Muscidae are a megadiverse dipteran family that exhibits extraordinary diversity in morphology and life history as both immatures and adults. The classification of Muscidae has been long debated, and most higher‐level relationships remain unknown. In this study, we used multilocus Sanger sequencing (mS‐seq), anchored hybrid enrichment (AHE) and restriction‐site associated DNA sequencing (RAD‐seq) approaches to examine relationships within Muscidae. The results from AHE and RAD‐seq largely correspond to those obtained from mS‐seq in terms of overall topology, yet phylogenomic approaches received much higher nodal support. The results from all molecular approaches contradict the traditional classification based predominantly on adult morphology, but provide an opportunity to re‐interpret the morphology of immature stages. Rearrangements in Muscidae classification are proposed as follows: (i) Mesembrina Meigen and Polietes Rondani are transferred from Muscinae to Azeliinae; (ii) Reinwardtiinae stat. rev. is resurrected as a subfamily distinct from Azeliinae; (iii) Eginia Robineau‐Desvoidy, Neohelina Malloch, Syngamoptera Schnabl and Xenotachina Malloch are transferred to Reinwardtiinae stat. rev.
Factors influencing diversification rates may be of intrinsic (e.g. morphological novelties) or extrinsic (e.g. long-distance dispersal, availability of ecological niches) nature. Growth habit may influence diversification rates because herbaceous plants often have shorter generation times and a more pronounced r reproductive strategy than their woody relatives. We examined life history and habit evolution, wood anatomy and biogeographical history of Apiaceae tribe Apieae in conjunction with diversification rate analysis to explore which factors may have affected clade species richness and to elucidate the constraints on the evolution of secondary woodiness in this group. We demonstrate that diversification rates are similar in morphologically homogeneous and diverse clades and in herbaceous and woody lineages. The only clade with a significantly elevated diversification rate is Southern Hemisphere Apium, in which diversity probably resulted from several long-distance dispersal events. We also show that wood anatomy in herbaceous and woody species does not differ considerably regardless of their continental or insular origin, but it is affected by stem architecture and plant reproductive strategy. As the taxonomy of Apieae suffers from inflation with numerous monotypic genera, we propose to include Canaria in Rutheopsis, and Foeniculum, Schoenoselinum, Ridolfia and Pseudoridolfia in Anethum.
The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae, and Scandicinae—that originated ca. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae, with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well‐supported topologies, irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups, thus confirming the relationship inferred from morphology. We conclude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.
The Polleniidae (Diptera) are a family of flies best known for species of the genus Pollenia, which overwinter inside human dwellings. Previously divided across the Calliphoridae, Tachinidae and Rhinophoridae, the polleniid genera have only recently been united. Several studies have utilized molecular data to analyse polleniid phylogenetic relationships, although all have suffered from low taxon sampling or insufficient phylogenetic signal in molecular markers. To alleviate these problems, we utilized two automated organellar genome extraction software, GetOrganelle and MitoFinder, to assemble mitogenomes from genome skimming data from 22 representatives of the polleniid genera: Dexopollenia, Melanodexia, Morinia, Pollenia and Xanthotryxus. From these analyses, we provide 14 new mitogenomes for the Polleniidae and perform phylogenetic analyses of 13 protein-coding mitochondrial genes using both maximum likelihood and Bayesian inference. Subfamilial phylogenetic relationships within the Polleniidae are interrogated and Pollenia is found to form a monophyletic clade sister to Melanodexia, Morinia and Dexopollenia, providing no evidence for the synonymisation of any of these genera. Our topology conflicts with previous morphology-based cladistic interpretations, with the amentaria, griseotomentosa, semicinerea and viatica species-groups resolving as non-monophyletic. We provide support for our topology through analysis of adult morphology and male and female terminalia, while identifying new diagnostic characters for some of the clades of the Pollenia. To test the validity of the current diagnostic morphology in the Polleniidae, newly assembled cytochrome C oxidase subunit 1 (COI) data are combined with a polleniid COI barcode reference library and analysed using the species delimitation software ASAP. COI barcodes support the current morphologically defined species within the Pollenia.
