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Items: 1 to 50 of 67

1.

Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa.

Mitchell JD, Sumner JG, Holland BR.

Syst Biol. 2018 Sep 1;67(5):905-915. doi: 10.1093/sysbio/syy038.

PMID:
29788496
2.

Live bearing promotes the evolution of sociality in reptiles.

Halliwell B, Uller T, Holland BR, While GM.

Nat Commun. 2017 Dec 11;8(1):2030. doi: 10.1038/s41467-017-02220-w.

3.

Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway.

Worth JRP, Holland BR, Beeton NJ, Schönfeld B, Rossetto M, Vaillancourt RE, Jordan GJ.

Ann Bot. 2017 Oct 17;120(4):539-549. doi: 10.1093/aob/mcx086.

PMID:
28961707
4.

Maximum likelihood estimates of pairwise rearrangement distances.

Serdoz S, Egri-Nagy A, Sumner J, Holland BR, Jarvis PD, Tanaka MM, Francis AR.

J Theor Biol. 2017 Jun 21;423:31-40. doi: 10.1016/j.jtbi.2017.04.015. Epub 2017 Apr 20.

PMID:
28435014
5.

Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants.

Sumner JG, Taylor A, Holland BR, Jarvis PD.

J Math Biol. 2017 Dec;75(6-7):1619-1654. doi: 10.1007/s00285-017-1129-2. Epub 2017 Apr 22.

PMID:
28434023
6.

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon.

Steane DA, Potts BM, McLean EH, Collins L, Holland BR, Prober SM, Stock WD, Vaillancourt RE, Byrne M.

Genome Biol Evol. 2017 Feb 1;9(2):253-265. doi: 10.1093/gbe/evw290.

7.

Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization.

Stark TL, Liberles DA, Holland BR, O'Reilly MM.

BMC Evol Biol. 2017 Jan 31;17(1):38. doi: 10.1186/s12862-016-0848-0.

8.

Simulating and Summarizing Sources of Gene Tree Incongruence.

Woodhams MD, Lockhart PJ, Holland BR.

Genome Biol Evol. 2016 May 9;8(5):1299-315. doi: 10.1093/gbe/evw065.

9.

Evaluation of Monitoring Schemes for Wastewater-Based Epidemiology to Identify Drug Use Trends Using Cocaine, Methamphetamine, MDMA and Methadone.

Humphries MA, Bruno R, Lai FY, Thai PK, Holland BR, O'Brien JW, Ort C, Mueller JF.

Environ Sci Technol. 2016 May 3;50(9):4760-8. doi: 10.1021/acs.est.5b06126. Epub 2016 Apr 13.

PMID:
27007609
10.

Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease.

Brüniche-Olsen A, Austin JJ, Jones ME, Holland BR, Burridge CP.

PLoS One. 2016 Mar 1;11(3):e0147875. doi: 10.1371/journal.pone.0147875. eCollection 2016.

11.

Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans.

Schmid J, Magee PT, Holland BR, Zhang N, Cannon RD, Magee BB.

Curr Genet. 2016 Feb;62(1):81-5. doi: 10.1007/s00294-015-0516-8. Epub 2015 Sep 9. Review.

PMID:
26353943
12.

Selective Advantages of a Parasexual Cycle for the Yeast Candida albicans.

Zhang N, Magee BB, Magee PT, Holland BR, Rodrigues E, Holmes AR, Cannon RD, Schmid J.

Genetics. 2015 Aug;200(4):1117-32. doi: 10.1534/genetics.115.177170. Epub 2015 Jun 10.

13.

A tensorial approach to the inversion of group-based phylogenetic models.

Sumner JG, Jarvis PD, Holland BR.

BMC Evol Biol. 2014 Dec 4;14:236. doi: 10.1186/s12862-014-0236-6.

14.

Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease.

Brüniche-Olsen A, Jones ME, Austin JJ, Burridge CP, Holland BR.

Biol Lett. 2014 Nov;10(11):20140619. doi: 10.1098/rsbl.2014.0619.

15.

Quantification of historical livestock importation into New Zealand 1860-1979.

Binney BM, Biggs PJ, Carter PE, Holland BR, French NP.

N Z Vet J. 2014 Nov;62(6):309-14. doi: 10.1080/00480169.2014.914861. Epub 2014 Jun 26. Erratum in: N Z Vet J. 2015 Nov;63(6):347. Holland, B M [corrected to Holland, B R].

PMID:
24869627
16.

Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand.

