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

MRI-Seed-Wizard: combining deep learning algorithms with magnetic resonance imaging enables advanced seed phenotyping

Evaluation of relevant seed traits is an essential part of most plant breeding and biotechnology programmes. There is a need for non-destructive, three-dimensional assessment of the morphometry, composition, and internal features of seeds. Here, we introduce a novel tool, MRI-Seed-Wizard, which integrates deep learning algorithms with non-invasive magnetic resonance imaging (MRI) for use in a new domain-plant MRI. The tool enabled in vivo quantification of 23 grain traits, including volumetric parameters of inner seed structure. Several of these features cannot be assessed using conventional techniques, including X-ray computed tomography. MRI-Seed-Wizard was designed to automate the manual processes of identifying, labeling, and analysing digital MRI data. We further provide advanced MRI protocols that allow the evaluation of multiple seeds simultaneously to increase throughput. The versatility of MRI-Seed-Wizard in seed phenotyping is demonstrated for wheat (Triticum aestivum) and barley (Hordeum vulgare) grains, and it is applicable to a wide range of crop seeds. Thus, artificial intelligence, combined with the most versatile imaging modality, MRI, opens up new perspectives in seed phenotyping and crop improvement.

Recent Southern Hemisphere Lamprimine Stag Beetle in Cretaceous Burmese Amber and Its Biogeographic Implications (Coleoptera: Lucanidae)

A new stag beetle fossil, Prostreptocerus burmiticus Yu & Cai gen. et sp. nov., is described based on a single male specimen. This is the first representative of the subfamily Lampriminae (Coleoptera: Scarabaeoidea: Lucanidae) from mid-Cretaceous Burmese amber. The new species is distinctive among Lucanidae due to its well-developed, right-angled mandible, frons featuring a pair of large protuberances, a coarse and sparsely punctate elytral disc, and large tubercles on the humeri. Prostreptocerus Yu & Cai is placed within Lampriminae based on several key characteristics. Morphologically, it is most similar to the extant Streptocerus Fairmaire, 1850. The current distribution of Streptocerus and Lampriminae is primarily restricted to the Southern Hemisphere, suggesting that this lineage is ancient and existed on Gondwanaland, which has significant geographical implications. This discovery extends the fossil record of Lampriminae and provides additional evidence for the existence of sexual dimorphism and potential combat behavior in Mesozoic lucanids. Additionally, Electraesalopsis Bai, Zhang & Qiu, 2017, previously placed as Lucanidae incertae sedis, shares many characteristics with Prostreptocerus Yu & Cai and is also assigned to Lampriminae based on a suite of traits.

Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants

The aquatic plant Nymphaea, a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae, has been extensively studied. However, the availability of chloroplast genome data for this genus is incomplete, and phylogenetic relationships within the order Nymphaeales remain controversial. In this study, 12 chloroplast genomes of Nymphaea were assembled and analyzed for the first time. These genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also report on codon usage, RNA editing sites, microsatellite structures, and new repetitive sequences in this genus. Comparative genomics revealed that expansion and contraction of IR regions can lead to changes in the gene numbers. Additionally, it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic regions. Furthermore, the phylogenetic tree showed the order Nymphaeales was divided into three families, and the genus Nymphaea can be divided into five (or three) subgenera, with the subgenus Nymphaea being the oldest. The divergence times of nymphaealean taxa were analyzed, with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years, respectively. The results of the phylogenetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00242-0.

A light in the dark: a mid-Cretaceous bioluminescent firefly with specialized antennal sensory organs

The beetle superfamily Elateroidea comprises the most biodiverse bioluminescent insects among terrestrial light-producing animals. Recent exceptional fossils from the Mesozoic era and phylogenomic studies have provided valuable insights into the origin and evolution of bioluminescence in elateroids. However, due to the fragmentary nature of the fossil record, the early evolution of bioluminescence in fireflies (Lampyridae), one of the most charismatic lineages of insects, remains elusive. Here, we report the discovery of the second Mesozoic bioluminescent firefly, Flammarionella hehaikuni Cai, Ballantyne & Kundrata gen. et sp. nov., from the Albian/Cenomanian of northern Myanmar (ca 99 Ma). Based on the available set of diagnostic characters, we interpret the specimen as a female of stem-group Luciolinae. The fossil possesses deeply impressed oval pits on the apices of antennomeres 3-11, representing specialized sensory organs likely involved in olfaction. The light organ near the abdominal apex of Flammarionella resembles that found in extant light-producing lucioline fireflies. The growing fossil record of lampyrids provides direct evidence that the stunning light displays of fireflies were already established by the late Mesozoic.

Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus (Rhamnaceae)

Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01331-7.

Fossil flowers of Phylica support a 250 Ma origin for Rhamnaceae

A new fossil discovery reported by Shi et al. changes our understanding of the biogeographic history of the cosmopolitan family, Rhamnaceae. Flowering shoots of the African genus Phylica (Rhamnaceae) dated at 100 million years ago (Ma) imply a 250 Ma origin of the family in fire-prone Gondwanan vegetation that enabled overland dispersal to all continents where it is currently widespread.

