State Reconstruction Analysis Research Articles

Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini).

The Laufeia clade is a peculiar lineage of euophryine jumping spiders showing rapid divergence of male genital structures, especially the embolic complex that directly interacts with female genitalia during sperm transfer. With the rapid growth of species discovery and the perplexing morphology of male genitalia in the Laufeia clade, the controversy in its classification has become a crucial problem. In this study, we applied a phylogenomic approach using ultra-conserved elements data to infer the phylogeny of the Laufeia clade with extensive taxon sampling. A comparative morphological study was performed to evaluate diagnostic characters and understand the evolution of the male embolic complex within the Laufeia clade. The evolution of microhabitats (foliage, tree trunk, rock and surface litter) was also investigated to uncover the potential link between the microhabitat shifts and male embolic complex divergence. The results provide a strongly supported phylogenetic framework and updated generic concepts for the Laufeia clade. The synapomorphies for the updated genera within the Laufeia clade were identified through character mapping on the phylogeny. Ancestral state reconstruction analyses revealed that the Type I embolic complex (characterized by a disc-like embolic disc with a lamina as its outer edge) was ancestral and gradually evolved into the Type II (without lamina of embolic disc, base of embolic complex often modified into a functional "conductor") and Type III (lacking lamina of embolic disc and base of embolic complex) embolic complex, and that some embolic shapes evolved multiple times independently in different lineages of the Laufeia clade. The shift from foliage-dwelling to tree trunk-dwelling in the common ancestor of the Laufeia clade may have facilitated the divergent evolution of male embolic complex in the Laufeia clade. This study provides a solid foundation for future studies of systematics and evolution of this group.

The discovery of novel variants reveals the genetic diversity and potential origin of Seoul orthohantavirus.

Seoul orthohantavirus (SEOV) has been identified as one of the main causative agents of hemorrhagic fever with renal syndrome (HFRS) in China. The virus was found circulating in rodent populations in almost all provinces of the country, reflecting the wide distribution of HFRS. Here, using the direct immunofluorescence assay (DFA) and real-time quantitative reverse transcription PCR (qRT-PCR) approach, we performed screening in 1784 small mammals belonging to 14 species of three orders captured in the main areas of HFRS endemicity in Yunnan province (southwestern China) and identified 37 SEOV-positive rats (36 Rattus norvegicus and 1 Rattus tanezumi). A 3-year surveillance of HFRS epidemics and dynamics of rodent reservoir density and virus prevalence implied a potential correlation between them. The subsequent meta-transcriptomic sequencing and phylogenetic analyses revealed three SEOV variants, among which two are completely novel. The ancestral character state reconstruction (ACSR) analysis based on both novel variants and documented strains from 5 continents demonstrated that SEOV appeared to originate near the southwestern area (Yunnan-Kweichow Plateau) of China, then could spread to other regions and countries by their rodent carriers, resulting in a global distribution today. In summary, these data furthered the understanding regards genetic diversity and the potential origin for SEOV. However, the expanding endemic foci in the province suggest that the virus is spreading over a wider region and is much more diverse than previous depicted, which means that increased sampling is necessary.

Senecavirus cetus a novel picornavirus isolated from cetaceans represents a major host switching to the marine environment

Senecavirus A (SVA), an emerging virus that causes vesicular disease in swine, was, until recently, the only member of the Senecavirus genus (Picornaviridae). Here, we report the isolation and complete genome sequence of two isolates of cetacean picornavirus 1 (Senecavirus cetus), a novel picornavirus species of the Senecavirus genus from dead stranded cetaceans from Alaska. One isolate was from a harbor porpoise stranded in 2017, and another from a beluga whale, stranded in 2019. Whole-genome sequencing of Senecavirus cetus strains showed a genome-wide nucleotide identity of 98.8% and a genome size of 7455 nucleotides. The Senecavirus cetus genomes are most similar to SVA with a 58.3% genome-wide pairwise nucleotide identity. Infection of eleven available cell lines from terrestrial and aquatic animals showed that beluga and sheep cells were susceptible to infection by Senecavirus cetus. Phylogenetic and ancestral state reconstruction analyses supported the novel virus being a member of the Senecavirus genus and provided the first evidence of Senecavirus-like picornavirus infecting marine mammals and likely descending from a terrestrial host ancestor. These discoveries provided important information on the evolutionary relationships and taxonomy of picornaviruses and increased our understanding of the genomic characteristics and potential host range of Senecavirus cetus.

Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.

The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.

Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence

BackgroundBaolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences.ResultsWe sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat.ConclusionsComparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).

Phylogeny, character evolution and historical biogeography of Scurrulinae (Loranthaceae): new insights into the circumscription of the genus Taxillus

BackgroundExploring the relationship between parasitic plants and answering taxonomic questions is still challenging. The subtribe Scurrulinae (Loranthaceae), which has a wide distribution in Asia and Africa, provides an excellent example to illuminate this scenario. Using a comprehensive taxon sampling of the subtribe, this study focuses on infer the phylogenetic relationships within Scurrulinae, investigate the phylogeny and biogeography of the subtribe, and establish a phylogenetically-based classification incorporating both molecular and morphological evidence. We conducted phylogenetic, historical biogeography, and ancestral character state reconstruction analyses of Scurrulinae based on the sequences of six DNA regions from 89 individuals to represent all five tribes of the Loranthaceae and the dataset from eleven morphological characters.ResultsThe results strongly support the non-monophyletic of Scurrulinae, with Phyllodesmis recognized as a separate genus from its allies Taxillus and Scurrula based on the results from molecular data and morphological character reconstruction. The mistletoe Scurrulinae originated in Asia during the Oligocene. Scurrulinae was inferred to have been widespread in Asia but did not disperse to other areas. The African species of Taxillus, T. wiensii, was confirmed to have originated in Africa from African Loranthaceae ca. 17 Ma, and evolved independently from Asian members of Taxillus.ConclusionsThis study based on comprehensive taxon sampling of the subtribe Scurrulinae, strongly supports the relationship between genera. The taxonomic treatment for Phyllodesmis was provided. The historical biogeography of mistletoe Scurrulinae was determined with origin in Asia during the Oligocene. Taxillus and Scurrula diverged during the climatic optimum in the middle Miocene. Taxillus wiensii originated in Africa from African Loranthaceae, and is an independent lineage from the Asian species of Taxillus. Diversification of Scurrulinae and the development of endemic species in Asia may have been supported by the fast-changing climate, including cooling, drying, and the progressive uplift of the high mountains in central Asia, especially during the late Pliocene and Pleistocene.

Lilium liangiae, a new species in the genus Lilium (Liliaceae) that reveals parallel evolution within morphology.

The former genus Nomocharis, which has been merged as a clade within the genus Lilium (Liliaceae), represents one of the most complicated and unclear groups included in the latter. Research on members of the Nomocharis clade has been quite limited due to the sampling difficulties caused by its selective environmental preferences. In this study, we propose a new species within this clade, Lilium liangiae, as a further bridge connecting the former genus Nomocharis with other members of the genus Lilium. We conducted morphological clustering, phylogenetic, and comparative genomics analyses of nuclear internal spacers and the newly generated complete chloroplast genome, in conjunction with previously published sequences, and performed ancestral state reconstruction to clarify the evolutionary pattern of important traits in Lilium. The clustering results of 38 morphological traits indicated that the new species is allied to Nomocharis, further increasing the morphological polymorphism in the latter. The phylogenetic results and morphological clustering both supported L. liangiae belonging to the subclade Ecristata in Nomocharis, its closest affinity being Lilium gongshanense. Inconsistencies in phylogenetic relationships were detected between nuclear and plastid datasets, possibly due to ancient hybridization and ongoing introgression. Comparative genomics revealed the conservation and similarity of their chloroplast genomes, with variations observed in the expansion and contraction of the IR regions. A/T and palindromic repeat sequences were the most abundant. Seven highly variable regions (Pi≥0.015) were identified as potential molecular markers based on the chloroplast genomes of 47 species within Lilium. Both nuclear and plastid genes exhibited very low variability within the Nomocharis clade, contrasting with their highly variable morphological appearance. The ancestral state reconstruction analysis suggests that the campanulate flower form, as in L. liangiae, arose at least three times within the genus Lilium, revealing parallel evolution in the latter. Overall, this study adds important genetic and morphological evidence for understanding the phylogenetic relationships and parallel evolution patterns of species within the genus Lilium.

