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Oxelman, Bengt
Publications (10 of 22) Show all publications
Britton, T., Svennblad, B., Erixon, P. & Oxelman, B. (2007). Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument.. Mathematical Medicine and Biology, 24(4), 401-411
Open this publication in new window or tab >>Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument.
2007 (English)In: Mathematical Medicine and Biology, ISSN 1477-8599, E-ISSN 1477-8602, Vol. 24, no 4, p. 401-411Article in journal (Refereed) Published
Abstract [en]

In phylogenetic inference, the support of an estimated phylogenetic tree topology and its interior branches is usually measured either with non-parametric bootstrap support (BS) values or with Bayesian posterior probabilities (BPPs). Extensive empirical evidence indicates that BPP values are systematically larger than BS when measured on the same data set, but there are no theoretical results supporting such a systematic difference. In the present note, we give a heuristic mathematical argument supporting the empirically observed phenomenon. The argument uses properties of the marginal and profile likelihoods of the normal distribution. The heuristic arguments are supported in a simulation study evaluating different steps in the argument.

Keywords
Bayesian posterior probability, bootstrap support, marginal likelihood, phylogenetic inference, profile likelihood
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-14578 (URN)10.1093/imammb/dqm008 (DOI)000255415800003 ()17977880 (PubMedID)
Available from: 2008-02-04 Created: 2008-02-04 Last updated: 2017-12-11Bibliographically approved
Popp, M. & Oxelman, B. (2007). Origin and evolution of North American Polyploid Silene (Caryophyllaceae). American Journal of Botany, 94(3), 330-349
Open this publication in new window or tab >>Origin and evolution of North American Polyploid Silene (Caryophyllaceae)
2007 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 3, p. 330-349Article in journal (Refereed) Published
Abstract [en]

Nuclear DNA sequences from introns of the low-copy nuclear gene family encoding the second largest subunit of RNA polymerases and the ribosomal internal transcribed spacer (ITS) regions, combined with the psbE-petL spacer and the rps16 intron from the chloroplast genome were used to infer origins and phylogenetic relationships of North American polyploid Silene species and their closest relatives. Although the vast majority of North American Silene species are polyploid, which contrasts to the diploid condition dominating in other parts of the world, the phylogenetic analyses rejected a single origin of the North American polyploids. One lineage consists of tetraploid Silene menziesii and its diploid allies. A second lineage, Physolychnis s.l., consists of Arctic, European, Asian, and South American taxa in addition to the majority of the North American polyploids. The hexaploid S. hookeri is derived from an allopolyploidization between these two lineages. The tetraploid S. nivea does not belong to any of these lineages, but is closely related to the European diploid S. baccifera. The poor resolution within Physolychnis s.l. may be attributed to rapid radiation, recombination among homoeologues, homoplasy, or any combination of these factors. No extant diploid donors could be identified in Physolychnis s.l.

Keywords
Caryophyllaceae, cpDNA, low-copy nuclear DNA, molecular phylogeny, North America, rapid radiation, RNA polymerase, Silene
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-91244 (URN)10.3732/ajb.94.3.330 (DOI)000245097500005 ()
Available from: 2004-01-13 Created: 2004-01-13 Last updated: 2017-12-14Bibliographically approved
Rautenberg, A. & Oxelman, B. (2007). Recombination between distinct lineages in Silene?. In: Abstracts - XI Congress European Society for Evolutionary Biology.
Open this publication in new window or tab >>Recombination between distinct lineages in Silene?
2007 (English)In: Abstracts - XI Congress European Society for Evolutionary Biology, 2007Conference paper, Published paper (Other scientific)
Abstract [en]

One of the challenges of evolutionary biologists is to reconstruct phylogenies, which are essential in order to understand the mechanisms of evolution. In systematic research, often only very small portions of the total genome are analyzed and assumed to reflect the species phylogeny. In principle, however, the resulting phylogenies do not reflect the history of the species, but rather the history of the individual DNA regions themselves. Sometimes the phylogenies show incongruences when based on different genomes, different genes, different copies of a gene, or different parts of a gene. These conflicts can either reflect complex phylogenetic patterns, or simply highlight errors and problems in lab procedures and/or phylogenetic methods. An example of a plant taxon with cases of conflicting gene phylogenies is Sileneae DC. (Caryophyllaceae). Silene section Elisanthe contains dioecious taxa with a X/Y chromosome system similar to that in humans. In order to understand the evolution of dioecy in Silene section Elisanthe, we compare the dioeciuos taxa with their closest relatives, using several molecular markers. We also test the utility of the potentially useful low-copy nuclear gene SlX1/SlY1, and its homologues in hermaphroditic taxa. We discovered that Elisanthe change places in the phylogenetic trees based on different parts of the SlX1/SlY1 alignment. We show that this may indicate that recombination between phylogenetically distant SlX1/SlY1 lineages has taken place.

