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Items: 50

1.

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements.

Andermann T, Fernandes AM, Olsson U, Töpel M, Pfeil B, Oxelman B, Aleixo A, Faircloth BC, Antonelli A.

Syst Biol. 2018 May 15. doi: 10.1093/sysbio/syy039. [Epub ahead of print]

PMID:
29771371
2.

Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot.

Bacon CD, Velásquez-Puentes FJ, Hinojosa LF, Schwartz T, Oxelman B, Pfeil B, Arroyo MTK, Wanntorp L, Antonelli A.

PeerJ. 2018 Mar 16;6:e4388. doi: 10.7717/peerj.4388. eCollection 2018.

3.

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae).

Eriksson JS, de Sousa F, Bertrand YJK, Antonelli A, Oxelman B, Pfeil BE.

BMC Evol Biol. 2018 Jan 27;18(1):9. doi: 10.1186/s12862-018-1127-z.

4.

Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L.

Sousa F, Bertrand YJK, Doyle JJ, Oxelman B, Pfeil BE.

Syst Biol. 2017 Nov 1;66(6):934-949. doi: 10.1093/sysbio/syx035.

PMID:
28177088
5.

Molecular phylogeny of the cosmopolitan aquatic plant genus Limosella (Scrophulariaceae) with a particular focus on the origin of the Australasian L. curdieana.

Ito Y, Tanaka N, Albach DC, Barfod AS, Oxelman B, Muasya AM.

J Plant Res. 2017 Jan;130(1):107-116. doi: 10.1007/s10265-016-0872-6. Epub 2016 Nov 18.

PMID:
27864639
6.

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA.

Syst Biol. 2017 Mar 1;66(2):152-166. doi: 10.1093/sysbio/syw066.

7.

Species delimitation without prior knowledge: DISSECT reveals extensive cryptic speciation in the Silene aegyptiaca complex (Caryophyllaceae).

Toprak Z, Pfeil BE, Jones G, Marcussen T, Ertekin AS, Oxelman B.

Mol Phylogenet Evol. 2016 Sep;102:1-8. doi: 10.1016/j.ympev.2016.05.024. Epub 2016 May 24.

PMID:
27233442
8.

Colonization and diversification in the African 'sky islands': insights from fossil-calibrated molecular dating of Lychnis (Caryophyllaceae).

Gizaw A, Brochmann C, Nemomissa S, Wondimu T, Masao CA, Tusiime FM, Abdi AA, Oxelman B, Popp M, Dimitrov D.

New Phytol. 2016 Jul;211(2):719-34. doi: 10.1111/nph.13937. Epub 2016 Apr 1.

9.

Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (papaveraceae).

Bertrand YJ, Scheen AC, Marcussen T, Pfeil BE, de Sousa F, Oxelman B.

Syst Biol. 2015 May;64(3):448-71. doi: 10.1093/sysbio/syv004. Epub 2015 Jan 20.

PMID:
25604357
10.

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent.

Jones G, Aydin Z, Oxelman B.

Bioinformatics. 2015 Apr 1;31(7):991-8. doi: 10.1093/bioinformatics/btu770. Epub 2014 Nov 23.

PMID:
25422051
11.

Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing.

de Sousa F, Bertrand YJ, Nylinder S, Oxelman B, Eriksson JS, Pfeil BE.

PLoS One. 2014 Oct 17;9(10):e109704. doi: 10.1371/journal.pone.0109704. eCollection 2014. Erratum in: PLoS One. 2015;10(5):e0127130.

12.

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).

Marcussen T, Heier L, Brysting AK, Oxelman B, Jakobsen KS.

Syst Biol. 2015 Jan;64(1):84-101. doi: 10.1093/sysbio/syu071. Epub 2014 Oct 3.

13.

Marginal likelihood estimate comparisons to obtain optimal species delimitations in Silene sect. Cryptoneurae (Caryophyllaceae).

Aydin Z, Marcussen T, Ertekin AS, Oxelman B.

PLoS One. 2014 Sep 12;9(9):e106990. doi: 10.1371/journal.pone.0106990. eCollection 2014. Erratum in: PLoS One. 2014;9(12):e116266.