Morphology, Phylogeny, and Evolution of the Rarely Known Genus Admetella McIntosh, 1885 (Annelida, Polynoidae) with Recognition of Four New Species from Western Pacific Seamounts

The polynoid genus Admetella constitutes a deep‐sea assemblage of polychaetes, notable for their large bodies adorned with antennal scales positioned dorsally to the bases of lateral antennae. Furthermore, the genus exhibits swimming proficiencies facilitated by elongated parapodia and flattened chaetae. Despite the frequent encounters with Admetella members during various deep‐sea explorations, a substantial gap in our comprehension of their diversity, phylogeny, and evolutionary trajectories still exists. Our thorough morphological and phylogenetic investigations of specimens obtained from three seamounts located in the tropical western Pacific have unveiled six species belonging to the genus Admetella, four of these being newly identified as Admetella multiseta sp. nov., A. levensteini sp. nov., A. nanhaiensis sp. nov., and A. undulata sp. nov. The other two species of Admetella remain unidentifiable at the species level due to the loss of crucial details. Our phylogenetic analysis, grounded on 13 mitochondrial protein‐coding genes and the inclusion of 12S, 16S, 18S, 28S rRNA, and ITS1–ITS2 genes, substantiates the monophyly of Admetella. Admetella is positioned at an intermediate node within the phylogenetic tree, situated between representative shallow‐water and deep‐sea subfamilies. The independent evolution of antennal scales within Admetella among polynoids constitutes a synapomorphy for this genus. Ancestral state reconstruction (ASR) analyses suggest that deep‐sea polynoids evolved from shallow‐water ancestors that possessed lateral antennae, which were subsequently lost in members inhabiting extreme marine environments, such as deep‐sea hydrothermal vents and anchialine caves. The analysis further implicates that swimming ability independently evolved at least four times within the Polynoidae family.

Ancestral state reconstruction reveals extensive homoplasy in nutlet characters of Cynoglossinae (Boraginaceae, subfam. Cynoglossoideae, tribe Cynoglosseae)

Recent phylogenetic studies have challenged the traditional classification of the subtribe Cynoglossinae, which was based on nutlet characteristics. To investigate the evolution of fruit traits related to dispersal modes in this complex group, we conducted a study using scanning electron microscopy to examine 28 taxa representing all previously recognized lineages of the subtribe. Cynoglossinae displays four main types of nutlets: marginate, emarginate, flat wing, and incurved wing. Our findings reveal the arrangement of glochids and their structure, including the number of apical hooks, and their surface ornamentation is highly variable both across and within these four main types. We reconstructed the phylogenetic tree with four main clades (i.e., Clades I–IV) using Maximum likelihood analysis. In addition, we mapped four nutlet traits (i.e., nutlet margin, nutlet glochid, glochid sculpture, and glochid hooks) associated with different dispersal modes using ancestral state reconstruction analysis. The ancestor of subtribe Cynoglossinae was inferred to have marginate and glochidiate nutlets, with glochids externally provided with complex spiny tubercles and bearing at least four hooks at the tip as well as epizoochory dispersal mode. These ancestral states have been retained in Clade II (East Asian-Australian-African Cynoglossum-Lindelofia clade) and Clade III (Mediterranean-Asian Cynoglossum-Solenanthus-Trachelanthus clade), with several independent shifts to emarginate fruits. Transitions from marginate to wide-winged nutlets have occurred at least four independent times, facilitating wind-assisted dispersal in Clade I (Microparacaryum clade), Clade IV (Paracaryum-Mattiastrum-Rindera clade), Rindera tetraspis, and Mattiastrum crista-galli (both belonging to Clade III), where a transition from tuberculate to papillate surface has also occurred.

