Diversity Patterns Research Articles

Diversification and extinction of Hemiptera in deep time

Untangling the patterns and drivers behind the diversification and extinction of highly diversified lineages remains a challenge in evolutionary biology. While insect diversification has been widely studied through the “Big Four” insect orders (Coleoptera, Hymenoptera, Lepidoptera and Diptera), the fifth most diverse order, Hemiptera, has often been overlooked. Hemiptera exhibit a rich fossil record and are highly diverse in present-day ecosystems, with many lineages closely associated to their host plants, making them a crucial group for studying how past ecological shifts—such as mass extinctions and floral turnovers—have influenced insect diversification. This study leverages birth-death models in a Bayesian framework and the fossil record of Hemiptera to estimate their past diversity dynamics. Our results reveal that global changes in flora over time significantly shaped the evolutionary trajectories of Hemiptera. Two major faunal turnovers particularly influenced Hemiptera diversification: (i) the aftermath of the Permo-Triassic mass extinction and (ii) the Angiosperm Terrestrial Revolution. Our analyses suggest that diversification of Hemiptera clades was driven by floristic shifts combined with competitive pressures from overlapping ecological niches. Leveraging the extensive fossil record of Hemiptera allowed us to refine our understanding of diversification patterns across major hemipteran lineages.

The proteotranscriptomic characterization of venom in the white seafan Eunicella singularis elucidates the evolution of Octocorallia arsenal.

All the members of the phylum Cnidaria are characterized by the production of venom in specialized structures, the nematocysts. Venom of jellyfish (Medusozoa) and sea anemones (Anthozoa) has been investigated since the 1970s, revealing a remarkable molecular diversity. Specifically, sea anemones harbour a rich repertoire of neurotoxic peptides, some of which have been developed in drug leads. However, venoms of the vast majority of Anthozoa species remain uncharacterized, particularly in the class Octocorallia. To fill this gap, we applied a proteo-transcriptomic approach to investigate venom composition in Eunicella singularis, a gorgonian species common in Mediterranean hard-bottom benthic communities. Our results highlighted the peculiarities of the venom of E. singularis with respect to sea anemones, which is reflected in the presence of several toxins with novel folds, worthy of functional characterization. A comparative genomic survey across the octocoral radiation allowed us to generalize these findings and provided insights into the evolutionary history, molecular diversification patterns and putative adaptive roles of venom toxins. A comparison of whole-body and nematocyst proteomes revealed the presence of different cytolytic toxins inside and outside the nematocysts. Two instances of differential maturation patterns of toxin precursors were also identified, highlighting the intricate regulatory pathways underlying toxin expression.

Evolutionary lability of a key innovation spurs rapid diversification.

Rates of lineage diversification vary considerably across the tree of life, often asa result of evolutionary innovations1-5. Although the ability to produce new traits can vary between clades and may drive ecological transitions6-9, the impact of differences in the pace at which innovations evolve at macroevolutionary scales has been overlooked. Complex teeth are one innovation that contributed to the evolutionary success of major vertebrate lineages10-12. Here we show that evolutionary lability of tooth complexity, but not complexity itself, spurs rapid diversification across ray-finned fishes. Speciation rates are five times higher when transitions between simple and complex teeth occur rapidly. We find that African cichlids are unique among all fishes; they are dominated by lineages that transition between simple and complex teeth at unparalleled rates. This innovation interacted with the ecological versatility of complex teeth to spur rapid adaptive radiations in lakes Malawi, Victoria and Barombi Mbo. The marked effect on diversification stems from the tight association of tooth complexity with microhabitat and diet. Our results show that phylogenetic variation in how innovations evolve can have a stronger effect on patterns of diversification than the innovation itself. Investigating the impact of innovations from this new perspective will probably implicate more traits in causing heterogeneous diversification rates across the tree of life.

Revisiting the backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes.

