Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form

Human immunodeficiency virus type I (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high level of genetic diversity within HIV-1 and to its worldwide distribution, this classification system is widely used in fields as diverse as vaccine development, evolution, epidemiology, viral fitness, and drug resistance. Here, we demonstrate how the high recombination rates of HIV-1 may confound the study of its evolutionary history and classification. Our data show that subtype G, currently classified as a pure subtype, has in fact a recombinant history, having evolved following recombination between subtypes A and J and a putative subtype G parent. In addition, we find no evidence for recombination within one of the lineages currently classified as a CRF, CRF02 -AG. Our analysis indicates that CRF02_AG was the parent of the recombinant subtype G, rather than the two having the opposite evolutionary relationship, as is currently proposed. Our results imply that the current classification of HIV-1 subtypes and CRFs is an artifact of sampling history, rather than reflecting the evolutionary history of the virus. We suggest a reanalysis of all pure subtypes and CRFs in order to better understand how high rates of recombination have influenced HIV-1 evolutionary history.</p

Vestiges of the history of popular science [Essay Review]

Robert Chambers, Vestiges of the Natural History of Creation and Other Evolutionary Writings, ed. James A. Secord. Chicago: University of Chicago Press. 1994. Pp. xlviii, vi, 390, viii, 254. US$ 19.95 PB. The title of Robert Chambers' anonymous evolutionary work, Vestiges of the natural history of creation, has long been familiar to even the most casual readers of the history of evolutionary theorising. From as early as 1861—when Charles Darwin first appended his 'historical sketch of the recent progress of opinion on the origin of species' to the third edition of his own more famous work on the subject—down to the present time, no history of what Loren Eiseley called 'evolution and the men who discovered it' has been complete without a discussion of this book. Yet as Eiseley's rather unfortunate phrase makes particularly clear, such histories of evolution are historiographically problematic. Indeed, it has become increasingly common over recent years to question altogether the value of 'evolution' as an object of historical study for any period before the middle of the nineteenth century, when the word began to acquire its familiar modern sense (viz., the origin of animal and plant species by a process of development from other forms). The great danger of evolution historiography is that it can unwittingly lead to teleological, present-centred history—more subtly so, perhaps, than in Eiseley's case, but nonetheless carrying the implication that Darwin's theory of natural selection (if not the modern evolutionary synthesis) was always out there, waiting to be 'discovered'

The extraordinary evolutionary history of the reticuloendotheliosis viruses

The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs—unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events

Discrete and continuous character-based disparity analyses converge to the same macroevolutionary signa. A case study from captorhinids

The relationship between diversity and disparity during the evolutionary history of a clade provides unique insights into evolutionary radiations and the biological response to bottlenecks and to extinctions. Here we present the first comprehensive comparison of diversity and disparity of captorhinids, a group of basal amniotes that is important for understanding the early evolution of high-fiber herbivory. A new fully resolved phylogeny is presented, obtained by the inclusion of 31 morphometric characters. The new dataset is used to calculate diversity and disparity through the evolutionary history of the clade, using both discrete and continuous characters. Captorhinids do not show a decoupling between diversity and disparity, and are characterized by a rather symmetric disparity distribution, with a peak in occupied morphospace at about the midpoint of the clade’s evolutionary history (Kungurian). This peak represents a delayed adaptive radiation, identified by the first appearance of several high-fiber herbivores in the clade, along with numerous omnivorous taxa. The discrete characters and continuous morphometric characters indicate the same disparity trends. Therefore, we argue that in the absence of one of these two possible proxies, the disparity obtained from just one source can be considered robust and representative of a general disparity pattern

Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201

Night at the museum: Contribution of small RNA from historical herbarium specimens in the reconstruction of evolutionary histories of geminiviruses

Emerging infectious diseases of plants, almost half of which are caused by viruses, are recognized as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors that underlie the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient DNA and RNA, it is now possible to sequence historical viral genomes, which provides us direct access to the dimension of time in evolutionary studies. Herbarium collections are an enormous source of dated, identified and well-preserved material that can be used to elucidate the emergence and evolutionary history of viral plant pathogens. Geminiviruses are responsible for many of the emerging plant diseases worldwide with a major economic impact on food crops such as cassava, which are a vital source of dietary calories in many sub-Saharan African countries. Their high potential for evolution, with high rates of mutation and recombination, makes such viruses an ideal model for understanding the epidemiological and evolutionary processes associated with viral emergence. Our proof of concept study investigated whether small interfering RNA (siRNA) can be used to reconstruct a complete geminivirus DNA genome from a herbarium sample despite the existence of post-mortem nucleic acid damage. Using a metagenomics approach based on the high-throughput sequencing of siRNA, we obtained a siRNA database from cassava leaf samples presenting typical symptoms of cassava mosaic disease that were collected in 1928 from Madagascar and 1968 from Cameroon, and then stored in the National Museum of Natural History herbarium in Paris. Our preliminary results demonstrate our ability to reconstruct the almost complete sequence of bipartite begomoviruses in particular from a 90-year-old herbarium specimen. These sequences are now used in phylogenetic, comparative genomic and phylogeographic studies to elucidate the emergence and evolutionary history of this important crop pathogen

Session 4: Evolutionary Indeterminism

Proceedings of the Pittsburgh Workshop in History and Philosophy of Biology, Center for Philosophy of Science, University of Pittsburgh, March 23-24 2001 Session 4: Evolutionary Indeterminis

Session 5: Development, Neuroscience and Evolutionary Psychology

Proceedings of the Pittsburgh Workshop in History and Philosophy of Biology, Center for Philosophy of Science, University of Pittsburgh, March 23-24 2001 Session 5: Development, Neuroscience and Evolutionary Psycholog