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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Systematic Entomology Laboratory » Research » Publications at this Location » Publication #382956

Research Project: Systematics of Beetles (Coleoptera) in Support of U.S. Agriculture, Arboriculture, and Biological Control of Pests

Location: Systematic Entomology Laboratory

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

item SMITH, AARON DENNIS - Purdue University
item KAMINSKI, MARCIN JAN - Northern Arizona University
item Kanda, Kojun
item SWEET, ANDREW - Arkansas State University
item BETANCOURT, JULIO - Us Geological Survey (USGS)
item HOLMGREN, CAMILLE - Buffalo State College
item HEMPEL, ELISABETH - University Of Potsdam
item ALBERTI, FEDERICA - University Of Potsdam
item HOFREITER, MICHAEL - University Of Potsdam

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2021
Publication Date: 6/16/2021
Citation: Smith, A., Kaminski, M., Kanda, K.N., Sweet, A., Betancourt, J., Holmgren, C.A., Hempel, E., Alberti, F., Hofreiter, M. 2021. Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing. Scientific Reports. 11:12635.

Interpretive Summary: Global shifts in climate affect the composition of insect communities. In agricultural systems, these shifts in insect communities can alter the composition of beneficial insects such as native pollinators or facilitate the introduction of potential pests. Studying how insect communities responded to past climate change events can help predict future shifts in these communities. However, because insects tend to be small and fragile, they do not preserve well over long stretches of time and it is difficult to characterize past insect communities based on fragmentary remains. In this study we present a method for identifying insect fragments ranging in age from 1,615 to 34,355 years old using DNA sequences. We demonstrate that even subfossils of small insect legs that were recovered from arid environments still contain DNA of the organism, and that this DNA can help identify to which species the insect legs belonged. This study will be useful for ecologists and evolutionary biologists studying insect communities in agricultural areas. The methods described in the paper will also be useful to anybody who needs to reliably identify fragmentary insect remains such as agricultural and port inspectors.

Technical 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.