The angiosperm tribe of Elsholtzieae (Lamiaceae) is characterized by complex inflorescences and has notable medicinal and economic significance. Relationships within Elsholtzieae, including the monophyly of Elsholtzia and Keiskea, and relationships among Mosla, Keiskea and Perilla, remain uncertain, hindering insights into inflorescence evolution within the tribe. Using hybridization capture sequencing and deep genome skimming data analysis, we reconstruct a phylogeny of Elsholtzieae using 279 orthologous nuclear loci from 56 species. We evaluated uncertainty among relationships using concatenation, coalescent and network approaches. Using a time-calibrated phylogeny, we reconstructed ancestral inflorescence traits to elucidate the patterns in their evolution within the tribe. Our analyses consistently support the paraphyly of the genus Elsholtzia. Phylogenetic network analyses, confirmed by PhyloNetworks and SplitsTree, showed reticulation events among the major lineages of Elsholtzieae. The unstable polyphyly of Keiskea observed in ASTRAL (accurate species tree algorithm), ML (maximum likelihood) and MP (maximum parsimony) analyses may be related to introgression from Perilla and Mosla. Based on the analyses of phylogenetic trees within Elsholtzieae, the evolutionary trajectory of inflorescences demonstrates a pattern of diversification, with specialization as one aspect of this process. Elsholtzieae support the hypothesis that compressed inflorescences evolved from larger and more complex ancestral forms through successive compressions of the inflorescence axis. Additionally, certain lineages within the tribe display a trend towards simplified inflorescences, characterized by a reduction in the number of florets. This highlights both the specialization and the diversity in the evolution of inflorescence structures within the tribe.

Rapid speciation of Chinese hypogean fishes driven by paleogeoclimatic and morphological adaptations

Abstract Major geoclimatic events trigger clade divergence, shaping diversification patterns. However, the influence of historical geoclimatic events on the diversification of subsurface biota remains poorly understood. This study investigates the phylogeny and evolutionary history of under-recognized hypogean fishes in the Nemacheilidae family (HFN) in southwestern China, using mitogenome and nuclear gene sequencing. Our phylogeny supports the current genus-level classification but reveals conflicts between mitochondrial and nuclear gene topologies, suggesting past hybridization events. The ancestor of the HFN originated in eastern China–Korean Peninsula–Japanese Islands, north of northwest China–Mongolian Plateau, the Qinghai-Xizang (Tibetan) Plateau–Hengduan Mountains during the late Eocene (~36 million years ago (Mya)) and early Miocene (~16 Mya), and dispersed twice into the karst region of southwestern China. An ancient radiation event occurred from 22.44 Mya to 12.25 Mya. In situ diversification is the major speciation event, originating around 30 Mya and increasing sharply at ~11 Ma, with three peaks at ~7 Mya, ~3 Mya, and 1 Mya, and two valleys at ~5 Mya and ~2 Mya. Ancestral state reconstruction suggests at least four independent origins for the colorless, eye-blind, and troglobitic species morphs, as opposed to two events for the caudal adipose keel, and that these traits have undergone multiple reversals. These results highlight the role of geological processes and climatic events in the evolution of hypogean fishes and provide insights for conservation efforts, particularly in specialized cave habitats.

A New Pattern of Species Diversification Revealed by Populus on the Qinghai-Tibet Plateau

A New Pattern of Species Diversification Revealed by Populus on the Qinghai-Tibet Plateau

Dataset on the patterns of livelihood diversification in farming systems of the Eastern Gangetic Plains of South Asia

Dataset on the patterns of livelihood diversification in farming systems of the Eastern Gangetic Plains of South Asia

Integrating Historical biogeography and Pliocene climate fluctuation to Unraveling the evolution of Tigris-Euphrates drainage basin through widespread freshwater Barbinae (Cypriniformes: Cyprinidae)

