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1. 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 ( October 2023 , Systematic Entomology)

   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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2. 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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3. Molecular phylogeny of the Cyathocotylidae (Digenea, Diplostomoidea) necessitates systematic changes and reveals a history of host and environment switches

   https://doi.org/10.1111/zsc.12360  

   Achatz, Tyler J. ; Pulis, Eric E. ; Junker, Kerstin ; Binh, Tran Thi ; Snyder, Scott D. ; Tkach, Vasyl V. ( May 2019 , Zoologica Scripta)

   The Cyathocotylidae is a globally distributed family of digeneans parasitic as adults in fish, reptiles, birds and mammals in both freshwater and marine environments. Molecular phylogenetic analysis of interrelationships among cyathocotylids is lacking with only a few species included in previous studies. We used sequences of the nuclear 28S rRNA gene to examine phylogenetic affinities of 11 newly sequenced taxa of cyathocotylids and the closely related family Brauninidae collected from fish, reptiles, birds and dolphins from Australia, Southeast Asia, Europe, North America and South America. This is the first study to provide sequence data from adult cyathocotylids parasitic in fish and reptiles. Our analyses demonstrated that the members of the genusBraunina(family Brauninidae) belong to the Cyathocotylidae, placing the Brauninidae into synonymy with the Cyathocotylidae. In addition, our DNA sequences supported the presence of a second species in the currently monotypicBraunina. Our phylogeny revealed thatCyathocotylespp. from crocodilians belong to a separate genus (Suchocyathocotyle, previously proposed as a subgenus) and subfamily (Suchocyathocotylinae subfam. n.). Morphological study ofGogatea serpentum indicumsupported its elevation to species asGogatea mehri. The phylogeny did not supportHolostephanoideswithin the subfamily Cyathocotylinae; instead,Holostephanoidesformed a strongly supported clade with members of the subfamily Szidatiinae (GogateaandNeogogatea). Therefore, we transferHolostephanoidesinto the Szidatiinae. DNA sequence data revealed the potential presence of cryptic species reported under the nameMesostephanus microbursa. Our phylogeny indicated at least two major host switching events in the evolutionary history of the subfamily Szidatiinae which likely resulted in the transition of these parasites from birds to fish and snakes. Likewise, the transition to dolphins byBrauninarepresents another major host switching event among the Cyathocotylidae. In addition, our phylogeny revealed more than a single transition between freshwater and marine environments demonstrated in our dataset byBrauninaand someMesostephanus.

    

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4. A timeframe for mint evolution: towards a better understanding of trait evolution and historical biogeography in Lamiaceae

   https://doi.org/10.1093/botlinnean/boab104  

   Rose, Jeffrey P ; Xiang, Chun-Lei ; Sytsma, Kenneth J ; Drew, Bryan T ( March 2022 , Botanical Journal of the Linnean Society)

   Abstract Lamiaceae are one of the largest and most economically important families of flowering plants. Despite focused study on relationships within subclades, higher-level relationships have been under-studied. Moreover, the herbaceous habit of much of the family has resulted in a poor fossil record and has hampered estimates of divergence times. Using a new dataset of five plastid loci from 178 members of Lamiaceae representing all subfamilies and nearly all tribes, we clarify major infrafamilial relationships and present a robust set of divergence times. We use this phylogenetic hypothesis as a platform to test previous hypotheses regarding the historical biogeography and evolution of major traits in the family. We confirm the placement of subfamily Nepetoideae, show continued uncertainty in the placement of subfamilies Ajugoideae and Premnoideae and highlight extreme discordance with recent results from nuclear data. Lamiaceae originated during the Late Cretaceous as woody plants with nutlet fruits and four stamens, probably in South-East Asia. Most subfamilies diverged during the Eocene, perhaps facilitated by climatic cooling. Our results provide a valuable set of secondary dates for Lamiaceae and highlight the need for focused study of subfamilies Callicarpoideae and Viticoideae. Our results also provide several hypotheses regarding trait or range-dependent diversification. 

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5. Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)

   https://doi.org/10.1111/syen.12590  

   Espeland, Marianne ; Nakahara, Shinichi ; Zacca, Thamara ; Barbosa, Eduardo P. ; Huertas, Blanca ; Marín, Mario A. ; Lamas, Gerardo ; Benmesbah, Mohamed ; Brévignon, Christian ; Casagrande, Mirna M. ; et al ( April 2023 , Systematic Entomology)

   The diverse, largely Neotropical subtribe Euptychiina is widely regarded as one of the most taxonomically challenging groups among all butterflies. Over the last two decades, morphological and molecular studies have revealed widespread paraphyly and polyphyly among genera, and a comprehensive, robust phylogenetic hypothesis is needed to build a firm generic classification to support ongoing taxonomic revisions at the species level. Here, we generated a dataset that includes sequences for up to nine nuclear genes and the mitochondrial COI ‘barcode’ for a total of 1280 specimens representing 449 described and undescribed species of Euptychiina and 39 out‐groups, resulting in the most complete phylogeny for the subtribe to date. In combination with a recently developed genomic backbone tree, this dataset resulted in a topology with strong support for most branches. We recognize eight major clades that each contain two or more genera, together containing all but seven Euptychiina genera. We provide a summary of the taxonomy, diversity and natural history of each clade, and discuss taxonomic changes implied by the phylogenetic results. We describe nine new genera to accommodate 38 described species:LazulinaWillmott, Nakahara & Espeland,gen.n.,SauronaHuertas & Willmott,gen.n.,ArgentariaHuertas & Willmott,gen.n.,TaguaibaFreitas, Zacca & Siewert,gen.n.,XenovenaMarín & Nakahara,gen.n.,DeltayaWillmott, Nakahara & Espeland,gen.n.,ModicaZacca, Casagrande & Willmott,gen.n.,OccultaNakahara & Willmott,gen.n., andTricoNakahara & Espeland,gen.n.We also synonymizeNubilaViloria, Andrade & Henao, 2019 (syn.n.) withSplendeuptychiaForster, 1964,MacrocissiaViloria, Le Crom & Andrade, 2019 (syn.n.) withSatyrotaygetisForster, 1964, andRudyphthimoidesViloria, 2022 (syn.n.) withMalaveriaViloria & Benmesbah, 2020. Overall, we revised the generic placement of 79 species (74 new generic combinations and five revised combinations), and as a result all but six described species of Euptychiina are accommodated within 70 named, monophyletic genera. For all newly described genera, we provide illustrations of representative species, drawings of wing venation and male and (where possible) female genitalia, and distribution maps, and summarize the natural history of the genus. For three new monotypic genera,Occultagen.n.,Tricogen.n.andXenovenagen.n.we provide a taxonomic revision with a review of the taxonomy of each species and data from examined specimens. We provide a revised synonymic list for Euptychiina containing 460 valid described species, 53 subspecies and 255 synonyms, including several new synonyms and reinstated species.

    

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