Phylogenetic reconstruction of Corydioidea (Dictyoptera: Blattodea) provides new insights on the placement of Latindiinae and supports the proposal of the new subfamily Ctenoneurinae

AbstractRepresentatives of the cockroach superfamily Corydioidea are less sampled than members of the two other cockroach superfamilies (Blaberoidea and Blattoidea) due to the difficulty of collecting them in the field, accentuated by a general lack of knowledge on their biology. Their evolutionary relationships have not yet been investigated with a relevant sampling and are therefore poorly known. Here, we assess the phylogenetic relationships of 35 Corydioidea species with mitochondrial genomes and two nuclear gene fragments. Our sampling for Corydiidae comprises Corydiinae and Euthyrrhaphinae representatives, whereas our sampling for the remaining Corydioidea includes species belonging to genera Beybienkonus Qiu, Wang and Che, Compsodes Hebard, Ctenoneura Hanitsch and Nocticola Bolívar. We further infer their divergence times with molecular dating analyses relying on five fossil calibrations. We also carry out reconstructions of ancestral character states for 11 phenotypic and one biological traits. Our results recover two major Corydioidea clades, one consisting solely of Corydiidae (except Latindiinae) and the other of all remaining Corydioidea taxa. Based on the results of phylogenetic analyses, an updated classification of extant Corydioidea is proposed, where Latindiinae Handlirsch stat.rev. and Ctenoneurinae Qiu and Che, subfam.nov. are assigned to the family Nocticolidae Bolívar sensu nov. A new genus Pseudoeupolyphaga Qiu and Che, gen.nov. is also established within Corydiinae. Both the origin of crown Corydioidea and the divergence of the two major lineages are estimated to have occurred during the Triassic–Jurassic boundary. Ancestral character state reconstruction analyses also suggest an adaptive relationship between phenotypic characteristics and habitat preferences.

Bathymetric evolution of black corals through deep time.

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250-3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

New perspectives on the evolutionary history of xiphosuran development through comparison with other fossil euchelicerates

IntroductionEuchelicerata is a diverse group encompassing Xiphosura, Chasmataspidida, Eurypterida, and Arachnida. Xiphosura represents an extant group with a rich fossil record dating back to the Ordovician period. Xiphosurans are often referred to as “living fossils” due to their seemingly unchanged morphology over millions of years. Numerous studies have contributed to the understanding of xiphosuran development, revealing changes in the timing and rate of their growth. These changes have been mainly associated with the freshwater invasion of early xiphosuran forms. However, limited research has been conducted to compare the developmental patterns of xiphosurans with other euchelicerates inhabiting aquatic environments.MethodsThis study compares the developmental patterns of xiphosurans with that of the fossil clades of eurypterids and chasmataspidids. By incorporating environmental and phylogenetic information within ancestral state reconstruction analyses, and then testing different evolutionary scenarios, the influence of the environment on the evolution of developmental patterns of euchelicerates is examined.ResultsThe results confirm that the developmental changes in Xiphosura throughout their evolutionary history are correlated with the exploitation of different environments. However, the inclusion of eurypterids and chasmataspidids indicates that the entirety of changes seen for Xiphosura represent only a small portion of the total variability recovered for euchelicerates.DiscussionOur results emphasize the importance of considering phylogenetic relationships and outgroup comparisons to understand the evolutionary dynamics of Xiphosura.

Comparative genomics, microsynteny, ancestral state reconstruction and selection pressure analysis across distinctive genomes and sub-genomes of Brassicaceae for analysis of evolutionary history of VQ gene family.

The online version contains supplementary material available at 10.1007/s12298-023-01347-z.

Insights into the morphology and evolution of orbicules in the Spermacoce clade (Spermacoceae-Rubiaceae) and implications for systematics

Abstract The orbicules are tiny structures of sporopollenin that occur on the interior wall of anthers in several groups of plants, and they are associated with pollen grains and tapetal cells. Although their function remains still unresolved, they have been widely used in systematics. Rubiaceae is one of the most studied families in this aspect. However, scarce information is available about the orbicules in the tribe Spermacoceae, especially in the Spermacoce clade. The main objectives of this work were to investigate the occurrence, general morphology, evolution, and systematic utility of the orbicular characters in the Spermacoce clade. We investigated the presence/absence, size, abundance, shape, and ornamentation of orbicules in 104 specimens from 84 species in the Spermacoce clade using scanning electron microscopy (SEM). On the basis of these features, the ancestral state reconstruction analyses were performed on a custom-made phylogeny by stochastic character mapping. The orbicules are present in 38 (44%) of 84 analysed species, corresponding to 13 genera (56%) of the Spermacoce clade. Seven genera have orbicules in all analysed species, eight genera lack orbicules in all analysed species, and six genera show both presence and absence of orbicules. The absence of orbicules was estimated to be the ancestral state for the Spermacoce clade and the presence of orbicules evolved several times independently within Clade B. The absence of orbicules in the common ancestor of the Spermacoce clade can be seen as one of the independent losses that occurred during the evolutionary history of the Rubiaceae.

