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Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to leap to the next level.

Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.

When and why did variations in placental structure and function evolve? Such questions cannot be addressed without a reliable version of mammalian phylogeny. Twenty-five years ago, the mammalian tree was reshaped by molecular phylogenetics. Soon it was shown, in contrast to prevailing theories, that the common ancestor of placental mammals had invasive placentation. Subsequently, evolution of many other features of extraembryonic membranes was addressed. This endeavour stimulated research to fill gaps in our knowledge of placental morphology. Last year the mammalian tree was again revised based on a large set of genomic data. With that in mind, this review provides an update on placentation in the nineteen orders of placental mammals, incorporating much recent data. The principal features such as shape, interdigitation, the interhaemal barrier and the yolk sac are summarized in synoptic tables. The evolution of placental traits and its timing is then explored by reference to the revised mammalian tree. Examples are the early appearance of epitheliochorial placentation in the common ancestor of artiodactyls, perissodactyls, pangolins and carnivores (with reversion to invasive forms in the latter) and later refinements such as the binucleate trophoblast cells and placentomes of ruminants. In primates, the intervillous space gradually evolved from the more basic labyrinth whereas trophoblast invasion of the decidua was a late development in humans and great apes. Only seldom can we glimpse the "why" of placental evolution. The best examples concern placental hormones, including some striking examples of convergent evolution such as the chorionic gonadotropins of primates and equids. In concluding, I review current ideas about what drives placental evolution and identify significant gaps in our knowledge of placentation, including several relevant to the evolution of placentation in primates. [Display omitted] • Placental evolution in mammals is interpreted from the newly revised phylogenomic tree. • Traits with a deep origin include the four-chambered allantoic sac of afrotherians • Traits with a late origin include the intervillous space of haplorrhine primates. • Some morphological traits can be linked to hormone secretion in ruminants, horses, rodents and primates. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis based on whole-genome sequences is the gold standard for monkeypox virus (MPXV) phylogeny. However, genomic epidemiology capability and capacity are lacking or limited in resource poor countries of sub-Saharan Africa. Therefore, these make real-time genome surveillance of MPXV virtually impossible. We hypothesized that phylogenetic analysis based on single, conserved genes will produce phylogenetic tree topology consistent with MPXV whole-genome phylogeny, thus serving as a reliable proxy to phylogenomic analysis. In this study, we analyzed 62 conserved MPXV genes and showed that Bayesian phylogenetic analysis based on five genes (OPG 066/E4L, OPG068/E6R, OPG079/I3L, OPG145/A18R, and OPG150/A23R) generated phylogenetic trees with 72.2–96.3% topology similarity index to the reference phylogenomic tree topology. Our results showed that phylogenetic analysis of the identified five genes singly or in combination can serve as surrogate for whole-genome phylogenetic analysis, and thus obviates the need for whole-genome sequencing and phylogenomic analysis in regions where genomic epidemiology competence and capacity are lacking or unavailable. This study is relevant to evolution and genome surveillance of MPXV in resource limited countries. [ABSTRACT FROM AUTHOR]

Leptocircini is a dazzling tribe of Papilionidae, including dragontails, kite swallowtails and swordtails. This tribe is widely distributed, notably throughout the tropics of Africa, Southeast Asia and the Americas, making it a fascinating model in evolutionary biology. However, despite accounting for 25% of the global swallowtail butterfly diversity, Leptocircini have been surprisingly neglected in phylogenetic analyses. This has left unanswered questions about their taxonomy and systematics. Here, we present a new taxonomic working list for Leptocircini, featuring 162 valid species. Using a combination of long and short reads data, we produced five new reference genomes, and we generated highly covered and scaffolded whole genomes for 148 individuals to infer densely sampled phylogenetic hypotheses. Based on mitochondrial or thousands of nuclear genes and multiple phylogenetic approaches, a robust phylogenomic tree is recovered, representing approximately 90% of the known species, which allowed examination of several key phylogenetic hypotheses. We found the monotypic genus Protographium Munroe to be sister of genus Graphium Scopoli. Additionally, we found that subgenus Paranticopsis Wood‐Mason and de Nicéville is nested within subgenus Pathysa Reakirt, which we found is likely attributed to an ancient gene flow. We therefore synonymize Paranticopsis, syn.rest. To keep a consistent approach to subgeneric classification across the tribe and family, we devided genus Eurytides Hübner into three subgenera: Mimoides Brown, Eurytides sensu stricto and Protesilaus Swainson. This led to several taxonomic implications: Asiographium Möhn, syn.rest., Boreographium Grishin, syn.n., Hyalaus Grishin, syn.n. and Neographium Möhn, syn.n. are synonymized with Eurytides (Mimoides); and Eurygraphium Möhn, syn.rest. is synonymized with Eurytides (Eurytides). Our analyses finally raised concerns about potential taxonomic inflation in two species‐groups within Graphium and Eurytides (Protesilaus). This study illuminates the clade's evolutionary history and paves the way for further research on this diverse group of charismatic butterflies. [ABSTRACT FROM AUTHOR]

