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1. An updated tribal classification of Lamiaceae based on plastome phylogenomics

   https://doi.org/10.1186/s12915-020-00931-z  

   Zhao, Fei; Chen, Ya-Ping; Salmaki, Yasaman; Drew, Bryan T.; Wilson, Trevor C.; Scheen, Anne-Cathrine; Celep, Ferhat; Bräuchler, Christian; Bendiksby, Mika; Wang, Qiang; et al (December 2021, BMC Biology)

   null (Ed.)

   Abstract Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract 

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2. Plastid Phylogenomic Analysis of Podostemaceae with an Emphasis on Neotropical Podostemoideae

   https://doi.org/10.1600/036364424X17267811220470  

   Ruhfel, Brad R; Larson, Drew A; Koenig, Nick; Rutishauser, Rolf; Bove, Claudia P; Philbrick, C Thomas (November 2024, Systematic Botany)

   Abstract—Podostemaceae are a clade of aquatic flowering plants that form important components of tropical river ecosystems. Species in the family exhibit highly derived growth forms and high vegetative phenotypic plasticity, both of which contribute to taxonomic confusion. The backbone phylogeny of the family remains poorly resolved, many species remain to be included in a molecular phylogenetic analysis, and the monophyly of many taxa remains to be tested. To address these issues, we assembled sequence data for 73 protein-coding plastid genes from 132 samples representing 68 species (∼23% of described species) that span the breadth of most major taxonomic, morphological, and biogeographic groups of Podostemaceae. With these data, we conducted the first plastid phylogenomic analysis of the family with broad taxon sampling. These analyses resolved most nodes with high support, including relationships not recovered in previous analyses. No evidence of widespread, well-supported conflict among individual plastid genes and the concatenated phylogeny was observed. We present new evidence that four genera (Apinagia,Marathrum,Oserya, andPodostemum), as well as four species, are not monophyletic. In particular, we show thatPodostemum flagelliformeshould not be included inPodostemumand is better recognized asDevillea flagelliformis,and thatMarathrum capillaceumis embedded withinLophogynes.l. and should be recognized asLophogyne capillacea. We also place a previously unsampled and undescribed species that likely represents a new genus. In contrast to previous studies, the neotropical generaDiamantina,Ceratolacis,Cipoia,andPodostemumare resolved as successive sister groups to a clade of all paleotropical Podostemoideae taxa sampled, suggesting a single dispersal event from the neotropics to the paleotropics in the history of the subfamily. These results provide a strong basis for improving the classification of Podostemaceae and a framework for future phylogenomic studies of the clade employing data from the nuclear genome. 

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3. Higher-Level Phylogeny and Reclassification of Lampyridae (Coleoptera: Elateroidea)

   https://doi.org/10.1093/isd/ixz024  

   Martin, Gavin J; Stanger-Hall, Kathrin F; Branham, Marc A; Da Silveira, Luiz F; Lower, Sarah E; Hall, David W; Li, Xue-Yan; Lemmon, Alan R; Moriarty Lemmon, Emily; Bybee, Seth M (November 2019, Insect Systematics and Diversity)

   Jordal, Bjarte (Ed.)

   Abstract Fireflies (Lampyridae Rafinesque) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ features. Due in part to their morphological diversity, the classification within the Lampyridae has long been in flux. Here we use an anchored hybrid enrichment approach to reconstruct the most extensive molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and use this phylogeny to evaluate the higher-level classification of the group. None of the currently recognized subfamilies were recovered as monophyletic with high support. We propose several classification changes supported by both phylogenetic and morphological evidence: 1) Pollaclasis Newman, Vestini McDermott (incl. Vesta Laporte, Dodacles Olivier, Dryptelytra Laporte, and Ledocas Olivier), Photoctus McDermott, and Araucariocladus Silveira & Mermudes are transferred to Lampyridae incertae sedis, 2) Psilocladinae Mcdermott, 1964status novum is reestablished for the genus Psilocladus Blanchard, 3) Lamprohizini Kazantsev, 2010 is elevated to Lamprohizinae Kazantsev, 2010status novum and Phausis LeConte is transferred to Lamprohizinae, 4) Memoan Silveira and Mermudes is transferred to Amydetinae Olivier, and 5) Scissicauda McDermott is transferred to Lampyrinae Rafinesque. 