Amplicon capture phylogenomics provides new insights into the phylogeny and evolution of alpine Parnassius butterflies (Lepidoptera: Papilionidae)

AbstractThe alpine butterfly genus Parnassius is a popular model group for studying biogeography, evolution, conservation biology, and ecology. Despite its scientific importance, a comprehensive and robust phylogeny of this group is still lacking. In this study, we used an amplicon capture strategy to sequence 144 nuclear protein‐coding genes and complete mitochondrial genomes for 60 Parnassius specimens covering 42 species and all eight subgenera of Parnassius. Our results strongly support the monophyly of the genus and eight subgenera. The relationships among subgenera are robustly resolved as (Sachaia, (Kreizbergia, (Driopa, (Parnassius, (Tadumia, Lingamius), (Kailasius, Koramius))))), which is different from all previous results. Biogeographic and divergence time analyses indicate that the ancestor of Parnassius originated in an area including the Himalayas and Tibetan Plateau (HTP) and Mongolian steppes in the middle Miocene approximately 13.19 Mya. The middle Miocene global cooling event (starting from ~13.9 Mya) probably provided climatic opportunities for the diversification of cold‐adapted Parnassius. The ancestral state reconstruction analyses suggest that the ancestor of Parnassius butterflies most likely lived in a medium elevational area (2000–4000 m) and fed on Papaveraceae plants. The host shift from Papaveraceae to Crassulaceae in the subgenus Parnassius increases the species diversity of this subgenus, concurring with the “escape and radiate” hypothesis. Overall, our work provides valuable nuclear gene and mitochondrial genome data and a robust phylogenetic framework of Parnassius for future studies of the taxonomy, evolution, and ecology of this group.

Chemical and evolutionary analysis of the scent gland secretions of two species of Gonyleptes Kirby, 1819 (Arachnida: Opiliones: Laniatores)

The subfamily Gonyleptinae is the second largest in Gonyleptidae, harboring over 100 species. Gonyleptinae is polyphyletic, nestled in the clade K92, and despite its richness, several species of that subfamily have not had their chemicals of the defensive secretions analyzed. Among these are Gonyleptes curticornis (Mello-Leitão, 1940) and G. horridus Kirby, 1819, the latter being particularly important, because it is the type species of the genus, which in turn names the subfamily Gonyleptinae. Gonyleptes horridus is also used in many phylogenetic analyses, be it using morphological or molecular data. The chemical study of the secretions of these two species by GC–MS and 1H NMR showed the presence of 1-(6-isopropyl-3,4-dihydro-2H-pyran-2-yl)-methylbutanone, 1-(6-isopropyl-3,4-dihydro-2H-pyran-2-yl) isobutanone and 4-methyl-1-hepten-3-one in both species. On the other hand, 4-methyl-1-hexen-3-one was observed only in G. curticornis, and 7-methyl-2-octanol is exclusive of G. horridus. All vinyl-ketones identified have already been described for Gonyleptidae. We ran an Ancestral Character State Reconstruction (ASR) analysis under three different conditions to infer the evolution of the identified compounds (based on modified characters of a previous study) and their chemical nature (multistate character, either as alkylphenol, benzoquinone or vinyl-ketone) on a modified Gonyleptidae phylogeny. Our results corroborate previous studies that alkylphenol is the ancestral most condition, changing to benzoquinone in the ancestor of Gonyleptidae or even earlier in a grassatorean ancestor depending on the analysis. Vinyl-ketones are a synapomorphy of K92. We briefly discuss character codifications and use of weights of ASR analyses of specific compounds, which were inconclusive. 1-(6-isopropyl-3,4-dihydro-2H-pyran-2-yl) isobutanone is shared by both Gonyleptes species and described for the genus Sodreana Mello-Leitão, 1922. 1-(6-(1-methyl-propyl)3,4-dihydro-2H-pyran-2yl)2-methylbutanone and 4-methyl-1-hepten-3-one are also shared by both Gonyleptes species and described for Moreiranula saprophila. From a taxonomic standpoint, combinations of specific compounds might help to diagnose supraspecific groups but given our limited sample, such decision should be taken with care and further tested. Finally, 7-methyl-2-octanol is described for the first time in Gonyleptidae, emphasizing the chemical diverse nature in the K92 clade.