National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-15013 (URN)
Available from: 2008-02-01 Created: 2008-02-01
Frajman, B. & Oxelman, B. (2007). Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences. Molecular Phylogenetics and Evolution, 43(1), 140-155
Open this publication in new window or tab >>Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences
2007 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 140-155Article in journal (Refereed) Published
Abstract [en]

The Balkan Peninsula is known to be one of the most diverse and species-rich parts of Europe, but its biota has gained much less attention in phylogenetic and evolutionary studies compared to other southern European mountain systems. We used nuclear ribosomal internal transcribed spacer (ITS) sequences and intron sequences of the chloroplast gene rps16 to examine phylogenetic and biogeographical patterns within the genus Heliosperma (Sileneae, Caryophyllaceae). The ITS and rps16 intron sequences both support monophyly of Heliosperma, but the data are not conclusive with regard to its exact origin. Three strongly supported clades are found in both data sets, corresponding to Heliosperma alpestre, Heliosperma macranthum and the Heliosperma pusillum clade, including all other taxa. The interrelationships among these three differ between the nuclear and the plastid data sets. Hierarchical relationships within the H. pusillum clade are poorly resolved by the ITS data, but the rps16 intron sequences form two well-supported clades which are geographically, rather than taxonomically, correlated. A similar geographical structure is found in the ITS data, when analyzed with the NeighbourNet method. The apparent rate of change within Heliosperma is slightly higher for rps16 as compared to ITS. In contrast, in the Sileneae outgroup, ITS substitution rates are more than twice as high as those for rps16, a situation more in agreement with what has been found in other rate comparisons of noncoding cpDNA and ITS. Unlike most other Sileneae ITS sequences, the H. pusillum group sequences display extensive polymorphism. A possible explanation to these patterns is extensive hybridization and gene flow within Heliosperma, which together with concerted evolution may have eradicated the ancient divergence suggested by the rps16 data. The morphological differentiation into high elevation, mainly widely distributed taxa, and low elevation narrow endemics is not correlated with the molecular data, and is possibly a result of ecological differentiation.

Keywords
Heliosperma, Ixoca, Balkan biogeography, ITS, rps16, Reticulate evolution
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96103 (URN)10.1016/j.ympev.2006.11.003 (DOI)000245936000011 ()17188521 (PubMedID)
Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
Eggens, F., Popp, M., Nepokroeff, M., Wagner, W. L. & Oxelman, B. (2007). The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae). American Journal of Botany, 94(2), 210-218
Open this publication in new window or tab >>The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)
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2007 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 2, p. 210-218Article in journal (Refereed) Published
Abstract [en]

The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.

Keywords
Caryophyllaceae, Hawaiian Silene, ITS, phylogeny, RPB2, rps16, Silene antirrhina, woodiness
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-95251 (URN)10.3732/ajb.94.2.210 (DOI)000244241800008 ()
Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2017-12-14Bibliographically approved
Brysting, A. K., Oxelman, B., Huber, K. T., Moulton, V. & Brochmann, C. (2007). Untangling complex histories of genome mergings in high polyploids. Systematic Biology, 56(3), 467-476
Open this publication in new window or tab >>Untangling complex histories of genome mergings in high polyploids
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2007 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 3, p. 467-476Article in journal (Refereed) Published
Abstract [en]

Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.

Keywords
Allopolyploidy, low-copy number gene, network construction, reticulate evolution
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-14579 (URN)10.1080/10635150701424553 (DOI)000248168200001 ()17562470 (PubMedID)
Available from: 2008-02-04 Created: 2008-02-04 Last updated: 2017-12-11Bibliographically approved
Huber, K. T., Oxelman, B., Lott, M. & Moulton, V. (2006). Reconstructing the evolutionary history of polyploids from multilabeled trees. Molecular biology and evolution, 23(9), 1784-1791
Open this publication in new window or tab >>Reconstructing the evolutionary history of polyploids from multilabeled trees
2006 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 23, no 9, p. 1784-1791Article in journal (Refereed) Published
Abstract [en]

In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/similar to a043878/padre.html.

Keywords
polyploid, phylogenetic tree, multilabeled trees, phylogenetic network
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-26501 (URN)10.1093/molbev/msl045 (DOI)000239905100017 ()16798795 (PubMedID)
Available from: 2007-02-18 Created: 2007-02-18 Last updated: 2017-12-07Bibliographically approved
Oxelman, B., Kornhall, P., Olmstead, R. G. & Bremer, B. (2005). Further disintegration of Scrophulariaceae. TAXON, 54, 411-425
Open this publication in new window or tab >>Further disintegration of Scrophulariaceae
2005 (English)In: TAXON, Vol. 54, p. 411-425Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-77104 (URN)
Available from: 2006-03-10 Created: 2006-03-10 Last updated: 2011-01-11
Popp, M., Erixon, P., Eggens, F. & Oxelman, B. (2005). Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae).. Systematic Botany, 30, 302-311
Open this publication in new window or tab >>Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae).
2005 (English)In: Systematic Botany, Vol. 30, p. 302-311Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-77107 (URN)
Available from: 2006-03-10 Created: 2006-03-10 Last updated: 2011-01-11
Rautenberg, A., Filatov, D. & Oxelman, B. (2005). Phylogenetic origins of dioecy in Silene. In: Abstracts IBC XVII.
Open this publication in new window or tab >>Phylogenetic origins of dioecy in Silene
2005 (English)In: Abstracts IBC XVII, 2005Conference paper, Published paper (Other scientific)
Abstract [en]

The aim of this project is to provide a phylogenetic/taxonomic framework for the evolution of dioecy within Silene (Caryophyllaceae). There are several dioecious taxa within the genus, traditionally classified in the sections Elisanthe and Otites. To understand how dioecy has evolved, these dioecious taxa need to be compared with their closest relatives. Available data suggest that the dioecious taxa within Elisanthe do not form a monophyletic group with the hermaphrodites in the section. Instead they seem more related to section Conoimorpha. This study is based on data from several Silene genes: (i) a gene sex-linked in the dioecious Elisanthe species (SlXY1) and a homologous autosomal gene in hermaphroditic taxa, (ii) intron sequences from the genes encoding the second largest subunits in the RNA polymerase gene family (RPA2, RPB2, RPD2) and (iii) chloroplast DNA. Remarkably, preliminary data suggest recombination between phylogenetically distant SIXY1 lineages.

National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-77215 (URN)
Available from: 2006-03-13 Created: 2006-03-13
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