Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing

Marcin J. Kamiński,Kojun Kanda,Andrew D. Sweet,Aaron D. Smith,Julio L. Betancourt,Federica Alberti,Michael Hofreiter,Elisabeth Hempel,Camille A. Holmgren

doi:10.1038/s41598-021-91896-8

Abstract

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.

Highlights

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species
The estimated probabilities of assigning sequences to a given taxonomic level were low. These studies illustrate a main trend in insect aDNA studies, which have been mostly focused on demonstrating the feasibility of extracting endogenous DNA rather than investigating particular biological problems—unlike published aDNA studies on vertebrates[4]
To estimate the overall endogenous DNA content of the studied ancient samples (Table 1), recovered sequence data were mapped to the only available Tenebrionidae nuclear genome assembly—that from Tribolium castaneum44—a distantly related species from the subfamily Tenebrioninae, that likely diverged from Pimeliinae ~ 145 million years ago[51]

Summary

Introduction

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals They are largely neglected in ancient DNA studies. The advantages of insect-based studies are highlighted, especially in the context of understanding past climate change In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time. The estimated probabilities of assigning sequences to a given taxonomic level were low These studies illustrate a main trend in insect aDNA studies, which have been mostly focused on demonstrating the feasibility of extracting endogenous DNA rather than investigating particular biological problems—unlike published aDNA studies on vertebrates[4]. The amount of sequenced DNA in these studies was insufficient for species-level identification

Methods

Results

Conclusion