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Raptor roosts as invasion archives: insights from the first black rat mitochondrial genome sequenced from the Caribbean

Abstract

Raptor roosts, as accumulations of expelled pellets and nest material, serve as archives of past and present small mammal communities and could therefore be used to track invasive species population dynamics over time. We tested the utility of this resource and added new information towards reconstructing the phylogeographic history of a globally invasive species in the Caribbean, the black rat (Rattus rattus) using skeletal remains from a raptor roost deposit located within a limestone cave in the Dominican Republic (Tres Bocas). As a tropical environment, Caribbean bones are typically poorly preserved. Thus, we applied next generation sequencing techniques commonly used in ancient DNA (aDNA) studies to reconstruct a nearly complete R. rattus mitochondrial genome from such a deposit. Phylogenetic analyses indicated a putative source R. rattus haplotype clade A-I for the Tres Bocas sample, which originates from southern India. Our results serve as a proof-of-concept that aDNA techniques could be used to unlock past histories of small mammal populations from raptor roost deposits in tropical island settings, where invasive mammals are among the greatest conservation concerns.

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Acknowledgements

We thank members of Grupo Jaragua, Gerson Feliz, Caridad Nova, Siobhan Cooke, and Kevin Chovanec for field assistance in the Dominican Republic. Tom Guilderson at Lawrence Livermore National Lab guided radiocarbon date processing. Staff at the Museo Nacional de Historia Natural "Prof. Eugenio de Jesús Marcano” provided invaluable logistical support and guidance. We thank Jesper Stenderup for technical assistance.

Funding

Laboratory funding was provided by NSF-DEB 1600728 awarded to AMM and the University of Puerto Rico Mayagüez Seed Grant to AVD. MEA was supported by the Villum Foundation (Young Investigator Grant 10120) and the Independent Research Fund Denmark (Sapere Aude Grant 7027-00147B). Bioinformatics infrastructure support funding for AVD was via NSF-XSEDE Grant TG-BIO150070. Publication costs were funded in by USDA-NIFA-HSI-006731 Grant Number 1016816 to AVD.

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Contributions

Conceived and designed the experiments: AVD, MEA. Collected the Samples: JNA. Conducted the Laboratory Experiments and Contributed Materials: MEA, AVD, AMM. Analyzed the Data: MME, AMM, AVD, MEA. Wrote the paper: MME, MEA, AMM, AVD.

Corresponding author

Correspondence to Alex R. Van Dam.

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Massini Espino, M., Mychajliw, A.M., Almonte, J.N. et al. Raptor roosts as invasion archives: insights from the first black rat mitochondrial genome sequenced from the Caribbean. Biol Invasions (2021). https://doi.org/10.1007/s10530-021-02636-y

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Keywords

  • Raptor roosts
  • Rattus rattus
  • Island
  • Cave
  • Caribbean
  • Ancient DNA