http://amborella.net/2010PlantSystematics/DATA/3-24-APG%202003%20Bot%20J%20Linn%20Soc%20APGII.pdf

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.2012.00644.x

The revised classification of eukaryotes

Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective.

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

Polyploidy and angiosperm diversification

This is an abbreviated version of a paper that appears in full in the Electronic supplement to Taxon. Phylogenetic definitions are provided for the names of 20 clades of vascular plants (plus 33 others in the electronic supplement). Emphasis has been placed on well-supported clades that are widely known to non-specialists and/or have a deep origin within Tracheophyta or Angiospermae. These treatments follow the draft PhyloCode and illustrate the application ofphylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy-based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of the PhyloCode) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named "Pan-X", where "X" is the name of the crown (e.g., Pan-Spermatophyta for the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name "X" that is based etymologically on an apomorphy is applied to the crown, the name "Apo-X" is applied to the clade for which this trait is synapomorphic (e.g., Apo-Spermatophyta for the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node-based and branch-modified node-based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of the PhyloCode on real definitions rather than simplified hypothetical ones.

/pdf/towards-a-phylogenetic-nomenclature-of-tracheophyta-1gj7bstl5l.pdf

Towards a phylogenetic nomenclature of Tracheophyta

A preliminary cladistic analysis suggests that the Labiatae are polyphyletic as presently circumscribed. The gynobasic-styled Labiatae emerge as a clade, nested within a larger group characterized by suprareticulate pollen and a fruit composed of nutlets. The latter includes the bulk of the Labiatae plus the verbenaceous genera Garrettia and Holmskioldia; its closest relatives are in tribe Viticeae (Verbenaceae). In contrast, Teucrium and five other genera of Ajugeae (Labiatae) belong to a large clade characterized by pollen with branched to granular columellae, most members of which are currently assigned to tribes Clerodendrea and Caryopterideae (Verbenaceae) (...)

Evidence for a polyphyletic origin of the Labiatae

Lamiaceae, the sixth largest angiosperm family, contains more than 7000 species distributed all over the world. However, although considerable progress has been made in the last two decades, its phylogenetic backbone has never been well resolved. In the present study, a large-scale phylogenetic reconstruction of Lamiaceae using chloroplast sequences was carried out with the most comprehensive sampling of the family to date (288 species in 191 genera, representing approximately 78% of the genera of Lamiaceae). Twelve strongly supported primary clades were inferred, which form the phylogenetic backbone of Lamiaceae. Six of the primary clades correspond to the current recognized subfamilies Ajugoideae, Lamioideae, Nepetoideae, Prostantheroideae, Scutellarioideae, and Symphorematoideae, and one corresponds to a portion of Viticoideae. The other five clades comprise: 1) Acrymia and Cymaria; 2) Hymenopyramis, Petraeovitex, Peronema, and Garrettia; 3) Premna, Gmelina, and Cornutia; 4) Callicarpa; and 5) Tectona. Based on these results, three new subfamilies-Cymarioideae, Peronematoideae, and Premnoideae-are described, and the compositions of other subfamilies are updated based on new findings from the last decade. Furthermore, our analyses revealed five strongly supported, more inclusive clades that contain subfamilies, and we give them phylogenetically defined, unranked names: Cymalamiina, Scutelamiina, Perolamiina, Viticisymphorina, and Calliprostantherina.

/pdf/a-large-scale-chloroplast-phylogeny-of-the-lamiaceae-sheds-35yyyrh69x.pdf

A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification.

A subfamilial level classification of Labiatae, originally proposed by G. Erdtman on the basis of pollen features, has received substantial corroboration in the European literature but remains little known in North America. In subfam. Lamioideae, pollen is usually tricolpate and shed in a two-celled stage; in subfam. Nepetoideae (Dumortier) Luerssen, it is usually hexacolpate and shed in a three-celled stage. The number of pollen cells and colpi are reported here for 108 genera of Labiatae, including 93 for which one or both had not previously been reported. The established relationship between number of colpi and pollen cells is consistent in 95% of the labiate genera for which data are available. In the remaining genera, one pollen character is constant while the other varies; in no genus is the pollen consistently tricolpate and three-celled when shed or consistently hexacolpate and two-celled. Other characters whose variation patterns closely parallel the pollen characters include occurrence of endosperm, embryo shape, cotyledon shape, volatile terpenoid content, occurrence of rosmarinic acid, occurrence of iridoid glycosides, degree of un- saturation of fatty acids in the seed oils, and myxospermy. Erdtman's subfamilies appear to be the primary phenetic groupings of the Labiatae, but only subfam. Nepetoideae can be shown to be monophyletic on the basis of synapomorphies. Briquet's (1895-1897) widely used classification is highly incongruent with Erdtman's, and it is recommended that the former be abandoned. A tabulation is provided of the component genera of each of Erdtman's subfamilies, along with the character state data upon which subfamilial assignments were based.

Philip D. Cantino

Papers

Towards a phylogenetic nomenclature of Tracheophyta

Evidence for a polyphyletic origin of the Labiatae

A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification.

Subfamilial Classification of Labiatae

The phylogenetic significance of Stomata and trichomes in the Labiatae and Verbenaceae