Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees

IncP-1  plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet

(2012) Y. Stolze et al.   MICROBIOLOGY-SGM

Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes

(2011) Diya Sen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Role of IncP-1β Plasmids pWDL7::rfpand pNB8c in Chloroaniline Catabolism as Determined by Genomic and Functional Analyses

(2011) J. E. Król et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination

(2011) Peter Norberg et al.   Nature Communications

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Conjugative Plasmids of Neisseria gonorrhoeae

(2010) Emilia Pachulec et al.   PLoS One

Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids

(2009) Géraldine A. Van der Auwera et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

PGA4genomics for comparative genome assembly based on genetic algorithm optimization

(2009) Fangqing Zhao et al.   GENOMICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone

(2009) Diya Sen et al.   PLASMID

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids

(2008) Chu Thi Thanh Binh et al.   FEMS MICROBIOLOGY ECOLOGY