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Items: 27

1.

The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss).

de Abreu NL, Alves RJV, Cardoso SRS, Bertrand YJK, Sousa F, Hall CF, Pfeil BE, Antonelli A.

PeerJ. 2018 Jun 15;6:e4916. doi: 10.7717/peerj.4916. eCollection 2018.

2.

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.

3.

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
4.

A cryptic species produced by autopolyploidy and subsequent introgression involving Medicago prostrata (Fabaceae).

Eriksson JS, Blanco-Pastor JL, Sousa F, Bertrand YJK, Pfeil BE.

Mol Phylogenet Evol. 2017 Feb;107:367-381. doi: 10.1016/j.ympev.2016.11.020. Epub 2016 Dec 2.

PMID:
27919807
5.

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
6.

A voltage-dependent chloride channel fine-tunes photosynthesis in plants.

Herdean A, Teardo E, Nilsson AK, Pfeil BE, Johansson ON, Ünnep R, Nagy G, Zsiros O, Dana S, Solymosi K, Garab G, Szabó I, Spetea C, Lundin B.

Nat Commun. 2016 May 24;7:11654. doi: 10.1038/ncomms11654.

7.

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
8.

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.

9.

Phylogeny of the Centaurea group (Centaurea, Compositae) - geography is a better predictor than morphology.

Hilpold A, Vilatersana R, Susanna A, Meseguer AS, Boršić I, Constantinidis T, Filigheddu R, Romaschenko K, Suárez-Santiago VN, Tugay O, Uysal T, Pfeil BE, Garcia-Jacas N.

Mol Phylogenet Evol. 2014 Aug;77:195-215. doi: 10.1016/j.ympev.2014.04.022. Epub 2014 Apr 28.

PMID:
24784974
10.

Stereopsidales--a new order of mushroom-forming fungi.

Sjökvist E, Pfeil BE, Larsson E, Larsson KH.

PLoS One. 2014 Apr 28;9(4):e95227. doi: 10.1371/journal.pone.0095227. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e106204.

11.

On the biogeography of Centipeda: a species-tree diffusion approach.

Nylinder S, Lemey P, De Bruyn M, Suchard MA, Pfeil BE, Walsh N, Anderberg AA.

Syst Biol. 2014 Mar;63(2):178-91. doi: 10.1093/sysbio/syt102. Epub 2013 Dec 12.

12.

A six nuclear gene phylogeny of Citrus (Rutaceae) taking into account hybridization and lineage sorting.

Ramadugu C, Pfeil BE, Keremane ML, Lee RF, Maureira-Butler IJ, Roose ML.

PLoS One. 2013 Jul 16;8(7):e68410. doi: 10.1371/journal.pone.0068410. Print 2013.

13.

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.

14.

Function and evolution of channels and transporters in photosynthetic membranes.

Pfeil BE, Schoefs B, Spetea C.

Cell Mol Life Sci. 2014 Mar;71(6):979-98. doi: 10.1007/s00018-013-1412-3. Epub 2013 Jul 9. Review.

15.

Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria.

Blanco-Pastor JL, Vargas P, Pfeil BE.

PLoS One. 2012;7(6):e39089. doi: 10.1371/journal.pone.0039089. Epub 2012 Jun 29.

16.

Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine.

Ashfield T, Egan AN, Pfeil BE, Chen NW, Podicheti R, Ratnaparkhe MB, Ameline-Torregrosa C, Denny R, Cannon S, Doyle JJ, Geffroy V, Roe BA, Saghai Maroof MA, Young ND, Innes RW.

Plant Physiol. 2012 May;159(1):336-54. doi: 10.1104/pp.112.195040. Epub 2012 Mar 28.

17.

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
18.

Phylogenetic Analysis of the Thylakoid ATP/ADP Carrier Reveals New Insights into Its Function Restricted to Green Plants.

Spetea C, Pfeil BE, Schoefs B.

Front Plant Sci. 2012 Jan 9;2:110. doi: 10.3389/fpls.2011.00110. eCollection 2011.

19.

A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences.

Bayer RJ, Mabberley DJ, Morton C, Miller CH, Sharma IK, Pfeil BE, Rich S, Hitchcock R, Sykes S.

Am J Bot. 2009 Mar;96(3):668-85. doi: 10.3732/ajb.0800341. Epub 2009 Feb 12.

20.

The age and biogeography of Citrus and the orange subfamily (Rutaceae: Aurantioideae) in Australasia and New Caledonia.

Pfeil BE, Crisp MD.

Am J Bot. 2008 Dec;95(12):1621-31. doi: 10.3732/ajb.0800214. Epub 2008 Nov 7.

21.

Replication of nonautonomous retroelements in soybean appears to be both recent and common.

Wawrzynski A, Ashfield T, Chen NW, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai H, Del Campo SM, Metcalf M, O'Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND, Innes RW.

Plant Physiol. 2008 Dec;148(4):1760-71. doi: 10.1104/pp.108.127910. Epub 2008 Oct 24.

22.

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND.

Plant Physiol. 2008 Dec;148(4):1740-59. doi: 10.1104/pp.108.127902. Epub 2008 Oct 8.

23.

The reticulate history of Medicago (Fabaceae).

Maureira-Butler IJ, Pfeil BE, Muangprom A, Osborn TC, Doyle JJ.

Syst Biol. 2008 Jun;57(3):466-82. doi: 10.1080/10635150802172168.

PMID:
18570039
24.

Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice.

Sweeney MT, Thomson MJ, Pfeil BE, McCouch S.

Plant Cell. 2006 Feb;18(2):283-94. Epub 2006 Jan 6.

25.

Testing the polyploid past of soybean using a low-copy nuclear gene--is Glycine (Fabaceae: Papilionoideae) an auto- or allopolyploid?

Straub SC, Pfeil BE, Doyle JJ.

Mol Phylogenet Evol. 2006 May;39(2):580-4. Epub 2005 Dec 27. No abstract available.

PMID:
16384718
26.

Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families.

Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ.

Syst Biol. 2005 Jun;54(3):441-54.

PMID:
16012110
27.

Paralogy and orthology in the MALVACEAE rpb2 gene family: investigation of gene duplication in hibiscus.

Pfeil BE, Brubaker CL, Craven LA, Crisp MD.

Mol Biol Evol. 2004 Jul;21(7):1428-37. Epub 2004 Apr 14.

PMID:
15084680

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