Microstructural and crystallographic evolution of palaeognath (Aves) eggshells.

The avian palaeognath phylogeny has been recently revised significantly due to the advancement of genome-wide comparative analyses and provides the opportunity to trace the evolution of the microstructure and crystallography of modern dinosaur eggshells. Here, eggshells of all major clades of Palaeognathae (including extinct taxa) and selected eggshells of Neognathae and non-avian dinosaurs are analysed with electron backscatter diffraction. Our results show the detailed microstructures and crystallographies of (previously) loosely categorized ostrich-, rhea-, and tinamou-style morphotypes of palaeognath eggshells. All rhea-style eggshell appears homologous, while respective ostrich-style and tinamou-style morphotypes are best interpreted as homoplastic morphologies (independently acquired). Ancestral state reconstruction and parsimony analysis additionally show that rhea-style eggshell represents the ancestral state of palaeognath eggshells both in microstructure and crystallography. The ornithological and palaeontological implications of the current study are not only helpful for the understanding of evolution of modern and extinct dinosaur eggshells, but also aid other disciplines where palaeognath eggshells provide useful archive for comparative contrasts (e.g. palaeoenvironmental reconstructions, geochronology, and zooarchaeology).

Re-Evaluating Botryosphaeriales: Ancestral State Reconstructions of Selected Characters and Evolution of Nutritional Modes.

Botryosphaeriales (Dothideomycetes, Ascomycota) occur in a wide range of habitats as endophytes, saprobes, and pathogens. The order Botryosphaeriales has not been subjected to evaluation since 2019 by Phillips and co-authors using phylogenetic and evolutionary analyses. Subsequently, many studies introduced novel taxa into the order and revised several families separately. In addition, no ancestral character studies have been conducted for this order. Therefore, in this study, we re-evaluated the character evolution and taxonomic placements of Botryosphaeriales species based on ancestral character evolution, divergence time estimation, and phylogenetic relationships, including all the novel taxa that have been introduced so far. Maximum likelihood, maximum parsimony, and Bayesian inference analyses were conducted on a combined LSU and ITS sequence alignment. Ancestral state reconstruction was carried out for conidial colour, septation, and nutritional mode. Divergence times estimates revealed that Botryosphaeriales originated around 109 Mya in the early epoch of the Cretaceous period. All six families in Botryosphaeriales evolved in the late epoch of the Cretaceous period (66-100 Mya), during which Angiosperms also appeared, rapidly diversified and became dominant on land. Families of Botryosphaeriales diversified during the Paleogene and Neogene periods in the Cenozoic era. The order comprises the families Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae. Furthermore, current study assessed two hypotheses; the first one being "All Botryosphaeriales species originated as endophytes and then switched into saprobes when their hosts died or into pathogens when their hosts were under stress"; the second hypothesis states that "There is a link between the conidial colour and nutritional mode in botryosphaerialean taxa". Ancestral state reconstruction and nutritional mode analyses revealed a pathogenic/saprobic nutritional mode as the ancestral character. However, we could not provide strong evidence for the first hypothesis mainly due to the significantly low number of studies reporting the endophytic botryosphaerialean taxa. Results also showed that hyaline and aseptate conidia were ancestral characters in Botryosphaeriales and supported the relationship between conidial pigmentation and the pathogenicity of Botryosphaeriales species.

Evolutionary timescale of chalcidoid wasps inferred from over one hundred mitochondrial genomes.

Chalcidoidea is one of the most biologically diverse groups among Hymenoptera. Members are characterized by extraordinary parasitic lifestyles and extensive host ranges, among which several species attack plants or serve as pollinators. However, higher-level chalcidoid relationships remain controversial. Here, we performed mitochondrial phylogenomic analyses for major clades (18 out of 25 families) of Chalcidoidea based on 139 mitochondrial genomes. The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences. Our phylogenetic results supported the monophyly of 16 families and polyphyly of Aphelinidae and Pteromalidae. Our preferred topology recovered the relationship (Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+ remaining Chalcidoidea)))). The monophyly of Agaonidae and Sycophaginae was rejected, while the gall-associated ((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae)) relationship was supported in most results. A six-gene inversion may be a synapomorphy for most families, whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes. Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea. We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea. Ancestral state reconstruction analyses supported the hypothesis that gall-inducers were mainly derived from parasitoids of gall-inducers, while other gall-inducers were derived from phytophagous groups. Taken together, these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.

Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys.

Chloridium is a little-studied group of soil- and wood-inhabiting dematiaceous hyphomycetes that share a rare mode of phialidic conidiogenesis on multiple loci. The genus has historically been divided into three morphological sections, i.e. Chloridium, Gongromeriza, and Psilobotrys. Sexual morphs have been placed in the widely perceived genus Chaetosphaeria, but unlike their asexual counterparts, they show little or no morphological variation. Recent molecular studies have expanded the generic concept to include species defined by a new set of morphological characters, such as the collar-like hyphae, setae, discrete phialides, and penicillately branched conidiophores. The study is based on the consilience of molecular species delimitation methods, phylogenetic analyses, ancestral state reconstruction, morphological hypotheses, and global biogeographic analyses. The multilocus phylogeny demonstrated that the classic concept of Chloridium is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of Gongromeriza and Psilobotrys. We present a new generic concept and define Chloridium as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to Gongromeriza, two have been redisposed to the new genus Gongromerizella. Analysis of published metabarcoding data showed that Chloridium is a common soil fungus representing a significant (0.3 %) proportion of sequence reads in environmental samples deposited in the GlobalFungi database. The analysis also showed that they are typically associated with forest habitats, and their distribution is strongly influenced by climate, which is confirmed by our data on their ability to grow at different temperatures. We demonstrated that Chloridium forms species-specific ranges of distribution, which is rarely documented for microscopic soil fungi. Our study shows the feasibility of using the GlobalFungi database to study the biogeography and ecology of fungi. Taxonomic novelties: New genus: Gongromerizella Réblová; New sections: Chloridium section Cryptogonytrichum Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Gonytrichopsis Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Metachloridium Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Volubilia Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; New species: Chloridium bellum Réblová & Hern.-Restr., Chloridium biforme Réblová & Hern.-Restr., Chloridium detriticola Réblová & Hern.-Restr., Chloridium gamsii Réblová & Hern.-Restr., Chloridium guttiferum Réblová & Hern.-Restr., Chloridium moratum Réblová & Hern.-Restr., Chloridium peruense Réblová & Hern.-Restr., Chloridium novae-zelandiae Réblová & Hern.-Restr., Chloridium elongatum Réblová & Hern.-Restr., Chloridium volubile Réblová & Hern.-Restr.; New varieties: Chloridium bellum var. luteum Réblová & Hern.-Restr., Chloridium detriticola var. effusum Réblová & Hern.-Restr., Chloridium chloridioides var. convolutum Réblová & Hern.-Restr.; New combinations: Chloridium section Gonytrichum (Nees & T. Nees) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Mesobotrys (Sacc.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Pseudophialocephala (M.S. Calabon et al.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium simile (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium chloridioides (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium subglobosum (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium fuscum (Corda) Réblová & Hern.-Restr., Chloridium ypsilosporum (Hol.-Jech.) Réblová & Hern.-Restr., Chloridium costaricense (G. Weber et al.) Réblová & Hern.-Restr., Chloridium cuneatum (N.G. Liu et al.) Réblová & Hern.-Restr., Fusichloridium cylindrosporum (W. Gams & Hol.-Jech.) Réblová, Gongromeriza myriocarpa (Fr.) Réblová, Gongromeriza pygmaea (P. Karst.) Réblová, Gongromerizella lignicola (F. Mangenot) Réblová, Gongromerizella pachytrachela (W. Gams & Hol.-Jech) Réblová, Gongromerizella pini (Crous & Akulov) Réblová; New name: Chloridium pellucidum Réblová & Hern.-Restr.; Epitypifications (basionyms): Chaetopsis fusca Corda, Gonytrichum caesium var. subglobosum W. Gams & Hol.-Jech.; Lectotypification (basionym): Gonytrichum caesium Nees & T. Nees. Citation: Réblová M, Hernández-Restrepo M, Sklenář F, Nekvindová J, Réblová K, Kolařík M (2022). Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys. Studies in Mycology 103: 87-212. doi: 10.3114/sim.2022.103.04.