Centuries-Old DNA from an Extinct Population of Aesculapian Snake (Zamenis longissimus) Offers New Phylogeographic Insight

Diversity

Morten E. Allentoft¹  Hans Viborg Kristensen²  Arne Redsted Rasmussen³ 

[1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen K, Denmark;Natural History Museum of Aarhus, Wilhelm Meyers Allé 10, 8000 Aarhus C, Denmark;The Royal Danish Academy of Fine Arts, Schools of Architecture, Design and Conservation, Esplanaden 34, 1263 Copenhagen K, Denmark;

关键词: Aesculapian snake;    Zamenis longissimus;    ancient DNA;    relics;    DNA preservation;    museum specimens;    phylogeography;   

DOI  :  10.3390/d10010014

来源: DOAJ

【 摘 要 】

The Aesculapian snake (Zamenis longissimus) is distributed in Central and Southern Europe, the Balkans, Anatolia, and Iran, but had a wider mid-Holocene distribution into Northern Europe. To investigate the genetic affinity of a Danish population that went extinct in historical times, we analysed three ethanol-preserved individuals dating back to 1810 using a silica-in-solution ancient DNA extraction method, combined with next-generation sequencing. Bioinformatic mapping of the reads against the published genome of a related colubrid snake revealed that two of the three specimens contained endogenous snake DNA (up to 8.6% of the reads), and this was evident for tooth, bone, and soft tissue samples. The DNA was highly degraded, observed by very short average sequence lengths (<50 bp) and 11–15% C to T deamination damage at the first 5′ position. This is an effect of specimen age, combined with suboptimal, and possibly damaging, molecular preservation conditions. Phylogeographic analyses of a 1638 bp mtDNA sequence securely placed the two Danish Aesculapian snakes in the Eastern (Balkan glacial refugium) clade within this species, and revealed one previously-undescribed haplotype. These results provide new information on the past distribution and postglacial re-colonization patterns of this species.

【 授权许可】

Unknown