Awesome Evolution

A curated list of awesome Evolution resources. Please feel free to contribute!

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Awesome ERV List

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Contents

Primate Research Papers

  • Constructing primate phylogenies from ancient retrovirus sequences - 1999. Johnson and Coffin. This is the seminal paper testing the hypothesis that ERVs can be used to reconstruct primate phylogenies. The authors used a set of 12 ERV loci to construct a phylogeny of 10 primate species, and found that the resulting tree was consistent with the known phylogeny of these species.

  • Origin and Deep Evolution of Human Endogenous Retroviruses in Pan-Primates - 2022. Zhang and Cui. This paper provides a comprehensive analysis of the origin and evolution of human endogenous retroviruses (HERVs) in primates. The authors used a combination of phylogenetic and genomic analyses to trace the evolutionary history of HERVs in primates, and found that HERVs have been present in primate genomes for at least 40 million years.

  • The diversity and evolution of retroviruses: Perspectives from viral “fossils” - 2022. Zheng, Wei, Cui. This paper provides a comprehensive review of the diversity and evolution of retroviruses, with a focus on the insights gained from the study of endogenous retroviruses (ERVs). The authors discuss the various mechanisms by which retroviruses have evolved, including recombination, mutation, and selection, and highlight the importance of ERVs as “fossils” that can provide valuable information about the evolutionary history of retroviruses.

  • Journal Viruses: Special Issue - 2022. This special issue of the journal Viruses is dedicated to the study of endogenous retroviruses (ERVs). It includes a collection of research articles and reviews that cover various aspects of ERV biology, including their evolution, function, and impact on host genomes.

Vertebrate Research Papers

  • Koala retrovirus: a genome invasion in real time - 2006. Stoye. This paper provides an overview of the discovery and characterization of the koala retrovirus (KoRV), which is currently invading the koala genome. The author discusses the implications of this invasion for koala health and conservation, as well as the potential for KoRV to serve as a model for studying retroviral evolution and host-virus interactions.

  • Diversity and transmission of koala retrovirus: a case study in three captive koala populations - 2022. Joyce, et al. This paper provides a detailed analysis of the diversity and transmission of koala retrovirus (KoRV) in three captive koala populations. The authors used a combination of genomic and epidemiological analyses to investigate the prevalence and diversity of KoRV in these populations, and found that KoRV is highly diverse and can be transmitted both vertically and horizontally.

  • Endogenous avian leukosis virus subgroup E elements of the chicken reference genome - 2020. Lee, et al. This paper provides a comprehensive analysis of the endogenous avian leukosis virus (ALV) subgroup E elements in the chicken reference genome. The authors used a combination of genomic and bioinformatic approaches to identify and characterize the ALV-E elements, and found that they are highly diverse and have undergone extensive recombination and mutation.

General ERV Papers

  • Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements - 2006. Marie Dewannieux, et al. The Phoenix Virus. This paper describes the identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. The authors used a combination of molecular and virological approaches to reconstruct the infectious progenitor, providing insights into the origin and evolution of HERV-K elements in the human genome.

  • Variation in proviral content among human genomes mediated by LTR recombination - 2018. Thomas, et al. This paper investigates the variation in proviral content among human genomes, focusing on the role of LTR recombination. The authors used a combination of genomic and bioinformatic approaches to analyze the diversity and distribution of proviral elements, providing insights into the mechanisms driving variation in human endogenous retroviruses.

  • Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: Implications for human and viral evolution - 2004. Hughes, et al. This paper investigates the formation of solo-LTRs and insertional polymorphisms of human endogenous retrovirus K (HERV-K) elements, providing insights into their impact on human and viral evolution. Captures solo-LTR formation “in the act,” documenting multiple loci where full-length HERV-K proviruses and their corresponding solo LTRs segregate as polymorphic alleles in modern humans.

  • Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses - 2006. Polavarapu, et al. This paper provides a comprehensive analysis of chimpanzee endogenous retroviruses (ERVs), including their identification, characterization, and comparative genomics. The authors used a combination of genomic and bioinformatic approaches to investigate the diversity and evolutionary history of ERVs in the chimpanzee genome.

  • Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations - 2019. Belyi, Levine, Skalka. This paper provides a comprehensive analysis of the segregation of endogenous retroviruses (ERVs) across wild and domestic host species populations. The authors used whole-genome sequencing data to investigate the distribution and diversity of ERVs in a variety of host species, and found that ERV segregation is influenced by both host population structure and viral evolutionary dynamics.

  • Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L - 2018. Lee, et al. This paper describes the reconstruction of a replication-competent ancestral murine endogenous retrovirus-L (ERV-L). The authors used a combination of phylogenetic and molecular techniques to reconstruct the ancestral ERV-L sequence, and demonstrated that the reconstructed virus is capable of replication in vitro. This study provides valuable insights into the evolution and biology of ERVs, and highlights the potential for using reconstructed viruses to study viral evolution and host-virus interactions.