Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark

Abstract

Objectives: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for largescale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark.Materials and Methods: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise Φ ST analysis.Results: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing.Discussion: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large

Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA

“…Baits were captured using 20 µL/rxn of the bead binding buffer, incubated at 55 °C for 2.5 min (60 °C for the second round), finger vortexed and spun down, then incubated for another 2.5 min. Beads were pelleted and the supernatant (the non-captured library fraction) was removed and stored at −20 °C as per Klunk et al 183 . The beads were resuspended in 180 µL of 60 °C Wash Buffer X per tube and washed four times following the Mybaits v4.1 protocol.…”

Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set

“…Capture enrichment involves designing a set of RNA probes or baits that closely match DNA sequences (including whole genomes) from organisms of interest, which are then allowed to hybridize to the predetermined target molecules that may be present in the DNA library. After hybridizing (either with in-solution biotinylated baits or on a solid-state microarray with pre-attached baits, see Marciniak et al, 2015, p. 29), the target molecules are sequestered while the non-target fraction is washed away for discard or storage for alternative use (Klunk et al, 2019). The technique allows for whole genome capture of multiple target organisms simultaneously, resulting in a huge increase in the proportion and diversity of informative sequenced DNA without the need for exponential PCR amplifications and the compounding biases therein—as well as substantially reduced costs compared to deep shotgun sequencing.…”

Toward a bioarchaeology of urbanization: Demography, health, and behavior in cities in the past

“…Recent work also shows the promise of using genomic data to estimate population‐level rates of migration. Klunk et al (2019) use large‐scale genomic analysis to explore demographic shifts in 14th century CE Europe, following the Great European Famine and the Black Death, and reveal evidence of a high frequency of female migration during this period. The increasing application of ancient DNA and isotopic methodologies in bioarchaeology in general means that it is at least theoretically possible that the issue of migration can be substantively addressed to a greater extent in the future.…”