Ancient Rhamnaceae flowers impute an origin for flowering plants exceeding 250-million-years ago

Setting the molecular clock to newly described 100-million-year-old flowering shoots of Phylica in Burmese amber enabled us to recalibrate the phylogenetic history of Rhamnaceae. We traced its origin to ∼260 million years ago (Ma) that can explain its migration within and beyond Gondwana since that time and implies an origin for flowering plants that stretches well beyond 290 Ma. Ancestral trait assignments also revealed that hard-seededness, fire-proneness, and to a lesser extent, heat-released seed dormancy, have a similarly long history in this clade.

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100-million-year-old fossils of Phylica (Rhamnaceae) have recently been described

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Phylogenetic reconstruction using them reveals a crown age for Rhamnaceae at 259 Ma

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Ancestral trait reconstruction shows the associated vegetation was fire prone 259 Ma

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These are the oldest flowering-plant ages and fire-related traits obtained so far

New Genus and Species of Empheriidae (Insecta: Psocodea: Trogiomorpha) and Their Implication for the Phylogeny of Infraorder Atropetae

Two species of psocids discovered from the Mid-Cretaceous Burmese amber, Latempheria kachinensis Li, Yoshizawa, and Yao, gen. et sp. nov. and Burmempheria curvatavena Li, Yoshizawa, and Yao, sp. nov., are described and assigned to the Empheriidae (Trogiomorpha: Atropetae) family. A phylogenetic analysis of the infraorder Atropetae is conducted based on 38 morphological characters of three outgroups and fifteen ingroups, which supported the monophyly of Atropetae including fossil and extant taxa. In the phylogenetic result, all the genera of fossil families Empheriidae and Archaeatropidae form a monophyletic group, sister to the extant members of Atropetae. The two fossil families also share a lot of similarities in morphology, locality, and geological period. Recently discovered fossil species exhibited combined morphological characters of both families. Based on these observations and the results of the phylogenetic analysis, Archaeatropidae is treated here as a new junior synonym of Empheriidae.

A New Subgenus and Species of Priochirus from Mid-Cretaceous Kachin Amber (Coleoptera: Staphylinidae: Osoriinae)

As one of the largest families of beetles (Coleoptera), the Staphylinidae (rove beetles and their relatives) are rich not only in extant species but also in a comparatively robust fossil record. Despite this preponderance of available fossil material, fossils of the diverse subfamily Osoriinae remain rare. Here, we describe a new ososriine species, Priochirus trisclerite sp. nov., from the mid-Cretaceous amber of Myanmar. The new specimen is similar to the only other definitive fossil of the genus, Priochirus thayerae Yamamoto 2019, and both are placed in the extinct subgenus Eopriochirus subgen. nov. The new species differs noticeably in a number of morphological details in relation to the submentum, gular sutures and protibial crenulae. The new fossil provides further evidence for understanding the radiation of staphylinoid beetles.

Fire-released seed dormancy - a global synthesis

Seed dormancy varies greatly between species, clades, communities, and regions. We propose that fireprone ecosystems create ideal conditions for the selection of seed dormancy as fire provides a mechanism for dormancy release and postfire conditions are optimal for germination. Thus, fire‐released seed dormancy should vary in type and abundance under different fire regimes. To test these predictions, we compiled data from a wide range of fire‐related germination experiments for species in different ecosystems across the globe. We identified four dormancy syndromes: heat‐released (physical) dormancy, smoke‐released (physiological) dormancy, non‐fire‐released dormancy, and non‐dormancy. In fireprone ecosystems, fire, in the form of heat and/or chemical by‐products (collectively termed ‘smoke’), are the predominant stimuli for dormancy release and subsequent germination, with climate (cold or warm stratification) and light sometimes playing important secondary roles. Fire (heat or smoke)‐released dormancy is best expressed where woody vegetation is dense and fires are intense, i.e. in crown‐fire ecosystems. In such environments, seed dormancy allows shade‐intolerant species to take advantage of vegetation gaps created by fire and synchronize germination with optimal recruitment conditions. In grassy fireprone ecosystems (e.g. savannas), where fires are less intense but more frequent, seed dormancy is less common and dormancy release is often not directly related to fire (non‐fire‐released dormancy). Rates of germination, whether controls or postfire, are twice as fast in savannas than in mediterranean ecosystems. Fire‐released dormancy is rare to absent in arid ecosystems and rainforests. The seeds of many species with fire‐released dormancy also possess elaiosomes that promote ant dispersal. Burial by ants increases insulation of seeds from fires and places them in a suitable location for fire‐released dormancy. The distribution of these dormancy syndromes across seed plants is not random – certain dormancy types are associated with particular lineages (phylogenetic conservatism). Heat‐released dormancy can be traced back to fireprone floras in the ‘fiery’ mid‐Cretaceous, followed by smoke‐released dormancy, with loss of fire‐related dormancy among recent events associated with the advent of open savannas and non‐fireprone habitats. Anthropogenic influences are now modifying dormancy‐release mechanisms, usually decreasing the role of fire as exaptive effects. We conclude that contrasting fire regimes are a key driver of the evolution and maintenance of diverse seed dormancy types in many of the world's natural ecosystems.