Skip to main content

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


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.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. Abdelkrim J, Pascal M, Samadi S (2005) Island colonization and founder effects: The invasion of the Guadeloupe islands by ship rats (Rattus rattus). Mol Ecol 14:2923–2931.

    CAS  Article  PubMed  Google Scholar 

  2. Allentoft ME, Sikora M, Sjögren K-G et al (2015) Population genomics of Bronze Age Eurasia. Nature 522:167–172.

    CAS  Article  PubMed  Google Scholar 

  3. Aplin KP, Stephen C, Suzuki H et al (2011) Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats. PLoS ONE.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Bernt M, Donath A, Jühling F et al (2013) MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–319.

    Article  PubMed  Google Scholar 

  5. Brace S, Thomas JA, Dalén L et al (2016) Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family. Mol Biol Evol 33:3095–3103.

    CAS  Article  PubMed  Google Scholar 

  6. Bushnell B (2015) BBMap short-read aligner, and other bioinformatics tools.

  7. Cooke SB, Dávalos LM, Mychajliw AM, Turvey ST, Upham NS (2017) Anthropogenic extinction dominates holocene declines of West Indian Mammals. Annu Rev Ecol Evol Syst 48:10–1146

    Article  Google Scholar 

  8. Darriba D, Weiß M, Stamatakis A (2016) Prediction of missing sequences and branch lengths in phylogenomic data. Bioinformatics 32:1331–1337.

    CAS  Article  PubMed  Google Scholar 

  9. Debrot AO, de Freitas JA, Brouwer A, van Marwijk KM (2000) The Curaçao Barn Owl: status and diet, 1987–1989. Caribb J Sci 37:185–193

    Google Scholar 

  10. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    CAS  Article  Google Scholar 

  11. Gansauge M-T, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8:737–748.

    CAS  Article  PubMed  Google Scholar 

  12. Gasc C, Peyretaillade E, Peyret P (2016) Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Guimaraes S, Pruvost M, Daligault J et al (2017) A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa. Mol Ecol Resour 17:405–417.

    CAS  Article  PubMed  Google Scholar 

  14. Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads - A baiting and iterative mapping approach. Nucleic Acids Res.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Harvey VL, Egerton VM, Chamberlain AT et al (2019) Interpreting the historical terrestrial vertebrate biodiversity of Cayman Brac (Greater Antilles, Caribbean) through collagen sequencing. The Holocene 29:531–542.

    Article  Google Scholar 

  16. Heisler LM, Somers CM, Poulin RG (2016) Owl pellets: A more effective alternative to conventional trapping for broad-scale studies of small mammal communities. Methods Ecol Evol 7:96–103.

    Article  Google Scholar 

  17. Hernández Muñoz A, Mancina CA (2011) La dieta de la lechuza (Tyto alba) (Aves: Strigiformes) en hábitats naturales y antropogénicos de la región central de Cuba Diet of Barn Owl (Tyto alba) (Aves: Strigiformes) in natural and anthropogenic habitat in central Cuba. Rev Mex Biodivers 82:217–226

    Google Scholar 

  18. Jónsson H, Ginolhac A, Schubert M et al (2013) MapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29:1682–1684.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Kehlmaier C, Barlow A, Hastings AK et al (2017) Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum. Proc R Soc B Biol Sci.

    Article  Google Scholar 

  20. Keith AR, Wiley JW, Latta SC, and Ottenwalder J (2003) The birds of Hispaniola, Haiti, and the Dominican Republic: an annotated checklist. BOU Checkl 21

  21. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21:936–939.

  24. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJournal 17:10–12.

    Article  Google Scholar 

  25. Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees. In Proceedings of the gateway computing environments workshop (GCE), 14 Nov. 2010, New Orleans, LA, pp 1–8

  26. Morgan M, Pagès H, Obenchain V, Hayden N (2018) Rsamtools: binary alignment (BAM), FASTA, variant call (BCF), and tabix file import.

  27. Morgan GS, MacPhee RDE, Woods R, Turvey S (2019) Late Quaternary fossil mammals from the Cayman Islands, West Indies. Bull Am Museum Nat Hist 428:

  28. Poulakakis N, Lymberakis P, Paragamian K, Mylonas M (2005) Isolation and amplification of shrew DNA from barn owl pellets. Biol J Linn Soc 85:331–340.

    Article  Google Scholar 

  29. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. Rambuat A (2018) FigTree v1.4.4.

  31. Rocha RG, Justino J, Leite YLR, Costa LP (2015) DNA from owl pellet bones uncovers hidden biodiversity. Syst Biodivers 13:403–412.

    Article  Google Scholar 

  32. Ronquist F, Teslenko M, Van Der Mark P et al (2012) MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst Biol 61:539–542.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Savidge JA, Hopken MW, Witmer GW et al (2012) Genetic evaluation of an attempted Rattus rattus eradication on Congo Cay, U.S. Virgin Islands, identifies importance of eradication units. Biol Invasions 14:2343–2354.

    Article  Google Scholar 

  34. Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313

    CAS  Article  Google Scholar 

  35. Stuiver M, Reimer PJ, Reimer RW (2018) CALIB 7.1

  36. Terry RC (2010) The dead do not lie: using skeletal remains for rapid assessment of historical small mammal community baselines. Proc R Soc Biol Sci 277:1193–1201

    Article  Google Scholar 

  37. Tollenaere C, Brouat C, Duplantier JM et al (2010) Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar. J Biogeogr 37:398–410.

    Article  Google Scholar 

  38. Woods R, Turvey ST, Brace S et al (2018) Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation. Proc Natl Acad Sci 115:12769–12774.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

Download references


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.


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.

Author information




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.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 5135 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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).

Download citation


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