Background One of the major trends in angiosperm evolution was the shift from woody to herbaceous habit. However, reversals known as derived woodiness have also been reported in numerous, distantly related clades. Among theories evoked to explain the factors promoting the evolution of derived woodiness are moderate climate theory and cavitation theory. The first assumes that woody habit evolves in response to mild climate allowing for prolonged life span, which in turn leads to bigger and woodier bodies. The second sees woodiness as a result of natural selection for higher cavitation resistance in seasonally dry environments. Here, we compare climatic niches of woody and herbaceous, mostly southern African, umbellifers from the Lefebvrea clade to assess whether woody taxa in fact occur in markedly drier habitats. We also calibrate their phylogeny to estimate when derived woodiness evolved. Finally, we describe the wood anatomy of selected woody and herbaceous taxa to see if life forms are linked to any particular wood traits. Results The evolution of derived woodiness in chamaephytes and phanerophytes as well as the shifts to short-lived annual therophytes in the Lefebvrea clade took place at roughly the same time: in the Late Miocene during a trend of global climate aridification. Climatic niches of woody and herbaceous genera from the Cape Floristic Region overlap. There are only two genera with distinctly different climatic preferences: they are herbaceous and occur outside of the Cape Floristic Region. Therefore, studied herbs have an overall climatic niche wider than their woody cousins. Woody and herbaceous species do not differ in qualitative wood anatomy, which is more affected by stem architecture and, probably, reproductive strategy than by habit. Conclusions Palaeodrought was likely a stimulus for the evolution of derived woodiness in the Lefebvrea clade, supporting the cavitation theory. The concurrent evolution of short-lived annuals withering before summer exemplifies an alternative solution to the same problem of drought-induced cavitation. Changes of the life form were most likely neither spurred nor precluded by any qualitative wood traits, which in turn are more affected by internode length and probably also reproductive strategy.
Apioideae is the biggest and the most diverse of four subfamilies recognised within Apiaceae. Except for a few, likely derived, woody clades, most representatives of this subfamily are herbaceous. In the present study, we assessed stem anatomy of 87, mostly therophytic and hemicryptophytic, species from at least 20 distinct lineages of Apioideae, and juxtaposed them with 67 species from our previous anatomical projects also focused on this subfamily. Comparing our data with the literature, we found that wood anatomy does not allow for a distinction between apioids and their close relatives (Azorelloideae, Saniculoideae), but more distantly related Mackinlayoideae differ from Apioideae in their perforation plate type. Vessel element and fibre length, and vessel diameter were positively correlated with plant height: phenomena already reported in literature. Similar pattern was retrieved for vertical intervessel pit diameter. Wood ground tissue in apioids ranges from entirely fibrous to parenchymatous. The shortening of internodes seems to favour the formation of parenchymatic ground tissue, whereas the early shift to flowering promotes the deposition of fibrous wood in monocarpic species. These results support a hypothesis on interdependence among internode length, reproductive strategy, and wood ground tissue type.
Dorema (Apiaceae) includes 12 species distributed in the Irano-Turanian region. The genus differs from other genera of subfamily Apioideae in having paniculate inflorescences with simple umbels. Recently, molecular phylogenetic analyses placed six species of Dorema, including the generitype, in Ferula, thus subsuming the former into the synonymy of the latter. The remaining six congeners have not been yet included in molecular analyses. Here, we fill this gap by determining the phylogenetic position of these species. Because of a low resolution in some parts of the Ferula tree in earlier studies, alongside standard set of markers—nuclear nrDNA ITS and plastid rps16 and rpoC1 introns and the rpoB-trnC intergenic spacer—we additionally assessed the utility of nrDNA ETS sequences in resolving infrageneric relationships in the genus. We included 43 ingroup species representing major infrageneric divisions recognised in the most recent taxonomic revision. Although we were not successful in obtaining all markers for all newly studied species, they were placed with high support in one clade within section Peucedanoides together with formerly studied congeners in all maximum likelihood and Bayesian analyses of nuclear, plastid, and combined data sets. The addition of the ETS marker to the combined phylogenetic analyses confirmed the most recent classification of Ferula with increased branch support in some parts of the tree. However, many branches still remained unresolved. In particular, the monophyly of former Dorema within section Peucedanoides as suggested by morphology has not been definitely confirmed. A new combination and two nomina nova are proposed.
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