Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity.

Weevils represent one of the most prolific radiations of beetles and the most diverse group of herbivores on land. The phylogeny of weevils (Curculionoidea) has received extensive attention, and a largely satisfactory framework for their interfamilial relationships has been established. However, a recent phylogenomic study of Curculionoidea based on anchored hybrid enrichment (AHE) data yielded an abnormal placement for the family Belidae (strongly supported as sister to Nemonychidae + Anthribidae). Here we reanalyse the genome-scale AHE data for Curculionoidea using various models of molecular evolution and data filtering methods to mitigate anticipated systematic errors and reduce compositional heterogeneity. When analysed with the infinite mixture model CAT-GTR or using appropriately filtered datasets, Belidae are always recovered as sister to the clade (Attelabidae, (Caridae, (Brentidae, Curculionidae))), which is congruent with studies based on morphology and other sources of molecular data. Although the relationships of the 'higher Curculionidae' remain challenging to resolve, we provide a consistent and robust backbone phylogeny of weevils. Our extensive analyses emphasize the significance of data curation and modelling across-site compositional heterogeneity in phylogenomic studies.

Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization.

Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian-Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian-Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental "Cambrian explosion" a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian-Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land.

A new marsh beetle from mid-Cretaceous amber of northern Myanmar (Coleoptera: Scirtidae).

As one of the earliest-diverging lineage of the megadiverse beetle suborder Polyphaga, marsh beetles (Scirtidae) are crucial for reconstructing the ancestor of all polyphagan beetles and the ecomorphological underpinnings of their remarkable evolutionary success. The phylogeny of marsh beetles has nonetheless remained challenging to infer, not least because of their fragmentary Mesozoic fossil record. Here we describe a new scirtid beetle genus and species, Varcalium lawrencei gen. et sp. nov., preserving internal tissue, from Albian-Cenomanian Kachin amber (ca 99 Ma), representing the second member of this family known from the deposit. Based on a formal morphological phylogenetic analysis, Varcalium is recovered within the crown-group of Scirtinae, forming a clade with other genera that possess subocular carinae. The finding suggests that the crown-group of Scirtinae has already diversified by the mid-Cretaceous.

Prolucanus beipiaoensis gen. et sp. nov.: The First Fossil Species of Lucaninae (Coleoptera: Lucanidae) from the Early Cretaceous of Northeastern China.

A new stag beetle fossil is described from the Yixian Formation in northeastern China. A new genus is established based on this well-preserved specimen. Prolucanus beipiaoensis gen. et sp. nov. is firmly placed in the extant lucanid subfamily Lucaninae based on its broad prosternal process and geniculate antennae. Our discovery represents the first fossil record of Lucaninae from the Late Mesozoic of China and the oldest reliable record belonging to the subfamily. We also summarize the fossil species of stag beetles found in China and the described fossil species of the subfamily Lucaninae found in the world. A key to all fossil genera of Lucanidae from China is provided.

The oldest fossil record of Pseudopsinae from the Lower Cretaceous Yixian Formation of northeastern China (Coleoptera: Staphylinidae: Pseudopsinae).

The Cretaceous witnessed a radiation of rove beetles (Staphylinidae), the most species-rich beetle family. Although most staphylinid subfamilies have been documented from Cretaceous strata over the world, there has been no fossil record of the subfamily Pseudopsinae until a recently reported fossil from the 99-Ma-old Myanmar amber. Here we describe a new compression fossil from the Lower Cretaceous Yixian Formation of northeastern China. It is described as Cretaceonanobius fossilis. gen. et sp. nov. and assigned to the extant subfamily Pseudopsinae, based on the well-preserved carinae on the pronotum, a carina on ventrites II and III, and distinctly separated mesocoxae. The discovery of Cretaceonanobius fossilis gen. et sp. nov. backdates the earliest fossils record of Pseudopsinae to 125 Ma in the Northern Hemisphere and sheds new lights on the evolution history and paleobiogeography of this subfamily.

Phylogenomics of Elongate-Bodied Springtails Reveals Independent Transitions from Aboveground to Belowground Habitats in Deep Time.

Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of paleontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher taxa (6 out of 8 families, 11 out of 16 subfamilies) of the order with an emphasis on the most problematic superfamily Tomoceroidea, applied whole-genome sequencing methods, and compared the performance of different combinations of data sets (universal single-copy orthologs [USCO] vs. ultraconserved elements]) and modeling schemes. The fossil-calibrated timetree was used to reconstruct the evolution of body size, sensory organs, and pigmentation to establish a time frame of the ecomorphological divergences. The resultant trees based on different analyses were congruent in most nodes. Several discordant nodes were carefully evaluated by considering method fitness, morphological information, and topology test. The evaluation favored the well-resolved topology from analyses using USCO amino acid matrices and complex site-heterogeneous models (CAT$+$GTR and LG$+$PMSF (C60)). The preferred topology supports the monophyletic superfamily Tomoceroidea as an early-diverging lineage and a sister relationship between Entomobryoidea and Isotomoidea. The family Tomoceridae was recovered as monophyletic, whereas Oncopoduridae was recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae and hence deserving a separate family status as Harlomillsiidae Yu and Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as surface-living, supporting independent origins of soil-living groups across the Paleozoic-Mesozoic, and highlighting the ancient evolutionary interaction between aboveground and belowground fauna. [Collembola; phylogenomics; soil-living adaptation; whole-genome sequencing.].