The formation history of the Tigris-Euphrates basins (TEB) and Karun River remains mostly unknown. To unravel the evolutionary history of the TEB and Karun River, we integrated the biogeography and climatic niche models of the freshwater fish with the largest natural distribution pattern. This study investigates 16 species of the Barbinae subfamily with wide distributions and high diversity. Mitochondrial Cytb and COI genes were obtained from various locations via GenBank and utilized to generate a dated phylogeny and reconstructed ancestral areas with the BioGeoBEARS model. We used the BAMM tools to estimate rates of diversification through time. Furthermore, by integrating potential geographic distribution with four spatial climate variables including max temperature of warmest month, min temperature of coldest month, temperature annual range and annual precipitation, we reconstruct ancestral predicted niche occupancy (PNO) profiles using ecological niche modeling (ENM) method. Based on the evolution of endemic TEB and Karun River Barbinae, we hypothesize that ancestral clades appeared in the TEB in the late Oligocene/early Miocene (∼23.12 Mya) and dispersed to the basin from the mid-Miocene onward (∼14.33 Mya). Our results suggest that the mid-Miocene uplift of the Zagros Mountains likely impacted Karun River flow in southwestern Iran, contributing to the observed diversification patterns in Barbinae. In addition, niche divergence was dominant in Barbinae diversification, alongside phylogenetic niche conservatism. The study introduces a method combining phylogenetic, biogeographic, and niche modeling data to explore freshwater fish evolution in the Tigris-Euphrates and Karun basins, highlighting geological impacts on biodiversity and diversification processes.

ECE-CYC1 Transcription Factor CmCYC1a May Interact with CmCYC2 in Regulating Flower Symmetry and Stamen Development in Chrysanthemum morifolium.

The attractive inflorescence of Chrysanthemum morifolium, its capitulum, is always composed of ray (female, zygomorphy) and disc (bisexual, actinomorphy) florets, but the formation mechanism remains elusive. The gene diversification pattern of the ECE (CYC/TB1) clade has been speculated to correlate with the capitulum. Within the three subclades of ECE, the involvement of CYC2 in defining floret identity and regulating flower symmetry has been demonstrated in many species of Asteraceae, including C. morifolium. Differential expression of the other two subclade genes, CYC1 and CYC3, in different florets has been reported in other Asteraceae groups, yet their functions in flower development have not been investigated. Here, a CYC1 gene, CmCYC1a, was isolated and its expression pattern was studied in C. morifolium. The function of CmCYC1a was identified with gene transformation in Arabidopsis thaliana and yeast two-hybrid (Y2H) assays were performed to explore the interaction between CmCYC1 and CmCYC2. CmCYC1a was expressed at higher levels in disc florets than in ray florets and the expression of CmCYC1a was increased in both florets during the flowering process. Overexpression of CmCYC1a in A. thaliana changed flower symmetry from actinomorphic to zygomorphic, with fewer stamens. Furthermore, CmCYC1a could interact with CmCYC2b, CmCYC2d, and CmCYC2f in Y2H assays. The results provide evidence for the involvement of CmCYC1a in regulating flower symmetry and stamen development in C. morifolium and deepen our comprehension of the contributions of ECE genes in capitulum formation.

Historical biogeography and systematics of yellow-bellied toads (Bombina variegata), with the description of a new subspecies from the Balkans

Abstract The Balkan Peninsula hosts a great proportion of Europe’s biodiversity, and this is well illustrated by amphibian richness and endemism. Among them, the yellow-bellied toad Bombina variegata has been a model in ecology and evolution, but several aspects of its phylogeography and taxonomy remain surprisingly poorly understood. In this study, we combine cytochrome b DNA barcoding data (1238 individuals from 355 localities), mitogenome phylogenetics (17.2 kb), gene-based nuclear phylogenetics (3.7 kb from four gene fragments) and multilocus phylogenomics (4759 loci / ~554 kb obtained by double digest Restriction Associated DNA sequencing; ddRAD-seq) to re-assess the diversification of B. variegata, and revisit its nomenclatural history to assign scientific names to phylogeographic lineages. The analyses support four major lineages, one assigned to B. v. variegata (Carpathians and northwestern ranges), one assigned to B. v. pachypus (Apennine Peninsula), and two assigned to B. v. scabra (Dinarides, Hellenides and Balkanides vs. the Rhodope mountains). Spatiotemporal patterns of diversification suggest a role for a Late Miocene marine incursion in the Pannonian Plain (Paratethys) as the initial trigger of divergence, followed by a vicariance event in the Apennines and a “sky island” process of Pleistocene differentiation in the Balkan Peninsula. As it reached the Dinarides during the Late Pleistocene, B. v. variegata potentially hybridized with B. v. scabra and captured its mitochondrial DNA, which resulted in a massive cyto-nuclear discordance across all northwestern European populations. Finally, we show that the two lineages of B. v. scabra significantly differ in morphology and ventral coloration patterns, and describe the Rhodope lineage as a new subspecies.

