu-Petri

• Master of Science
• Max Planck Institute for Evolutionary Anthropology

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. Nevertheless, demands in throughput continue t...

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS metho...

SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast screening method based on direct RT-qPCR to detect SARS-CoV-2 in single or pooled gargle lavages (...

It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3′ ends of single...

Background: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation...

SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast approach to detect SARS-CoV-2 in single or pooled gargle lavages ('mouthwashes'). With this approa...

DNA preserved in ancient bones, teeth and sediments is typically highly fragmented and present only in minute amounts. Here, we provide a highly versatile silica-based DNA extraction protocol that enables the retrieval of short (≥35 bp) or even ultrashort (≥25 bp) DNA fragments from such material with minimal carryover of substances that inhibit li...

Background The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation p...

Relationships among North Africans The general view is that Eurasians mostly descend from a single group of humans that dispersed outside of sub-Saharan Africa around 50,000 to 100,000 years ago. Present-day North Africans share a majority of their ancestry with present-day Near Easterners, but not with sub-Saharan Africans. To investigate this con...

By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1-3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide da...

Tracing our ancestors in cave sediments Analysis of DNA from archaic hominids has illuminated human evolution. However, sites where thousand-year-old bones and other remains can be found are relatively rare. Slon et al. wanted to exploit any trace remains that our ancestors left behind. They looked for ancient DNA of hominids and other mammals in c...

A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia a...

We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segme...

Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use pri...

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individ...

Differentially expressed genes. (XLSX)

GO enrichment results. (XLS)

PCA of gene expression variation. Blue: domesticated/tame rat, red: wild/aggressive rat; circles: females, squares: males. (PDF)

Domestication-related genes. (XLSX)

Full details on samples and sequencing runs performed for this study. (XLS)

Gene expression values used in the analyses, stored as R objects. (ZIP)

PCA of SNV data. Blue: domesticated/tame rat, red: wild/aggressive rat; circles: females, squares: males. (PDF)

Transcript sequence differences to the reference genome in genes with common expression in domesticated animals. For each gene, the median fold change of expression in domesticated vs. wild animals is plotted as a function of the difference between wild and domesticated mean sequence difference to the reference genome. The p-values are from Wilcoxo...

PCA of expression data in all 12 rabbit samples. Note the large distance separating A115 from all other samples. Blue: domesticated, red: wild, circles: females, squares: males. (PDF)

“Extreme” and random permutations when testing for shared gene expression across domestication events. (DOCX)

Shown is the number of genes that are 1∶1 orthologues in the given comparison and that are “expressed” in both pairs (i.e. have >0 counts in at least half the samples in both species pairs that are compared). (DOCX)

Extreme and random permutations when searching for genes with shared expression in domesticated animals. A detailed step-by-step description of this Figure is provided in Note S1. A. Expression levels of a hypothetical gene in three pairs (circles, squares, triangles) of domesticated (blue) and wild (red) animals. The dotted line is the overall mea...

Q-Q plots comparing the p-value distribution of the un-permuted data to all possible extreme permutations for the analyses without guinea pigs. p-values are for the effect of domestication in the ANOVA analyses of dogs, pigs and rabbits, and were −log10 transformed. The real, un-permuted data is shown on the y-axis compared to each of the respectiv...

Q-Q plots comparing the p-value distribution of the un-permuted data to all possible extreme permutations for the analyses including guinea pigs. p-values are for the effect of domestication in the ANOVA analyses of dogs, pigs, rabbits and guinea pigs, and were −log10 transformed. The real, un-permuted data is shown on the respective y-axis compare...

Sequence polymorphism in genes with common expression in domesticated animals. (DOCX)

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild spe...

Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineag...

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day...