Integrated phylogenomics and fossil data illuminate the evolution of beetles.

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.

Fire-prone Rhamnaceae with South African affinities in Cretaceous Myanmar amber.

The rapid Cretaceous diversification of flowering plants remains Darwin's 'abominable mystery' despite numerous fossil flowers discovered in recent years. Wildfires were frequent in the Cretaceous and many such early flower fossils are represented by charcoalified fragments, lacking complete delicate structures and surface textures, making their similarity to living forms difficult to discern. Furthermore, scarcity of information about the ecology of early angiosperms makes it difficult to test hypotheses about the drivers of their diversification, including the role of fire in shaping flowering plant evolution. We report the discovery of two exquisitely preserved fossil flower species, one identical to the inflorescences of the extant crown-eudicot genus Phylica and the other recovered as a sister group to Phylica, both preserved as inclusions together with burned plant remains in Cretaceous amber from northern Myanmar (~99 million years ago). These specialized flower species, named Phylica piloburmensis sp. nov. and Eophylica priscastellata gen. et sp. nov., exhibit traits identical to those of modern taxa in fire-prone ecosystems such as the fynbos of South Africa, and provide evidence of fire adaptation in angiosperms.

The evolution of insect biodiversity.

Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.

Salinella.

Erik Tihelka and Chenyang Cai introduce Salinella, a cryptic basal metazoan taxon.

Murcybolus gen. nov., a new net-winged beetle genus from mid-Cretaceous Burmese amber (Coleoptera: Lycidae: Burmolycini).

A new lycid beetle, Murcybolus longiantennus gen. et sp. nov., is reported from mid-Cretaceous Burmese amber (ca. 99 Ma). Murcybolus is placed in the recently erected fossil tribe Burmolycini based on the fully metamorphosed female, 10-segmented antennae, and pronotal disc with deep rounded punctures but without carinae. Murcybolus differs from the other genus in Burmolycini, Burmolycus, by its antennal morphology and elytral venation.

Angiosperm pollinivory in a Cretaceous beetle.

Despite the crucial importance of flower-visiting insects in modern ecosystems, there is little fossil evidence on the origins of angiosperm pollination. Most reports of pollination in the Mesozoic fossil record have been based on the co-occurrence of the purported pollinators with pollen grains and assumed morphological adaptations for vectoring pollen. Here, we describe an exceptionally preserved short-winged flower beetle (Cucujoidea: Kateretidae) from mid-Cretaceous amber, Pelretes vivificus gen. et sp. nov., associated with pollen aggregations and coprolites consisting mainly of pollen, providing direct evidence of pollen-feeding in a Cretaceous beetle and confirming that diverse beetle lineages visited early angiosperms in the Cretaceous. The exquisite preservation of our fossil permits the identification of the pollen grains as Tricolpopollenites (Asteridae or Rosidae), representing a record of flower beetle pollination of a group of derived angiosperms in the Mesozoic and suggesting that potentially diverse beetle lineages visited early angiosperms by the mid-Cretaceous.

Cretophengodidae, a new Cretaceous beetle family, sheds light on the evolution of bioluminescence.

Bioluminescent beetles of the superfamily Elateroidea (fireflies, fire beetles, glow-worms) are the most speciose group of terrestrial light-producing animals. The evolution of bioluminescence in elateroids is associated with unusual morphological modifications, such as soft-bodiedness and neoteny, but the fragmentary nature of the fossil record discloses little about the origin of these adaptations. We report the discovery of a new bioluminescent elateroid beetle family from the mid-Cretaceous of northern Myanmar (ca 99 Ma), Cretophengodidae fam. nov. Cretophengodes azari gen. et sp. nov. belongs to the bioluminescent lampyroid clade, and would appear to represent a transitional fossil linking the soft-bodied Phengodidae + Rhagophthalmidae clade and hard-bodied elateroids. The fossil male possesses a light organ on the abdomen which presumably served a defensive function, documenting a Cretaceous radiation of bioluminescent beetles coinciding with the diversification of major insectivore groups such as frogs and stem-group birds. The discovery adds a key branch to the elateroid tree of life and sheds light on the evolution of soft-bodiedness and the historical biogeography of elateroid beetles.

On the Nosodendridae from mid-Cretaceous amber of northern Myanmar (Coleoptera: Nosodendroidea).

Nosodendridae is a small polyphagan beetle family with a sparse fossil record. Herein, the fossil Nosodendridae from mid-Cretaceous Burmese amber (ca. 99 Ma) are systematically reviewed. Nosodendron cretaceum Deng et al. is transferred into Archaenosodendron Li Cai gen. nov., as A. cretaceum (Deng et al.) comb. nov., primarily based on the morphology of prosternum. Three new species of Archaenosodendron from Burmese amber, A. explanatum Li Cai sp. nov., A. remotidens Li Cai sp. nov., and A. angulare Li Cai sp. nov., are also described and illustrated. A key to nosodendrid genera and species from Burmese amber is provided.

