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Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the “reversed” gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC , and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.

This paper is the first in a series that documents the diversity, distribution, and evolution of palynological characters across angiosperms in a contemporary phylogenetic context, using modern optimization methods. The objectives of the series are: (1) to describe the diversity of pollen morphologies across the angiosperms; (2) to estimate ancestral palynological character states, diagnostic characters, and synapomorphies for monophyletic groups; (3) to highlight and interpret inferred patterns and processes of evolution in palynological characters; and (4) to provide a framework for the placement of enigmatic taxa (including fossil taxa) based on pollen morphology. This first paper examines the methods available for such a study and presents an overview of palynological characters across angiosperms as a whole. Using a well-supported, recent, molecular phylogeny, we consider the effects of coding strategy, method of optimization, and starting tree topology upon inference of trait evolution.Coding strategy and optimization method had significant effects upon inferred ancestral character states, the latter probably due to the different evolutionary models applied. Phylogenetic topology had little effect upon inferred ancestral character states, because the uncertainty in topology at this level involved only nodes where few character state changes occurred. Several palynological characters showed consistent, structured patterns in the context of phylogeny: angiosperms are distinguished from other seed plants by character states including supratectal elements echinate and less than 1 μm in size, and infratectum structure columellate; eudicots, as recognized in previous studies, may be defined by globose, isopolar, radially symmetrical grains with three equatorial apertures. We present a framework for the remainder of the series, in which the angiosperms are divided into nine monophyletic and paraphyletic groups each having a similar level of pollen variability, and a set of recommendations for the analysis of these groups. The series will provide a reference for future palynological and systematic studies and an approach that may be replicated for other character sets.

Apiaceae belong to angiosperm families with frequent plastome structural rearrangements, some of which are generally regarded as synapomorphic for large clades, although typically with limited taxon sampling. Our study aims to improve understanding of the structural rearrangements in plastome within the Tordylieae tribe (ApiaceaeApioideae) with a dense sampling scheme of its species. We showed that presence of psb A pseudogene in inverted repeats near the border with a large single-copy region, which is found in the Tordylieae tribe, may be a clade-specific synapomorphy.

Eukaryotic cells acquired novel organelles during evolution through mechanisms that remain largely obscure. The existence of the unique oil body compartment is a synapomorphy of liverworts that represents lineage-specific acquisition of this organelle during evolution, although its origin, biogenesis, and physiological function are yet unknown. We find that two paralogous syntaxin-1 homologs in the liverwort Marchantia polymorpha are distinctly targeted to forming cell plates and the oil body, suggesting that these structures share some developmental similarity. Oil body formation is regulated by an ERF/AP2-type transcription factor and loss of the oil body increases M . polymorpha herbivory. These findings highlight a common strategy for the acquisition of organelles with distinct functions in plants, via periodical redirection of the secretory pathway depending on cellular phase transition. Liverworts have a unique oil body organelle unrelated to lipid stores found in other eukaryotes. Here the authors show that oil body formation is analogous to that of cell plates, relying on periodic redirection of the secretory pathway and a syntaxin-1 homolog, and that oil bodies contribute to defence against herbivory.

The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with the evolution of terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved with an ancestral OR co-receptor (Orco) after the origin of terrestriality and the OR/Orco system is an adaptation to winged flight in insects. We investigated genomes of the Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, and Ephemeroptera, and find ORs present in all insect genomes but absent from lineages predating the evolution of insects. Orco is absent only in the ancestrally wingless insect lineage Archaeognatha. Our new genome sequence of the zygentoman firebrat Thermobia domestica reveals a full OR/Orco system. We conclude that ORs evolved before winged flight, perhaps as an adaptation to terrestriality, representing a key evolutionary novelty in the ancestor of all insects, and hence a molecular synapomorphy for the Class Insecta.

Wingless and shorter winged stick insects are very common today, but most known extinct stick insects had fully developed wings, leading to contentious affinities among the extinct winged and extant groups. We report herein three male winged stick insects, assigned to Pterophasmatidae fam. nov., from mid-Cretaceous Myanmar (Burmese) amber. Pterophasmatidae fam. nov. are regarded as transitional taxa from extinct winged to modern wingless and shorter winged stick insects based on their similar tegmina venation with extinct Susumanioidea and some body features the same as extant Phasmatodea. However, their symmetric phallic organs comprising two consistent phallomeres are different from those of all living groups. Phylogenetic analyses suggest that the extinct winged taxa, including the new family, are the stem groups of modern stick and leaf insects, and all of them constitute the clade of Phasmatodea. New findings indicate winged and wingless stick insects' morphologies diversified significantly during or before the mid-Cretaceous.

• Hornworts are crucial to understand the phylogeny of early land plants. The emergence of ‘reverse’ U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort–tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. • We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. • Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. • We observe significant variants of the ‘classic’ DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.

Alvarezsauria is a group of early-branching maniraptoran theropods that are distributed globally from the Late Jurassic to the latest Cretaceous. Despite recent increases in the fossil record of this group, the scarcity of complete specimens still restricts interpreting their detailed anatomy, ecology, and evolution. Here, we report a new taxon of derived alvarezsaur, Jaculinykus yaruui gen. et sp. nov., from the Late Cretaceous of Mongolia, which represents a nearly complete and articulated skeleton. Our phylogenetic analysis reveals that Jaculinykus belongs to the sub-clade of Alvarezsauridae, Parvicursorinae, and forms a mononphyletic group with Mononykus and Shuvuuia . Its well-preserved manus has only two fingers, composed of a hypertrophied digit I and greatly reduced digit II, which implies an intermediate condition between the tridactyl manus of Shuvuuia and monodactyl manus of Linhenykus . This highlights a previously unrecognized variation in specialization of alvarezsaurid manus. Notably, the preserved posture of the specimen exhibits a stereotypical avian-like sleeping position seen in the troodontids Mei and Sinornithoides . Evidence of this behavior in the alvarezsaur Jaculinykus suggests that stereotypically avian sleeping postures are a maniraptoran synapomorphy, providing more evidence of bird-like traits being distributed broadly among avian ancestors.

Frostius pernambucensis is a phytotelm-breeding frog with endotrophic larvae. Although the larvae were formally described, no aspect of its internal morphology is known. In this paper, we re-describe the tadpole based on a large sample, describe its internal anatomy (buccopharyngeal cavity and musculo-skeletal system), provide data on natural history, and discuss the evolution of endotrophy and phytotelma colonization. The tadpoles of F. pernambucensis are highly modified, with depressed bodies, reduced mouthparts, and long tails. Many character-states described for these tadpoles can be related to its endotrophic development. Consequence of this highly modified phenotype, we propose several novel putative synapomorphies for the genus: (1) labial tooth row formula 1/1; (2) absence of pustulation in the buccal roof and (3) floor; (4) absence of median ridge; (5) absence of lateral ridge papillae; (6) absence of secretory ridges and pores; (7) absence of filter plates; (7) m. subarcualis rectus II–IV originating on ceratobranchial III; (8) m. subarcualis rectus II–IV inserting on ceratobranchial I; (8) ventral slip of the m. subarcualis rectus I inserting on the ceratobranchial III; (9) suprarostral corpora fused to the cornua trabeculae ; (10) commissura quadratoorbitalis absent; (11) cerabranchial II attached to the planum hypobranchiale ; and (12) ceratobranchial III attached to the planum hypobranchiale . Finally, we also propose that the presence of a single pair of infralabial papilla could represent a synapomorphy of bufonids. The colonization of phytotelma seem to have created a selective pression on the development of F. pernambucenis , favoring the evolution of endotrophy.