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Ancient DNA is preserved in fish fossils from tropical lake sediments
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  • Moritz Muschick,
  • Eliane Jemmi,
  • Nicholas Lengacher,
  • Stephanie Hänsch,
  • Nathan Wales,
  • Mary Kishe,
  • Salome Mwaiko,
  • Jorunn Dieleman,
  • Mark Lever,
  • Walter Salzburger,
  • Dirk Verschuren,
  • Ole Seehausen
Moritz Muschick
University of Bern

Corresponding Author:[email protected]

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Eliane Jemmi
University of Bern
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Nicholas Lengacher
University of Bern
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Stephanie Hänsch
University of Oslo
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Nathan Wales
University of York
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Mary Kishe
Tanzania Fisheries Research Institute
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Salome Mwaiko
Eawag Swiss Federal Institute of Aquatic Science and Technology
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Jorunn Dieleman
Ghent University
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Mark Lever
ETH Zurich
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Walter Salzburger
University of Basel
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Dirk Verschuren
Ghent University
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Ole Seehausen
Eawag Das Wasserforschungsinstitut des ETH-Bereichs
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Tropical freshwater lakes are well-known for their high biodiversity, and the East African Great Lakes in particular are renowned for their endemic cichlid fish adaptive radiations. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, evolutionary trajectories within lineages, impacts of environmental drivers, or the scope and nature of now-extinct diversity remain largely unknown. Time-structured paleodata from geologically young fossil records, such as fossil counts and particularly ancient DNA data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous ancient DNA (aDNA). Despite generally low endogenous content and high sample drop-out, high-throughput sequencing and in some cases sequence capture allowed for taxonomic assignment to family or tribe level and phylogenetic placement of individuals. Even skeletal remains weighing less than 1 mg and up to 2700 years of age could be phylogenetically placed. We find that the relationship of degradation of aDNA with the thermal age of samples is similar to that described for terrestrial samples from cold environments adjusted for elevated temperatures. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in water oxygenation at deposition. Our study demonstrates that sediments of tropical lakes preserve genetic information on rapidly diversifying taxa over time scales of millennia.
16 Apr 2023Submitted to Molecular Ecology
19 Apr 2023Submission Checks Completed
19 Apr 2023Assigned to Editor
19 Apr 2023Review(s) Completed, Editorial Evaluation Pending
27 Apr 2023Reviewer(s) Assigned
20 Jun 2023Editorial Decision: Revise Minor
30 Aug 20231st Revision Received
31 Aug 2023Submission Checks Completed
31 Aug 2023Assigned to Editor
31 Aug 2023Review(s) Completed, Editorial Evaluation Pending
25 Sep 2023Editorial Decision: Accept