First fossil pseudopsine rove beetle from mid-Cretaceous Burmese amber (Coleoptera: Staphylinidae: Pseudopsinae).

Pseudopsinae represented by four genera with just over 50 species in the Recent fauna represent one of the smallest subfamilies of the megadiverse family Staphylinidae. Here we describe the first fossil member of the subfamily Pseudopsinae. Cretopseudopsis maweii gen. et sp. nov. preserved in mid-Cretaceous Burmese amber (ca. 99 Ma) is distinguished from extant pseudopsine genera by head not carinate, apical maxillary palpomere only slightly narrower than penultimate segment, subocular carinae absent, temples short, pronotal lateral margin smoothly rounded, and mesocoxae separated by an elongate process of the mesoventrite. Our discovery of Cretopseudopsis gen. et sp. nov. provides evidence that the subfamily Pseudopsinae originated by the Albian-Cenomanian and suggests a Gondwanan distribution of the group in the Cretaceous.

Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera).

Western honey bees (Apis mellifera) are one of the most important pollinators of agricultural crops and wild plants. Despite the growth in the availability of sequence data for honey bees, the phylogeny of the species remains a subject of controversy. Most notably, the geographic origin of honey bees is uncertain, as are the relationships among its constituent lineages and subspecies. We aim to infer the evolutionary and biogeographical history of the honey bee from mitochondrial genomes. Here we analyse the full mitochondrial genomes of 18 A. mellifera subspecies, belonging to all major lineages, using a range of gene sampling strategies and inference models to identify factors that may have contributed to the recovery of incongruent results in previous studies. Our analyses support a northern African or Middle Eastern origin of A. mellifera. We show that the previously suggested European and Afrotropical cradles of honey bees are the result of phylogenetic error. Monophyly of the M, C, and O lineages is strongly supported, but the A lineage appears paraphyletic. A. mellifera colonised Europe through at least two pathways, across the Strait of Gibraltar and via Asia Minor.

Mimicry in Cretaceous Bugs.

Mimicry is ubiquitous in nature, yet understanding its origin and evolution is complicated by the scarcity of exceptional fossils that enable behavioral inferences about extinct animals. Here we report bizarre true bugs (Hemiptera) that closely resemble beetles (Coleoptera) from mid-Cretaceous amber. The unusual fossil bugs are described as Bersta vampirica gen. et sp. nov. and Bersta coleopteromorpha gen. et sp. nov. and are placed into a new family, Berstidae fam. nov. The specialized mouthparts of berstids indicate that they were predaceous on small arthropods. Their striking beetle-like appearance implies that they were either involved in defensive mimicry or mimicked beetles to attack unsuspecting prey. The latter would represent the first case of aggressive mimicry in the invertebrate fossil record. These findings enrich our understanding of the paleoecological associations and extinct behavioral strategies of Mesozoic insects.

Structural colours in diverse Mesozoic insects.

Structural colours, nature's most pure and intense colours, originate when light is scattered via nanoscale modulations of the refractive index. Original colours in fossils illuminate the ecological interactions among extinct organisms and functional evolution of colours. Here, we report multiple examples of vivid metallic colours in diverse insects from mid-Cretaceous amber. Scanning and transmission electron microscopy revealed a smooth outer surface and five alternating electron-dense and electron-lucent layers in the epicuticle of a fossil wasp, suggesting that multilayer reflectors, the most common biophotonic nanostructure in animals and even plants, are responsible for the exceptional preservation of colour in amber fossils. Based on theoretical modelling of the reflectance spectra, a reflective peak of wavelength of 514 nm was calculated, corresponding to the bluish-green colour observed under white light. The green to blue structural colours in fossil wasps, beetles and a fly most likely functioned as camouflage, although other functions such as thermoregulation cannot be ruled out. This discovery not only provides critical evidence of evolution of structural colours in arthropods, but also sheds light on the preservation potential of nanostructures of ancient animals through geological time.

Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga).

Diving beetles and their allies are an almost ubiquitous group of freshwater predators. Knowledge of the phylogeny of the adephagan superfamily Dytiscoidea has significantly improved since the advent of molecular phylogenetics. However, despite recent comprehensive phylogenomic studies, some phylogenetic relationships among the constituent families remain elusive. In particular, the position of the family Hygrobiidae remains uncertain. We address these issues by re-analyzing recently published phylogenomic datasets for Dytiscoidea, using approaches to reduce compositional heterogeneity and adopting a site-heterogeneous mixture model. We obtained a consistent, well-resolved, and strongly supported tree. Consistent with previous studies, our analyses support Aspidytidae as the monophyletic sister group of Amphizoidae, and more importantly, Hygrobiidae as the sister of the diverse Dytiscidae, in agreement with morphology-based phylogenies. Our analyses provide a backbone phylogeny of Dytiscoidea, which lays the foundation for better understanding the evolution of morphological characters, life habits, and feeding behaviors of dytiscoid beetles.