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4. Phylogenetic Systematics of the Millipede Family Xystodesmidae

   https://doi.org/10.1093/isd/ixab003  

   Means, Jackson C; Hennen, Derek A; Tanabe, Tsutomu; Marek, Paul E (March 2021, Insect Systematics and Diversity)

   Mikó, István (Ed.)

   Abstract The millipede family Xystodesmidae includes 486 species distributed primarily in temperate deciduous forests in North America and East Asia. Species diversity of the family is greatest in the Appalachian Mountains of the eastern United States, with 188 species. Although the group includes notable taxa such as those that are bioluminescent and others that display Müllerian mimicry, producing up to 600 mg of cyanide, basic alpha-taxonomy of the group is woefully incomplete and more than 50 species remain undescribed in the Appalachian Mountains alone. In order to establish a robust phylogenetic foundation for addressing compelling evolutionary questions and describing species diversity, we assembled the largest species phylogeny (in terms of species sampling) to date in the Diplopoda. We sampled 49 genera (out of 57) and 247 of the species in the family Xystodesmidae, recollecting fresh material from historical type localities and discovering new species in unexplored regions. Here, we present a phylogeny of the family using six genes (four mitochondrial and two nuclear) and include pivotal taxa omitted from previous studies including Nannaria, Erdelyia, taxa from East Asia, and 10 new species. We show that 6 of the 11 tribes are monophyletic, and that the family is paraphyletic with respect to the Euryuridae and Eurymerodesmidae. Prior supraspecific classification is in part inconsistent with the phylogeny and convergent evolution has caused artificial genera to be proposed. Subspecific classification is likewise incongruent with phylogeny and subspecies are consistently not sister to conspecifics. The phylogeny is used as a basis to update the classification of the family, diagnose monophyletic groups, and to inform species hypotheses. 

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5. Anchored phylogenomics and revised classification of the Miltogramminae (Diptera: Sarcophagidae)

   https://doi.org/10.1111/syen.12609  

   Johnston, Nikolas P.; Pape, Thomas; Piwczyński, Marcin; Wallman, James F.; Wiegmann, Brian M.; Cassel, Brian K.; Akbarzadeh, Kamran; Szpila, Krzysztof (January 2024, Systematic Entomology)

   Abstract The Miltogramminae (Diptera: Sarcophagidae) includes ~600 species across >40 genera, which constitute ~20% of global Sarcophagidae. While molecular phylogenetic hypotheses have been produced for this group, critical problems persist, including the presence of paraphyletic genera, uncertain relationships between genera, a bias of sampling towards Palaearctic taxa, and low support for many branches. The present study remedies these issues through the application of Anchored Hybrid Enrichment (AHE) to a sample including ~60% of the currently recognised genera (16% of known species) representing all biogeographic regions except the Neotropical. An alignment of 1,281 concatenated loci was analysed with maximum likelihood (RAxML, IQ‐TREE), Bayesian inference (ExaBayes) and coalescent‐based approaches (ASTRAL, SVDquartets), which resulted in highly supported and concordant topologies, providing unprecedented insight into the relationships of this subfamily of flesh flies, allowing a major update to miltogrammine classification. The AHE phylogenetic hypothesis supports the monophyly of a large proportion of genera. The monophyly ofMetopiaMeigen is restored by synonymy withAenigmetopiaMalloch,syn.n.To achieve monophyly ofMiltogrammaMeigen, eight species are transferred fromPterellaRobineau‐Desvoidy. The genusPterellais shown to be paraphyletic in its current circumscription, and to restore generic monophylyPterellais restricted to contain onlyPt. grisea(Meigen).ErioproctaEnderlein,stat.rev., is resurrected. The genusSenotainiaMacquart is reconstructed as paraphyletic. The monotypic genusMetopodiaBrauer & Bergenstamm is synonymised withTaxigrammaMacquart,syn.n.In light of our phylogenetic hypotheses, a new Miltogramminae tribal classification is proposed, composed of six tribes. 

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