Picornaviridae and Caliciviridae diversity in Madagascar fruit bats is driven by cross-continental genetic exchange.

Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Divergent Caliciviridae and Picornaviridae (families within the Picornavirales ) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Bats live in close proximity to and are consumed widely as a food source by humans in Madagascar, providing opportunities for zoonotic transmission. Prior work in Madagascar has described numerous evolutionarily divergent bat viruses, some with zoonotic potential. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats ( Eidolon dupreanum , Pteropus rufus , and Rousettus madagascariensis ), we recovered 13 full-length and 37 partial-length genomic sequences within the order Picornavirales (36 Picornaviridae and 14 Caliciviridae sequences), which we identify and describe here. We find evidence that genetic exchange between mainland African bat and Madagascar bat Picornavirales likely shaped the diversification patterns of these novel sequences through recombination events between closely related Picornavirales ; thus far, high host fidelity appears to have limited these viruses from spilling over into other species.

Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species.

Patterns of Genetic and Morphological Variability of Teucrium montanum sensu lato (Lamiaceae) on the Balkan Peninsula.

The Balkan Peninsula represents an important center of plant diversity, exhibiting remarkable ecological heterogeneity that renders it an optimal region for studying the diversification patterns of complex taxa such as Teucrium montanum. In the Balkan Peninsula, T. montanum is a highly plastic and morphologically variable species with unresolved taxonomic status. To ascertain the patterns of genetic and morphological diversification, a comparative genetic and morphological analysis was conducted. In total, 57 populations were subjected to analysis using AFLP and a multivariate morphometric approach. A Bayesian analysis of population structure distinguished two main genetic clusters, labelled A and B. Cluster B was found to be geographically restricted to the northwestern Dinarides, while cluster A occurred in the rest of the Balkans. Genetic cluster A was further subdivided into four subclusters that were spatially separated from each other. The contact populations between the subclusters exhibited a mixed genetic structure. There was a partial correlation between genetic and morphological diversification. The peripheral populations of the genetic clusters displayed morphological differences, while both genetic and morphological differences decreased in the contact zones. The observed genetic structure can be attributed to the reproductive biology of this species and the complex geological history of the Balkan Peninsula.

Comparative Analysis of Drosophila Bam and Bgcn Sequences and Predicted Protein Structural Evolution.

The protein encoded by the Drosophila melanogaster gene bag of marbles (bam) plays an essential role in early gametogenesis by complexing with the gene product of benign gonial cell neoplasm (bgcn) to promote germline stem cell daughter differentiation in males and females. Here, we compared the AlphaFold2 and AlphaFold Multimer predicted structures of Bam protein and the Bam:Bgcn protein complex between D. melanogaster, D. simulans, and D. yakuba, where bam is necessary in gametogenesis to that in D. teissieri, where it is not. Despite significant sequence divergence, we find very little evidence of significant structural differences in high confidence regions of the structures across the four species. This suggests that Bam structure is unlikely to be a direct cause of its functional differences between species and that Bam may simply not be integrated in an essential manner for GSC differentiation in D. teissieri. Patterns of positive selection and significant amino acid diversification across species is consistent with the Selection, Pleiotropy, and Compensation (SPC) model, where detected selection at bam is consistent with adaptive change in one major trait followed by positively selected compensatory changes for pleiotropic effects (in this case perhaps preserving structure). In the case of bam, we suggest that the major trait could be genetic interaction with the endosymbiotic bacteria Wolbachia pipientis. Following up on detected signals of positive selection and comparative structural analysis could provide insight into the distribution of a primary adaptive change versus compensatory changes following a primary change.

