Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification

JV Freudenstein, MW Chase - Annals of botany, 2015 - academic.oup.com
Abstract Background and Aims The largest subfamily of orchids, Epidendroideae, represents
one of the most significant diversifications among flowering plants in terms of pollination …

Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of Spiralia

TH Struck, AR Wey-Fabrizius… - Molecular biology …, 2014 - academic.oup.com
Based on molecular data three major clades have been recognized within Bilateria:
Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized …

BaCoCa–A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

P Kück, TH Struck - Molecular phylogenetics and evolution, 2014 - Elsevier
Abstract BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines
multiple statistical approaches (like RCFV and C value calculations) to identify biases in …

Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects

E Dell'Ampio, K Meusemann… - Molecular biology …, 2014 - academic.oup.com
Phylogenetic relationships of the primarily wingless insects are still considered unresolved.
Even the most comprehensive phylogenomic studies that addressed this question did not …

Systematics of spiny‐backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

KH Jungfer, J Faivovich, JM Padial… - Zoologica …, 2013 - Wiley Online Library
Spiny‐backed tree frogs of the genus O steocephalus are conspicuous components of the
tropical wet forests of the A mazon and the G uiana S hield. Here, we revise the phylogenetic …

Resolving rapid radiations within angiosperm families using anchored phylogenomics

É Léveillé-Bourret, JR Starr, BA Ford… - Systematic …, 2018 - academic.oup.com
Despite the promise that molecular data would provide a seemingly unlimited source of
independent characters, many plant phylogenetic studies are still based on only two …

Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons

MP Simmons - Journal of Systematics and Evolution, 2017 - Wiley Online Library
Both traditional as well as 10 more recent methods of coding characters from exons of
protein‐coding genes are reviewed. The more recent methods collectively blur the …

Plastid genomes and deep relationships among the commelinid monocot angiosperms

CF Barrett, JI Davis, J Leebens‐Mack, JG Conran… - …, 2013 - Wiley Online Library
The commelinid monocots comprise the orders Arecales (A), Commelinales (C), Poales
sensu Angiosperm Phylogeny Group III (APGIII)(P), Zingiberales (Z), plus the unplaced …

Misleading results of likelihood‐based phylogenetic analyses in the presence of missing data

MP Simmons - Cladistics, 2012 - Wiley Online Library
The amount of missing data in many contemporary phylogenetic analyses has substantially
increased relative to previous norms, particularly in supermatrix studies that compile …

Coalescence vs. concatenation: sophisticated analyses vs. first principles applied to rooting the angiosperms

MP Simmons, J Gatesy - Molecular phylogenetics and evolution, 2015 - Elsevier
It has recently been concluded that phylogenomic data from 310 nuclear genes support the
clade of (Amborellales, Nymphaeales) as sister to the remaining angiosperms and that …