Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Evolution and classification of figs (Ficus, Moraceae) and their close relatives (Castilleae) united by involucral bracts

(2020) Wendy L Clement et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Inferring processes of coevolutionary diversification in a community of Panamanian strangler figs and associated pollinating wasps

(2019) Jordan D. Satler et al.   EVOLUTION

LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference

(2019) Carlos J. Rivera-Rivera et al.   BMC BIOINFORMATICS

Genomic landscape of the global oak phylogeny

(2019) Andrew L. Hipp et al.   NEW PHYTOLOGIST

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

(2018) Diep Thi Hoang et al.   BMC EVOLUTIONARY BIOLOGY

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

OUP accepted manuscript

(2018)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Estimating divergence times and ancestral breeding systems in Ficus and Moraceae

(2018) Qian Zhang et al.   ANNALS OF BOTANY

First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)

(2017) Sam Bruun-Lund et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data

(2017) Silas Bossert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

(2017) David A Duchêne et al.   SYSTEMATIC BIOLOGY

Phylogenetic rooting using minimal ancestor deviation

(2017) Fernando Domingues Kümmel Tria et al.   Nature Ecology & Evolution

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

(2017) Uyen Mai et al.   PLoS One

RADIS:analysis ofRAD-seq data for interspecific phylogeny

(2016) Astrid Cruaud et al.   BIOINFORMATICS

LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa

(2016) Carlos J. Rivera-Rivera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Clustering Genes of Common Evolutionary History

(2016) Kevin Gori et al.   MOLECULAR BIOLOGY AND EVOLUTION

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

A review of methods for analysing insect structures — the role of morphology in the age of phylogenomics

(2016) Benjamin Wipfler et al.   Current Opinion in Insect Science

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees

(2015) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Morphology should not be forgotten in the era of genomics–a phylogenetic perspective

(2015) Gonzalo Giribet   ZOOLOGISCHER ANZEIGER

A New Classification of Ficus Subsection Urostigma (Moraceae) Based on Four Nuclear DNA Markers (ITS, ETS, G3pdh, and ncpGS), Morphology and Leaf Anatomy

(2015) Bhanumas Chantarasuwan et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

(2014) Bastien Boussau et al.   PLoS One

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

An Extreme Case of Plant–Insect Codiversification: Figs and Fig-Pollinating Wasps

(2012) Astrid Cruaud et al.   SYSTEMATIC BIOLOGY

Molecular phylogeny of Ficus section Ficus in China based on four DNA regions

(2012) Hong-Qing LI et al.   Journal of Systematics and Evolution

New insight into the phylogenetic and biogeographic history of genus Ficus: Vicariance played a relatively minor role compared with ecological opportunity and dispersal

(2011) Lei XU et al.   Journal of Systematics and Evolution

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Host sanctions and pollinator cheating in the fig tree-fig wasp mutualism

(2010) K. C. Jander et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Laying the foundations for a new classification of Agaonidae (Hymenoptera: Chalcidoidea), a multilocus phylogenetic approach

(2009) Astrid Cruaud et al.   CLADISTICS

Molecular dating and biogeography of fig-pollinating wasps

(2009) Carlos Lopez-Vaamonde et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Morphological Evolution in the Mulberry Family (Moraceae)

(2009) Wendy L. Clement et al.   SYSTEMATIC BOTANY

Evolutionary Ecology of Figs and Their Associates: Recent Progress and Outstanding Puzzles

(2008) Edward Allen Herre et al.   Annual Review of Ecology Evolution and Systematics

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One