Exploring latitudinal gradients and environmental drivers of amphipod biodiversity patterns regarding depth and habitat variations

Amphipods are known as umbrella species in conservation biology that their protection indirectly protects other species. Recent hypotheses suggest a bimodal latitudinal global species richness pattern for amphipods, irrespective of species’ depth or habitat type. Phylogeographic hypotheses suggested two distinct procedures for amphipod diversification: ecological radiation and Pangea fragmentation. This study aimed to revisit the bimodal latitudinal pattern of species richness for amphipods, investigate similarities in species composition and main environmental amphipod distribution drivers regarding their depth and habitat variations. The comprehensive database was collected from open-access data and a personal sampling database from the Persian Gulf and the Gulf of Oman. After rigorous data quality controls, the final dataset comprised 1,142,416 distribution records of 6,424 accepted marine amphipod species distributed from 0 to 10,900 m depth. All the species were grouped into pelagic and benthic, shallow-water (> 200 m), and deep-sea (< 200 m). Alpha and gamma species richness and the expected number of species per 50 random samples (ES50) were calculated. Our findings showed that species richness patterns in amphipods are shaped not only by habitat types but also by depth, and they are not significantly bimodal in all groups. Also, the Beta diversity of benthic species revealed distinct diversification patterns between benthic and pelagic species. The species similarity clusters revealed a fragmentation between Gondwana and Laurasia for shallow benthic species. However, the similarity between pelagic amphipod communities is more compatible with ecological parameters. Generalized Additive Models (GAMs) highlighted that environmental variables play a significant role in species distributions, for example, temperature and chlorophyll levels were the main predictors of species richness in shallow waters. However, a complete effect of multiple environmental variables is responsible for deep-sea species gradients. These findings are crucial information to be considered when managing the species richness and establishing conservation priorities for their habitats.

Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards.

-Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a 2 species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.

Tempo and mode of diversification of the red devil spiders (Araneae: Dysderidae) of the Canary Islands

AbstractThe study of adaptive radiations has shed light on our current understanding of evolution. However, previous studies examining the mode in which species diversified, how diversification rates varied, and how ecological specialisation affected these processes have found few different results across different taxa and geographic and ecological systems, showing how complex this process is. To gain a more complete picture of how species evolve, additional model systems that encompass alternative ecological requirements are needed. Here, we present the results of a study aimed at unravelling the diversification mode and evolutionary drivers of the spider genus Dysdera, the red devil spiders, endemic to the Canary Islands. These species exhibit remarkable phenotypic variability in their mouthparts, which has been related to different levels of specialisation in the predation of isopods. We explored patterns of lineage diversification and assessed the role of trophic specialisation as a driver of species diversification. Additionally, we used climatic variables, occurrence data and morphological information to unravel the underlying mode of speciation by means of joint species distribution models and age‐range correlation methods. Our results reveal that red devil spiders underwent an early burst of diversification, followed by a slowdown of diversification rates, which is a hallmark of adaptive radiation. We also found evidence that the trophic morphology shaped diversification, with specialist species exhibiting higher rates of diversification. Finally, our analyses suggest that speciation occurred mostly in allopatry, with subsequent secondary sympatry following range expansion.

Ecological and Evolutionary Factors Contribute to the Uneven Diversification of Firs in the Northern Hemisphere

ABSTRACTAimThe Northern Hemisphere harbours the greatest diversity of temperate plants on Earth, with East Asia having the highest species richness compared with North America and Europe. When and how this uneven diversification pattern emerged remains unclear. Here, we use a conifer genus that forms extensive forests in the Northern Hemisphere to explore a fundamental question in ecology and evolution: what processes underlie temperate biodiversity through time and space?LocationThe Northern Hemisphere.TaxonAbies.MethodsTo reconstruct a well‐supported framework for estimating diversification rate, we performed phylogenetic analyses using concatenation and coalescent methods based on 58 fir taxa and 56 nuclear single‐copy genes. Niche evolution was explored using species occurrence data and environmental factors based on the l1ou model. Multiple regression was carried out to identify correlations between species richness and environmental variables at global and regional scales, to evaluate factors of species diversity preference, and potentially to explain the evolutionary history of firs.ResultsWe identified East Asia as having the highest species diversity and speciation rate. Two clade‐specific niche shifts corresponding with the distribution of firs were detected, one in the Himalaya‐Hengduan Mountains (c. 12.2 Ma) and the other in the Mexican highlands (c. 14.3 Ma), but none in the Euro‐Mediterranean region. Fir species richness increased with cool temperatures both globally and regionally. Seasonal precipitation showed significant positive correlation to species richness on a global scale and in North America and the Euro‐Mediterranean region. Soil factors showed significant trends and moderate correlations with species richness in the Himalaya‐Hengduan Mountains and Mexican highlands.Main ConclusionsOur results indicate that modern firs prefer cool climates with seasonal rainfall. East Asian firs experienced niche shifts with the Himalayan orogeny in the Middle Miocene. Novel heterogeneous habitats due to changes in topography and the establishment of a monsoon climate, accompanied by niche shift, can account for the high speciation of firs in East Asia. A similar process is found in the Mexican highland firs. In contrast, cold–dry continental climate in North America since the late Paleogene and the lack of seasonal rainfall and relatively stable topography in the Euro‐Mediterranean region are the main limiting factors for fir diversification. Our study rejects the ‘clade age’ hypothesis but supports the hypothesis that niche shift related to high diversification rate triggered by environmental heterogeneity underlies the uneven species diversity of the Northern Hemisphere.

