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Bertrand, Yann
Publications (10 of 10) Show all publications
Bertrand, Y. J., Johansson, M. & Norberg, P. (2016). Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach. PLoS ONE, 11(10), Article ID e0164435.
Open this publication in new window or tab >>Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach
2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, article id e0164435Article in journal (Refereed) Published
Abstract [en]

The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31079 (URN)10.1371/journal.pone.0164435 (DOI)000386204000036 ()27760182 (PubMedID)2-s2.0-84992395862 (Scopus ID)
Funder
The Foundation for Baltic and East European Studies, 1330/42/2010Knowledge Foundation, 20150201
Available from: 2016-11-03 Created: 2016-11-03 Last updated: 2017-11-29Bibliographically approved
Bertrand, Y., Töpel, M., Elväng, A., Melik, W. & Johansson, M. (2012). First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses. PLoS ONE, 7(2), e31981
Open this publication in new window or tab >>First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses
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2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 2, p. e31981-Article in journal (Refereed) Published
Abstract [en]

The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus (TBEV). We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses about the ecological conditions that could account for the observed recombination.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-17058 (URN)10.1371/journal.pone.0031981 (DOI)000302875500062 ()2-s2.0-84857493482 (Scopus ID)
Funder
The Foundation for Baltic and East European Studies
Available from: 2012-09-13 Created: 2012-09-13 Last updated: 2018-12-17Bibliographically approved
Elväng, A., Melik, W., Bertrand, Y., Lönn, M. & Johansson, M. (2011). Sequencing of a Tick-Borne Encephalitis Virus from Ixodes ricinus Reveals a Thermosensitive RNA Switch Significant for Virus Propagation in Ectothermic Arthropods.. Vector Borne and Zoonotic Diseases, 11(6), 649-658
Open this publication in new window or tab >>Sequencing of a Tick-Borne Encephalitis Virus from Ixodes ricinus Reveals a Thermosensitive RNA Switch Significant for Virus Propagation in Ectothermic Arthropods.
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2011 (English)In: Vector Borne and Zoonotic Diseases, ISSN 1530-3667, E-ISSN 1557-7759, Vol. 11, no 6, p. 649-658Article in journal (Refereed) Published
Abstract [en]

Tick-borne encephalitis virus (TBEV) is a flavivirus with major impact on global health. The geographical TBEV distribution is expanding, thus making it pivotal to further characterize the natural virus populations. In this study, we completed the earlier partial sequencing of a TBEV pulled out of a pool of RNA extracted from 115 ticks collected on Torö in the Stockholm archipelago. The total RNA was sufficient for all sequencing of a TBEV genome (Torö-2003), without conventional enrichment procedures such as cell culturing or suckling mice amplification. To our knowledge, this is the first time that the genome of TBEV has been sequenced directly from an arthropod reservoir. The Torö-2003 sequence has been characterized and compared with other TBE viruses. In silico analyses of secondary RNA structures formed by the two untranslated regions revealed a temperature-sensitive structural shift between a closed replicative form and an open AUG accessible form, analogous to a recently described bacterial thermoswitch. Additionally, novel phylogenetic conserved structures were identified in the variable part of the 3'-untranslated region, and their sequence and structure similarity when compared with earlier identified structures suggests an enhancing function on virus replication and translation. We propose that the thermo-switch mechanism may explain the low TBEV prevalence often observed in environmentally sampled ticks. Finally, we were able to detect variations that help in the understanding of virus adaptations to varied environmental temperatures and mammalian hosts through a comparative approach that compares RNA folding dynamics between strains with different mammalian cell passage histories.

National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:sh:diva-6139 (URN)10.1089/vbz.2010.0105 (DOI)000291717500010 ()21254926 (PubMedID)2-s2.0-79959411565 (Scopus ID)
Available from: 2011-02-10 Created: 2011-02-10 Last updated: 2018-01-12Bibliographically approved
Bertrand, Y. (2008). Contrasting the general with the particular in phylogenetics - a proposal to keep the meanings of mono/paraphyletic and clade/grade separated. Taxon, 57(3), 705-708
Open this publication in new window or tab >>Contrasting the general with the particular in phylogenetics - a proposal to keep the meanings of mono/paraphyletic and clade/grade separated
2008 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 57, no 3, p. 705-708Article in journal (Refereed) Published
Abstract [en]

Clade and monophyletic group on one hand and grade and paraphyletic group on the other hand are commonly used as pairs of interchangeable terms. I question this apparent synonymy and propose that "monophyly" and "paraphyly" should refer to a property of a set, whereas "clade" and "grade" should apply to individuals resulting from evolutionary process.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:sh:diva-14140 (URN)000258974600003 ()2-s2.0-52249108872 (Scopus ID)
Available from: 2011-12-18 Created: 2011-12-16 Last updated: 2017-12-08Bibliographically approved
Bertrand, Y. & Härlin, M. (2008). Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names. Zoologica Scripta, 37(3), 337-347
Open this publication in new window or tab >>Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names
2008 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 3, p. 337-347Article in journal (Refereed) Published
Abstract [en]

When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.

