Biology subjects

Siekmann, A.

Publications and source records attributed to Siekmann, A..

3 recordsLinked to original sources

bioRxiv2026

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age ([~]1,700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged [~]11,500-3,700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities have been threatened by sheeppox for over 3,700 years, and provide new insights to the genomic evolution and potential host adaptation of sheeppox virus. TeaserAncient viral genomes from manuscripts and teeth illuminate the evolutionary history of sheeppox virus.

genetics↗

bioRxiv2025

Old Goats: 3,000 years of genetic connectivity of the domestic goat in Ireland

The domestic goat likely first arrived to the island of Ireland as part of the introduction of agriculture approximately 5,900 years ago, and remains a part of the islands biocultural heritage. However, due to the challenges of differentiating goat remains from that of sheep using traditional archaeozoological approaches, there are few specimens specifically identified as goat. To address this we employed genetic, proteomics, and archaeozoological techniques to assess faunal remains from the Late Bronze assemblage of Haugheys Fort (Armagh) and medieval assemblage of Carrickfergus (Antrim). We identify these specimens as goats using proteomics and genetics, and additionally determine their molecular sex. Genomic data recovered from a Haugheys Fort goat reveals a three-millenia genetic connection between herds in the Late Bronze Age, medieval period, and the indigenous Irish breed extant today, the Old Irish Goat. We additionally find varying levels of inbreeding within goats from the settlement of Carrickfergus, suggesting possible mixed use of herds within medieval Irish society. Our results demonstrate the continuing potential of combining archaeological and biomolecular techniques to clarify existing ambiguities and at the same time reveal new facets of the past.

genomics↗

bioRxiv2019

Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells

Hematopoietic stem cell (HSC) ontogeny is accompanied by dynamic changes in gene regulatory networks. We performed RNA-Seq and histone mark ChIP-Seq to define the transcriptomes and epigenomes of cells representing key developmental stages of HSC ontogeny in the mouse. The five populations analyzed were embryonic day 10.5 (E10.5) endothelium and hemogenic endothelium from the major arteries (dorsal aorta, umbilical and vitelline), an enriched population of pre-hematopoietic stem cells (pre-HSCs), fetal liver HSCs, and adult bone marrow HSCs. We observed dynamic and combinatorial epigenetic changes that mark regulatory DNA sequences including gene promoters and enhancers. Using epigenetic signatures, we identified enhancers for each developmental stage. Only 12% of enhancers are primed, and 78% are active, suggesting the vast majority of enhancers are established de novo at the developmental stages where they are required to control their target genes, without prior priming in earlier stages. We constructed developmental-stage-specific transcriptional regulatory networks during HSC ontogeny by linking enhancers and predicted bound transcription factors to their target promoters using a novel computational algorithm. Our computational analyses predicted known transcriptional regulators for the endothelial-to-hematopoietic transition, validating our overall approach, and identified putative novel transcription factors whose regulon activities correlate with the emergence of pre-HSCs. We validated roles for the broadly expressed transcription factors SP3 and MAZ in arterial hemogenic endothelium. Our data and computational analyses provide a useful resource for uncovering regulators of HSC formation.

developmental biology↗