14.

Evolution of sex determination systems with heterogametic males and females in silene.

Slancarova V, Zdanska J, Janousek B, Talianova M, Zschach C, Zluvova J, Siroky J, Kovacova V, Blavet H, Danihelka J, Oxelman B, Widmer A, Vyskot B.

Evolution. 2013 Dec;67(12):3669-77. doi: 10.1111/evo.12223. Epub 2013 Sep 2. Erratum in: Evolution. 2015 Feb;69(2):570. Evolution. 2015 Feb;69(2):570.

PMID:
24299418
15.

Introgressive hybridization between anciently diverged lineages of Silene (Caryophyllaceae).

Petri A, Pfeil BE, Oxelman B.

PLoS One. 2013 Jul 8;8(7):e67729. doi: 10.1371/journal.pone.0067729. Print 2013.

16.

Life-history strategy defends against disease and may select against physiological resistance.

Gibson AK, Petit E, Mena-Ali J, Oxelman B, Hood ME.

Ecol Evol. 2013 Jun;3(6):1741-50. doi: 10.1002/ece3.583. Epub 2013 May 8.

17.

Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting.

Jones G, Sagitov S, Oxelman B.

Syst Biol. 2013 May 1;62(3):467-78. doi: 10.1093/sysbio/syt012. Epub 2013 Feb 19.

PMID:
23427289
18.

Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions.

Fior S, Li M, Oxelman B, Viola R, Hodges SA, Ometto L, Varotto C.

New Phytol. 2013 Apr;198(2):579-92. doi: 10.1111/nph.12163. Epub 2013 Feb 5.

19.

Time to a single hybridization event in a group of species with unknown ancestral history.

Bartoszek K, Jones G, Oxelman B, Sagitov S.

J Theor Biol. 2013 Apr 7;322:1-6. doi: 10.1016/j.jtbi.2013.01.001. Epub 2013 Jan 11.

PMID:
23318988
20.

The taxonomic identity of the 30,000-y-old plant regenerated from fruit tissue buried in Siberian permafrost.

Oxelman B, Petri A, Elven R, Lazkov G.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):E2735; author reply E2736. doi: 10.1073/pnas.1207774109. Epub 2012 Aug 15. No abstract available.

21.

Use of allele-specific sequencing primers is an efficient alternative to PCR subcloning of low-copy nuclear genes.

Scheen AC, Pfeil BE, Petri A, Heidari N, Nylinder S, Oxelman B.

Mol Ecol Resour. 2012 Jan;12(1):128-35. doi: 10.1111/j.1755-0998.2011.03070.x. Epub 2011 Sep 22.

PMID:
21943046
22.

Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae).

Marcussen T, Jakobsen KS, Danihelka J, Ballard HE, Blaxland K, Brysting AK, Oxelman B.

Syst Biol. 2012 Jan;61(1):107-26. doi: 10.1093/sysbio/syr096. Epub 2011 Sep 14.

23.

Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences.

Rautenberg A, Hathaway L, Oxelman B, Prentice HC.

Mol Phylogenet Evol. 2010 Dec;57(3):978-91. doi: 10.1016/j.ympev.2010.08.003. Epub 2010 Aug 17.

PMID:
20723610
24.

Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae)--a multigene phylogenetic approach with relative dating.

Frajman B, Eggens F, Oxelman B.

Syst Biol. 2009 Jun;58(3):328-45. doi: 10.1093/sysbio/syp030. Epub 2009 Jul 3.

PMID:
20525587
25.

Distribution of the anther-smut pathogen Microbotryum on species of the Caryophyllaceae.

Hood ME, Mena-Alí JI, Gibson AK, Oxelman B, Giraud T, Yockteng R, Arroyo MT, Conti F, Pedersen AB, Gladieux P, Antonovics J.

New Phytol. 2010 Jul;187(1):217-29. doi: 10.1111/j.1469-8137.2010.03268.x. Epub 2010 Apr 12.

26.

Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae).

Marcussen T, Oxelman B, Skog A, Jakobsen KS.

BMC Evol Biol. 2010 Feb 16;10:45. doi: 10.1186/1471-2148-10-45.

27.

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae.

