Biology subjects

Runfeldt, G.

Publications and source records attributed to Runfeldt, G..

4 recordsLinked to original sources

bioRxiv2026

Mitotree: The Universal Human Mitochondrial Reference Phylogeny at 10x the Resolution

Mitochondrial DNA (mtDNA) is the oldest and most prevalent source of human molecular phylogenetic reconstruction. Everyone alive today traces their matrilines to one female African ancestor who lived some 145 thousand years ago. For decades, PhyloTree provided researchers with a moderately sized reference tree (v17: n=24,275 sequences, n=5,438 branches). However, hundreds of thousands of sequences are available today, and since PhyloTrees retirement in 2016, there is a need for an actively maintained phylogenetic reference system. In addition, no currently published method can wield such a large de novo reconstruction while dealing with the rampant homoplasy seen in mtDNA and adhering to the accuracy standards expected in this well-studied field. In this paper we introduce Mitotree, the largest human phylogeny ever described (n{approx}330,000 complete sequences, n{approx}54,000 branches), and a new recursive phylogenetic pipeline for estimating it. We incorporate ancient DNA, relaxed clock age estimates (TMRCAs), and public databases (e.g., GenBank, 1000 Genomes, HGDP, and SGDP). We report approximately 180 previously unknown branches older than 30,000 years. The median TMRCA of terminal haplogroups is 2,000 years more recent than PhyloTree. Our pipeline offers a novel divide-and-conquer approach that tackles huge heuristic searches within tractable runtimes, provides high accuracy, and reasonable confidence estimates. Our validation found a false negative rate of 3.5%, and a false positive rate of 1.0%. Among the most striking findings are an [~]83 kya split of African L2e (the oldest in our dataset), the resolution of Otzis K1f into a clade with living descendants, new ethnic founder haplogroups (e.g., Jewish diaspora), and placement of historical figures such as Abraham Lincoln. To our knowledge, Mitotree is the largest de novo haplotype phylogeny built for humanity, and is a continually improved resource for academic, genealogical, and medical research.

genetics↗

bioRxiv2026

Reconstructing their genomes confirms the historically attested genealogy of the two medieval emperors Otto I (the Great) and Heinrich II (Saint Henry)

The Medieval Ottonian dynasty had a lasting impact on European history. We obtained ancient genomic DNA from the purported remains of Otto I (912-973) and Heinrich (Henry) II (973-1024), the first and last emperors of this dynasty, preserved in the cathedrals of Magdeburg and Bamberg, respectively. Historical records attest that they were related as a great-uncle and a grandnephew via the paternal line. Whole-genome sequencing confirms such a relationship between the two individuals, as we identify a third-degree genetic relationship based on shared DNA segments and infer matching Y haplogroups. This genetic relatedness effectively identifies the remains of the two emperors. The authentication yields a valuable resource for refining and calibrating bio-archaeological methods. Because historical records provide the precise lifespans and dates of death of these individuals, their remains can serve as a "ground-truth" for methods such as radiocarbon dating and age-at-death estimates. They can provide calibration data to improve our understanding of the radiocarbon reservoir effects of Medieval elites. As the Ottonian lineage was closely linked to the mating networks of elites across Europe, the genomes of the two emperors are valuable resources for identifying other potential elite burials.

genetics↗

bioRxiv2025

Revisiting the lineages of the Cohanim using data from next-generation sequencing

BackgroundEarly studies using a handful of Y-chromosome markers showed that many self-declared Jewish priests (Cohanim) share related haplotypes, but the limited resolution left open how many priestly lineages exist, when they arose, and how they map onto Jewish population history. ObjectivesWe used whole-Y sequencing and modern phylogenetic tools to (i) catalogue Y-chromosome clades that are robustly enriched among Cohanim, (ii) date their most-recent common ancestors (TMRCAs) with pedigree-calibrated clocks, (iii) reconstruct their geographic dispersal across the Jewish Diaspora, and (iv) offer a stable, SNP-block nomenclature for future work. MethodsWe generated 104 new Big Y-700 sequences from rigorously documented Cohanim spanning 20 diaspora origins, and incorporated 215 legacy samples re-typed for diagnostic SNPs. Phylogenies and branch TMRCAs were built on the FTDNA and YFull backbones. A branch qualified as "Cohen" (CB) if [≥]5 men and [≥]50 % of branch members self-identified as Cohanim. ResultsNine Cohen branches met these criteria, and for the current study were designated CB-01 to CB-09 with numbering based on antiquity of SNP-block coalescence. CB-01 is the largest ([~]45 % of all Cohanim sampled), the most ancient (TMRCA {approx} 850 BCE), and the only lineage present in every major Jewish community. Its internal topology shows explosive branching between 700 and 300 BCE, stasis through the Roman-Byzantine era, and renewed expansion after 800 CE, mirroring known demographic pulses. CB-02 (TMRCA {approx} 700 BCE) and CB-03 ({approx} 550 BCE) likewise trace to Iron- or late Classical-period Judea but are geographically narrower. CB-04 - CB-07 are Near-Eastern clades whose priestly status may have crystallized 0-1000 CE, while CB-05, CB-08 and CB-09 appear to derive from Mediterranean host populations. Twenty percent of Cohanim fall outside any current CB, indicating that additional, rarer lineages remain to be characterized. ConclusionsHigh-resolution sequencing reveals a small set of divergent paternal lines comprising the Jewish priesthood, dominated by a pre-exilic Levantine lineage whose branch structure traces three millennia of geographically dispersed Jewish demographic history. The CB nomenclature, SNP catalogues and open dataset provided here supply a reproducible framework for genetic and historical studies which illustrate the broader power of dense uniparental phylogenies in population-genetic inference.

genomics↗

bioRxiv2023

Local population structure in Cambridgeshire during the Roman occupation

The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today the United Kingdom. While there is written evidence of high mobility into and out of Britain for administrators, traders and the military, the impact of imperialism on local population structure is invisible in the textual record. The extent of genetic change that occurred in Britain before the Early Medieval Period and how closely linked by genetic kinship the local populations were, remains underexplored. Here, using genome-wide data from 52 ancient individuals from Cambridgeshire, we show low levels of genetic ancestry differentiation between Romano-British sites and lower levels of runs of homozygosity over 4 centimorgans (cM than in the Bronze Age and Neolithic. We find fourteen cases of genetic relatedness within and one between sites without evidence of patrilineal dominance and one case of temporary mobility within a family unit during the Late Romano-British period. We also show that the modern patterns of genetic ancestry composition in Modern Britain emerged after the Roman period.

genetics↗