Mohan V, Stevenson M, Marshall J, Fearnhead P, Holland BR, Hotter G, French NP.

Microbiologyopen. 2013 Aug;2(4):659-73. doi: 10.1002/mbo3.102. Epub 2013 Jul 22.

17.

Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice.

Shavit Grievink L, Penny D, Holland BR.

Genome Biol Evol. 2013;5(4):681-7. doi: 10.1093/gbe/evt032.

18.

Reconstructing past changes in locus-specific recombination rates.

Cox MP, Holland BR, Wilkins MC, Schmid J.

BMC Genet. 2013 Feb 25;14:11. doi: 10.1186/1471-2156-14-11.

19.

The identification of concerted convergence in insect heads corroborates palaeoptera.

Blanke A, Greve C, Wipfler B, Beutel RG, Holland BR, Misof B.

Syst Biol. 2013 Mar;62(2):250-63. doi: 10.1093/sysbio/sys091. Epub 2012 Nov 23. Erratum in: Syst Biol. 2013 Sep;62(5):787.

PMID:
23179601
20.

Novel distances for dollo data.

Woodhams M, Steane DA, Jones RC, Nicolle D, Moulton V, Holland BR.

Syst Biol. 2013 Jan 1;62(1):62-77. doi: 10.1093/sysbio/sys071. Epub 2012 Aug 22.

PMID:
22914977
21.

Low-parameter phylogenetic inference under the general markov model.

Holland BR, Jarvis PD, Sumner JG.

Syst Biol. 2013 Jan 1;62(1):78-92. doi: 10.1093/sysbio/sys072. Epub 2012 Aug 22.

PMID:
22914976
22.

Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli.

Yu S, Fearnhead P, Holland BR, Biggs P, Maiden M, French N.

J Mol Evol. 2012 Jun;74(5-6):273-80. doi: 10.1007/s00239-012-9505-4. Epub 2012 Jul 6.

23.

Is the general time-reversible model bad for molecular phylogenetics?

Sumner JG, Jarvis PD, Fernández-Sánchez J, Kaine BT, Woodhams MD, Holland BR.

Syst Biol. 2012 Dec 1;61(6):1069-74. doi: 10.1093/sysbio/sys042. Epub 2012 Mar 22. No abstract available.

PMID:
22442193
24.

Gaps: an elusive source of phylogenetic information.

Saurabh K, Holland BR, Gibb GC, Penny D.

Syst Biol. 2012 Dec 1;61(6):1075-82. doi: 10.1093/sysbio/sys043. Epub 2012 Mar 21. No abstract available.

PMID:
22438330
25.

Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria).

Eytan RI, Hastings PA, Holland BR, Hellberg ME.

Mol Phylogenet Evol. 2012 Jan;62(1):159-73. doi: 10.1016/j.ympev.2011.09.028. Epub 2011 Oct 20.

PMID:
22040767
26.

The algebra of the general Markov model on phylogenetic trees and networks.

Sumner JG, Holland BR, Jarvis PD.

Bull Math Biol. 2012 Apr;74(4):858-80. doi: 10.1007/s11538-011-9691-z.

PMID:
21975643
27.

Supermatrices, supertrees and serendipitous scaffolding: inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data.

Johnson KA, Holland BR, Heslewood MM, Crayn DM.

Mol Phylogenet Evol. 2012 Jan;62(1):146-58. doi: 10.1016/j.ympev.2011.09.011. Epub 2011 Sep 22.

PMID:
21967784
28.

Faster exact maximum parsimony search with XMP.

White WT, Holland BR.

Bioinformatics. 2011 May 15;27(10):1359-67. doi: 10.1093/bioinformatics/btr147. Epub 2011 Mar 27.

PMID:
21444294
29.

Biogeography of circum-Antarctic springtails.

McGaughran A, Stevens MI, Holland BR.

Mol Phylogenet Evol. 2010 Oct;57(1):48-58. doi: 10.1016/j.ympev.2010.06.003. Epub 2010 Jun 15.

PMID:
20558307
30.

Identifying cliques of convergent characters: concerted evolution in the cormorants and shags.

Holland BR, Spencer HG, Worthy TH, Kennedy M.

Syst Biol. 2010 Jul;59(4):433-45. doi: 10.1093/sysbio/syq023. Epub 2010 May 14.

PMID:
20547779
31.

Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree.

Shavit Grievink L, Penny D, Hendy MD, Holland BR.

Syst Biol. 2010 May;59(3):288-97. doi: 10.1093/sysbio/syq003. Epub 2010 Mar 1.

