Narayan O, Clements JE. Biology and pathogenesis of lentiviruses. J Gen Virol. 1989;70(Pt 7):1617–39.

Article  CAS  Google Scholar 

van der Kuyl AC, Berkhout B. The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology. 2012;9:92.

Article  Google Scholar 

van Hemert F, van der Kuyl AC, Berkhout B. On the nucleotide composition and structure of retroviral RNA genomes. Virus Res. 2014;193:16–23.

Article  Google Scholar 

Yamashita M, Emerman M. Retroviral infection of non-dividing cells: old and new perspectives. Virology. 2006;344(1):88–93.

Article  CAS  Google Scholar 

Brown PO. Integration. In: Coffin JM, Hughes SM, Varmus HE, editors. Retroviruses. Cold Spring Harbor Laboratory Press: Cold Spring Harbor; 1997.

Google Scholar 

Gifford R, Tristem M. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes. 2003;26(3):291–315.

Article  CAS  Google Scholar 

Hayward A, Cornwallis CK, Jern P. Pan-vertebrate comparative genomics unmasks retrovirus macroevolution. Proc Natl Acad Sci U S A. 2015;112(2):464–9.

Article  CAS  Google Scholar 

Johnson WE. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat Rev Microbiol. 2019;17(6):355–70.

Article  CAS  Google Scholar 

Stoye JP. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol. 2012;10(6):395–406.

Article  CAS  Google Scholar 

Belshaw R, et al. Rate of recombinational deletion among human endogenous retroviruses. J Virol. 2007;81(17):9437–42.

Article  CAS  Google Scholar 

Gifford RJ. Viral evolution in deep time: lentiviruses and mammals. Trends Genet. 2012;28(2):89–100.

Article  CAS  Google Scholar 

Keckesova Z, et al. Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology. 2009;384(1):7–11.

Article  CAS  Google Scholar 

Halo JV, et al. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology. 2019;16(1):6.

Article  Google Scholar 

Diehl WE, et al. Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals. Elife. 2016;5: e12704.

Article  Google Scholar 

Compton AA, Malik HS, Emerman M. Host gene evolution traces the evolutionary history of ancient primate lentiviruses. Philos Trans R Soc Lond B Biol Sci. 2013;368(1626):20120496.

Article  Google Scholar 

Dewannieux M, et al. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 2006;16(12):1548–56.

Article  CAS  Google Scholar 

Blanco-Melo D, Gifford RJ, Bieniasz PD. Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. Elife. 2017. https://doi.org/10.7554/eLife.22519.

Article  Google Scholar 

Goldstone DC, et al. Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host Microbe. 2010;8(3):248–59.

Article  CAS  Google Scholar 

Katzourakis A, et al. Discovery and analysis of the first endogenous lentivirus. Proc Natl Acad Sci U S A. 2007;104(15):6261–5.

Article  CAS  Google Scholar 

Gifford RJ, et al. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc Natl Acad Sci U S A. 2008;105(51):20362–7.

Article  CAS  Google Scholar 

Gilbert C, et al. Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genet. 2009;5(3): e1000425.

Article  Google Scholar 

Han GZ, Worobey M. Endogenous lentiviral elements in the weasel family (Mustelidae). Mol Biol Evol. 2012;29(10):2905–8.

Article  CAS  Google Scholar 

Cui J, Holmes EC. Endogenous lentiviruses in the ferret genome. J Virol. 2012;86(6):3383–5.

Article  CAS  Google Scholar 

Hron T, et al. Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates. Retrovirology. 2014;11(1):84.

Google Scholar 

Han GZ, Worobey M. A primitive endogenous lentivirus in a colugo: insights into the early evolution of lentiviruses. Mol Biol Evol. 2015;32(1):211–5.

Article  CAS  Google Scholar 

Hron T, et al. Life history of the oldest lentivirus: characterization of ELVgv integrations in the dermopteran genome. Mol Biol Evol. 2016;33(10):2659–69.

Article  CAS  Google Scholar 

Zhu H, et al., Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database. bioRxiv, 2018.

Altschul SF, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuc Acids Res. 1997;25:3389–402.

Article  CAS  Google Scholar 

Kitts PA, et al. Assembly: a resource for assembled genomes at NCBI. Nucleic Acids Res. 2016;44(D1):D73-80.

Article  CAS  Google Scholar 

Dewannieux M, Heidmann T. Endogenous retroviruses: acquisition, amplification and taming of genome invaders. Curr Opin Virol. 2013;3(6):646–56.

Article  CAS  Google Scholar 

Gifford R, et al. Evolution and distribution of class II-related endogenous retroviruses. J Virol. 2005;79(10):6478–86.

Article  CAS  Google Scholar 

Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.

Article  CAS  Google Scholar 

Subramanian RP, et al. Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology. 2011;8:90.

Article  CAS  Google Scholar 

Rambaut A. Se-Al: sequence alignment editor. 1997: Edinburgh.

Gifford RJ. Lentivirus-GLUE. 2021; Available from: https://giffordlabcvr.github.io/Lentivirus-GLUE.

Ge D, et al. Evolutionary history of lagomorphs in response to global environmental change. PLoS ONE. 2013;8(4): e59668.

Article  CAS  Google Scholar 

Toljagić O, et al. Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands. Syst Biol. 2017;67(1):145–57.

Article  Google Scholar 

Law CJ. Evolutionary shifts in extant mustelid (Mustelidae: Carnivora) cranial shape, body size and body shape coincide with the Mid-Miocene Climate Transition. Biol Lett. 2019;15(5):20190155.

Article  Google Scholar 

Springer MS, et al. The historical biogeography of Mammalia. Philos Trans R Soc Lond B Biol Sci. 2011;366(1577):2478–502.

Article  Google Scholar 

Karanth KP, et al. Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates. Proc Natl Acad Sci U S A. 2005;102(14):5090–5.

Article  CAS  Google Scholar 

Poux C, et al. Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores, and rodents as inferred from nuclear genes. Syst Biol. 2005;54(5):719–30.

Article  Google Scholar 

Gifford RJ, et al. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology. 2018;15(1):59.

Article  Google Scholar 

Dimmic MW, et al. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol. 2002;55(1):65–73.

Article  CAS  Google Scholar 

Kumar S, et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Mol Biol Evol. 2017;34(7):1812–9.

Article  CAS  Google Scholar 

Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–15.

Article  CAS  Google Scholar