Sloan DB, Oxelman B, Rautenberg A, Taylor DR.

BMC Evol Biol. 2009 Oct 31;9:260. doi: 10.1186/1471-2148-9-260. Erratum in: BMC Evol Biol. 2010;10:12.

28.

Inferring polyploid phylogenies from multiply-labeled gene trees.

Lott M, Spillner A, Huber KT, Petri A, Oxelman B, Moulton V.

BMC Evol Biol. 2009 Aug 28;9:216. doi: 10.1186/1471-2148-9-216.

29.

Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene.

Rautenberg A, Filatov D, Svennblad B, Heidari N, Oxelman B.

BMC Evol Biol. 2008 Oct 30;8:299. doi: 10.1186/1471-2148-8-299.

30.

Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)?

Erixon P, Oxelman B.

Mol Phylogenet Evol. 2008 Jul;48(1):313-25. doi: 10.1016/j.ympev.2008.04.015. Epub 2008 Apr 14.

PMID:
18490181
31.

Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies.

Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, Sundberg P, Thollesson M.

Mol Phylogenet Evol. 2008 Jul;48(1):369-71. doi: 10.1016/j.ympev.2008.03.024. Epub 2008 Mar 21. No abstract available.

PMID:
18424089
32.
33.

Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument.

Britton T, Svennblad B, Erixon P, Oxelman B.

Math Med Biol. 2007 Dec;24(4):401-11. Epub 2007 Oct 31.

PMID:
17977880
34.

Untangling complex histories of genome mergings in high polyploids.

Brysting AK, Oxelman B, Huber KT, Moulton V, Brochmann C.

Syst Biol. 2007 Jun;56(3):467-76.

PMID:
17562470
35.

Origin and evolution of North American polyploid Silene (Caryophyllaceae).

Popp M, Oxelman B.

Am J Bot. 2007 Mar;94(3):330-49. doi: 10.3732/ajb.94.3.330.

36.

The origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae).

Eggens F, Popp M, Nepokroeff M, Wagner WL, Oxelman B.

Am J Bot. 2007 Feb;94(2):210-8. doi: 10.3732/ajb.94.2.210.

37.
38.

Reconstructing the evolutionary history of polyploids from multilabeled trees.

Huber KT, Oxelman B, Lott M, Moulton V.

Mol Biol Evol. 2006 Sep;23(9):1784-91. Epub 2006 Jun 23.

PMID:
16798795
39.

Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics.

Svennblad B, Erixon P, Oxelman B, Britton T.

Syst Biol. 2006 Feb;55(1):116-21.

PMID:
16507528
41.

Piecing together the "new" Plantaginaceae.

Albach DC, Meudt HM, Oxelman B.

Am J Bot. 2005 Feb;92(2):297-315. doi: 10.3732/ajb.92.2.297.

42.

Polyploid origins in a circumpolar complex in Draba (Brassicaceae) inferred from cloned nuclear DNA sequences and fingerprints.

Grundt HH, Popp M, Brochmann C, Oxelman B.

Mol Phylogenet Evol. 2004 Sep;32(3):695-710.

PMID:
15288048
43.

RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.

Oxelman B, Yoshikawa N, McConaughy BL, Luo J, Denton AL, Hall BD.

Mol Phylogenet Evol. 2004 Aug;32(2):462-79.

PMID:
15223030
44.

Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.

Erixon P, Svennblad B, Britton T, Oxelman B.

Syst Biol. 2003 Oct;52(5):665-73.

PMID:
14530133
45.

Phylogenetic dating with confidence intervals using mean path lengths.

Britton T, Oxelman B, Vinnersten A, Bremer K.

Mol Phylogenet Evol. 2002 Jul;24(1):58-65.

PMID:
12128028
46.

More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae).

Bremer B, Jansen RK, Oxelman B, Backlund M, Lantz H, Kim KJ.

Syst Biol. 1999 Sep;48(3):413-35.

PMID:
12066290
47.
48.

Two APETALA2-like genes of Picea abies are differentially expressed during development.

Vahala T, Oxelman B, von Arnold S.

J Exp Bot. 2001 May;52(358):1111-5.

PMID:
11432927

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