32.

Testing the effect of metabolic rate on DNA variability at the intra-specific level.

McGaughran A, Holland BR.

PLoS One. 2010 Mar 15;5(3):e9686. doi: 10.1371/journal.pone.0009686.

33.

Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2.

Zhang N, Cannon RD, Holland BR, Patchett ML, Schmid J.

PLoS One. 2010 Mar 9;5(3):e9614. doi: 10.1371/journal.pone.0009614. Erratum in: PLoS One. 2010;5(4). doi: 10.1371/annotation/a50e86c0-f779-4a4a-80e6-e634a11bbfa8.

34.

The emergence of predators in early life: there was no Garden of Eden.

de Nooijer S, Holland BR, Penny D.

PLoS One. 2009 Jun 3;4(6):e5507. doi: 10.1371/journal.pone.0005507.

35.

Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes.

Zhang N, Upritchard JE, Holland BR, Fenton LE, Ferguson MM, Cannon RD, Schmid J.

Infect Genet Evol. 2009 Jul;9(4):493-500. doi: 10.1016/j.meegid.2009.01.007. Epub 2009 Jan 30.

PMID:
19460314
36.

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.

Shavit Grievink L, Penny D, Hendy MD, Holland BR.

BMC Evol Biol. 2008 Nov 21;8:317. doi: 10.1186/1471-2148-8-317. Erratum in: BMC Evol Biol. 2009;9:200. doi:10.1186/1471-2148-9-200.

37.

Using supernetworks to distinguish hybridization from lineage-sorting.

Holland BR, Benthin S, Lockhart PJ, Moulton V, Huber KT.

BMC Evol Biol. 2008 Jul 14;8:202. doi: 10.1186/1471-2148-8-202.

38.

Optimizing automated AFLP scoring parameters to improve phylogenetic resolution.

Holland BR, Clarke AC, Meudt HM.

Syst Biol. 2008 Jun;57(3):347-66. doi: 10.1080/10635150802044037.

PMID:
18570031
39.

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.

Shepherd LD, Holland BR, Perrie LR.

Mol Phylogenet Evol. 2008 Jul;48(1):176-87. doi: 10.1016/j.ympev.2008.02.023. Epub 2008 Apr 4.

PMID:
18462954
40.

The problem of rooting rapid radiations.

Shavit L, Penny D, Hendy MD, Holland BR.

Mol Biol Evol. 2007 Nov;24(11):2400-11. Epub 2007 Aug 23.

PMID:
17720690
41.

Treeness triangles: visualizing the loss of phylogenetic signal.

White WT, Hills SF, Gaddam R, Holland BR, Penny D.

Mol Biol Evol. 2007 Sep;24(9):2029-39. Epub 2007 Jul 13.

PMID:
17630280
42.

Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2.

Holmes AR, Tsao S, Ong SW, Lamping E, Niimi K, Monk BC, Niimi M, Kaneko A, Holland BR, Schmid J, Cannon RD.

Mol Microbiol. 2006 Oct;62(1):170-86. Epub 2006 Aug 30.

43.

Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes.

Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, Penny D.

Mol Biol Evol. 2006 Oct;23(10):1966-75. Epub 2006 Jul 19.

44.

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

Auch AF, Henz SR, Holland BR, Göker M.

BMC Bioinformatics. 2006 Jul 19;7:350.

45.

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny.

Holland BR, Jermiin LS, Moulton V; SMBE Tri-National Young Investigators.

Mol Biol Evol. 2006 May;23(5):848-55. Epub 2005 Nov 9.

PMID:
16280536
46.
47.

Selecting representative model micro-organisms.

Holland BR, Schmid J.

BMC Microbiol. 2005 May 17;5:26.

48.

The MinMax Squeeze: guaranteeing a minimal tree for population data.

Holland BR, Huber KT, Penny D, Moulton V.

Mol Biol Evol. 2005 Feb;22(2):235-42. Epub 2004 Oct 13.

PMID:
15483326
49.

Using consensus networks to visualize contradictory evidence for species phylogeny.

Holland BR, Huber KT, Moulton V, Lockhart PJ.

Mol Biol Evol. 2004 Jul;21(7):1459-61. Epub 2004 Apr 14.

PMID:
15084681
50.

Upper bounds on maximum likelihood for phylogenetic trees.

Hendy MD, Holland BR.

Bioinformatics. 2003 Oct;19 Suppl 2:ii66-72.

PMID:
14534174

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