National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-6100 (URN)10.1111/j.1463-6409.2007.00323.x (DOI)000254954700008 ()2-s2.0-42149140801 (Scopus ID)
Available from: 2011-02-08 Created: 2011-02-08 Last updated: 2017-12-11Bibliographically approved
Bertrand, Y. (2008). Relationships between nomenclature, phylogenetics and systematics. (Doctoral dissertation). Göteborg: Göteborgs universitet
Open this publication in new window or tab >>Relationships between nomenclature, phylogenetics and systematics
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Systematists have become increasingly aware of the limits imposed by the current system of nomenclature for accurately representing evolutionary relationships and managing efficiently names associated with clades. In reaction, a new system of nomenclature, the PhyloCode is being developed that fully recognizes the historical nature of taxonomy and the importance of the cladistics revolution. As a consequence, questions emerge about the new historical entities of systematics, questions that can be apprehended through the lens of epistemology, philosophy of language and metaphysics. What is the ontological nature of entities that lack any other essential features besides spatiotemporal properties? How to depart from the fixed realm of immutable and transcendental essence into a worldview wherein all biological entities are characterized by their temporality and materiality? What are the consequences of nomenclatural decisions on other sectors of biology? With the ever growing sequencing capacity and tree reconstructing abilities, our conceptualization of phylogenetic relationships is changing at an unprecedented pace. Then it begs the question, what prevents communication break down when the references of clades’ names are changing almost on a daily basis. These are some of the fundamental issues I am tackling in the present work. Addressing the ontological issue, I argue that species and clades are best perceived as mereological sums of individuals, which means that each biological individual is the unique individual composed of all its less inclusive individuals and nothing more. I propose to separate the meanings of “clade” and “monophyletic group”. I suggest to use “monophyletic” for an epithet referring to a defining property of a set (a natural kind) and “clade” for a noun which corresponds to a historical entity (an individual) resulting from evolutionary process. I present the idea that a phyloname is not attached to a single clade but to a natural kind containing as members the clades that would be selected in counterfactual phylogenies. The defining properties of this natural kind are provided by the phylogenetic definition. Finally I stress that taxonomists are also driven by the will to narrate the same sort of history, when they adjust the reference of names in light of new phylogenetic data, which leads me to submit that taxa can also be perceived as narratives.

Place, publisher, year, edition, pages
Göteborg: Göteborgs universitet, 2008. p. 44
Keywords
PhyloCode, philosophy, systematics, individuality, natural kind, possible worlds, causal theory of reference
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31241 (URN)978-91-628-7544-2 (ISBN)
Public defence
2008-09-26, Föreläsningssalen, Department of Zoology, Medicinaregatan 18, Göteborg, 10:00 (English)
Opponent
Supervisors
Available from: 2016-11-29 Created: 2016-11-29 Last updated: 2016-11-29Bibliographically approved
Bertrand, Y. & Härlin, M. (2006). Stability and universality in the application of taxon names in phylogenetic nomenclature. Systematic Biology, 55(5), 848-858
Open this publication in new window or tab >>Stability and universality in the application of taxon names in phylogenetic nomenclature
2006 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 5, p. 848-858Article in journal (Refereed) Published
National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-6070 (URN)10.1080/10635150600960061 (DOI)000246721800012 ()2-s2.0-39049175702 (Scopus ID)
Available from: 2011-02-08 Created: 2011-02-07 Last updated: 2017-12-11Bibliographically approved
Bertrand, Y., Pteijel, F. & Rouse, G. W. (2006). Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks. Systematics and Biodiversity, 4(2), 149-159
Open this publication in new window or tab >>Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks
2006 (English)In: Systematics and Biodiversity, ISSN 1477-2000, E-ISSN 1478-0933, Vol. 4, no 2, p. 149-159Article in journal (Refereed) Published
Abstract [en]

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy tacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon-Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-14295 (URN)10.1017/S1477200005001908 (DOI)000238588700004 ()2-s2.0-33744806071 (Scopus ID)
Available from: 2011-12-20 Created: 2011-12-20 Last updated: 2017-12-08Bibliographically approved
Bertrand, Y. & Härlin, M.Historicism and essentialism in phylogenetic biology.
Open this publication in new window or tab >>Historicism and essentialism in phylogenetic biology
(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-6137 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-02-10 Created: 2011-02-10 Last updated: 2016-11-29Bibliographically approved
Bertrand, Y.Species individuality and integration.
Open this publication in new window or tab >>Species individuality and integration
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31240 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-11-29 Created: 2016-11-29 Last updated: 2016-11-29Bibliographically approved
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