Unified Assembly of Chloroplast Genomes: A Comparative Study of Grapes Representing Global Geographic Diversity

The genus Vitis, known for its economically important fruit—grape—is divided into three geographical groups, American, East Asian, and Eurasian, along with a hybrid group. However, previous studies on grape phylogeny using chloroplast genomes have been hindered by limited sample sizes and inconsistent methodologies, resulting in inaccuracies. In this study, we employed the GetOrganelle software with consistent parameters to assemble the chloroplast genomes of 21 grape cultivars, ensuring comprehensive representation across four distinct groups. A comparative analysis of the 21 grape cultivars revealed structural variation, showing chloroplast genome sizes ranging from 160,813 bp to 161,275 bp. In 21 Vitis cultivars, genome annotation revealed 134 to 136 genes, comprising 89 to 91 protein-coding genes (PCGs), 37 tRNAs, and 8 rRNAs. Our observations have pinpointed specific occurrences of contraction and expansion phenomena at the interfaces between inverted repeat (IR) regions and single-copy (SC) regions, particularly in the vicinity of the rpl2, ycf1, ndhF, and trnN genes. Meanwhile, a total of 193 to 198 SSRs were identified in chloroplast genomes. The diversification pattern of chloroplast genomes exhibited strong concordance with the phylogenetic relationships of the Euvitis subgenera. Phylogenetic analysis based on conserved chloroplast genome strongly clustered the grape varieties according to their geographical origins. In conclusion, these findings enhance our understanding of chloroplast genome variation in Vitis populations and have important implications for cultivar selection, breeding, and conservation efforts.

Phylogeny and evolution of larval feeding mode in the megadiverse superfamily Sciaroidea (Diptera)

Abstract Sciaroidea is a megadiverse clade within Diptera that exhibits diverse larval feeding modes. In this study, we explored the phylogenetic relationships and evolution of larval feeding modes within the superfamily using a fossil-calibrated time tree. We found that filtering out potentially fast-evolving sites altered the family-level tree topology, and that species within Sciaroidea incertae sedis might be crucial in determining the general tree topology. The most recent common ancestor of Sciaroidea was inferred to have originated in the Upper Triassic (~225 Ma). A major radiation of families occurred from the Uppermost Triassic to the Lowermost Jurassic (190–200 Ma). The ancestral larval feeding mode was inferred to be mycophagy. Most families retained this feature with only minor transitions occurring in some clades; however, Cecidomyiidae and Keroplatidae went through notable shifts in larval feeding mode. Cecidomyiidae underwent a transition from mycophagy to phytophagy in the Lower Cretaceous, in line with angiosperm radiation as suggested in previous studies. The larvae of stem Keroplatidae were inferred to be predators since the Jurassic. A transition back to mycophagy occurred within the subfamily Keroplatinae during the Paleogene to Uppermost Cretaceous, coinciding with the origin and radiation of species-rich mycophagous clades of other sciaroid families. Our study highlights the importance of taxon sampling and sequence filtering in phylogenetic analyses of Sciaroidea. We suggest, based on temporal patterns of lineage diversification, that the evolution of larval feeding modes within the group might be correlated with the diversification of mushroom-forming fungi and angiosperms.