Summary Grasses (Poaceae) comprise c. 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome‐scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1153‐tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a newly inferred 910‐tip plastome tree. We recovered most of the tribes and subfamilies previously established, despite pervasive incongruence among nuclear gene trees. The early diversification of the PACMAD clade could represent a hard polytomy. Gene tree–species tree reconciliation suggests that reticulation events occurred repeatedly. Nuclear–plastome incongruence is rare, with very few cases of supported conflict. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Vitamin B12, also known as cobalamin, is an essential organic cofactor for methionine synthase (METH), and is only synthesized by a subset of bacteria. Plants and fungi have an alternative methionine synthase (METE) that does not need B12 and are typically considered not to utilize it. Some algae facultatively utilize B12 because they encode both METE and METH, while other algae are dependent on B12 as they encode METH only. We performed phylogenomic analyses of METE, METH and 11 further proteins involved in B12 metabolism across more than 1600 plant and algal genomes and transcriptomes (e.g. from OneKp), demonstrating the presence of B12-associated metabolism deep into the streptophytes. METH and five further accessory proteins (MTRR, CblB, CblC, CblD and CblJ) were detected in the hornworts (Anthocerotophyta), and two (CblB and CblJ) were identified in liverworts (Marchantiophyta) in the bryophytes, suggesting a retention of B12-metabolism in the last common land plant ancestor. Our data further show more limited distributions for other B12-related proteins (MCM and RNR-II) and B12 dependency in several algal orders. Finally, considering the collection sites of algae that have lost B12 metabolism, we propose freshwater-to-land transitions and symbiotic associations to have been constraining factors for B12 availability in early plant evolution. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Plant chemical diversity is largely owing to a number of enzymes which catalyse reactions involved in the assembly, and in the subsequent chemical modifications, of the core structures of major classes of plant specialized metabolites. One such reaction is acylation. With this in mind, to study the deep evolutionary history of BAHD and the serine-carboxypeptidase-like (SCPL) acyltransferase genes, we assembled phylogenomic synteny networks based on a large-scale inference analysis of orthologues across whole-genome sequences of 126 species spanning Stramenopiles and Archaeplastida, including Arabidopsis thaliana, tomato (Solanum lycopersicum) and maize (Zea mays). As such, this study combined the study of genomic location with changes in gene sequences. Our analyses revealed that serine-carboxypeptidase (SCP)/serine-carboxypeptidase-like (SCPL) genes had a deeper evolutionary origin than BAHD genes, which expanded massively on the transition to land and with the development of the vascular system. The two gene families additionally display quite distinct patterns of copy number variation across phylogenies as well as differences in cross-phylogenetic syntenic network components. In unlocking the above observations, our analyses demonstrate the possibilities afforded by modern phylogenomic (syntenic) networks, but also highlight their current limitations, as demonstrated by the inability of phylogenetic methods to separate authentic SCPL acyltransferases from standard SCP peptide hydrolases. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

The Pleidae, or pygmy backswimmers, is a family of aquatic bugs (Hemiptera, Heteroptera, Nepomorpha) containing four genera. Here, we describe Plea cryptica sp. nov. and redescribe its sister species, Plea minutissima Leach, 1817. Whereas the morphological distinction of these closely related species is only possible for males, molecular data clearly separate them. As part of our taxonomic study, we provide comprehensive molecular data including more than 200 DNA barcodes from all over Europe, complete nuclear ribosomal DNA, full mitochondrial genome data, and 3D scans for both species. Furthermore, the same molecular markers are also presented for Neoplea striola (Fieber, 1844). We used Maximum Likelihood (ML) analyses to reconstruct the phylogeny of the Pleidae and Notonectoidea based on available mitogenomic data. Our study represents a successful implementation of the proposed concept of taxonomics, using data from high-throughput sequencing technologies for integrative taxonomic studies, and allowing high confidence for both biodiversity and ecological research. [ABSTRACT FROM AUTHOR]

Introduction: The Providencia genus is assuming greater clinical relevance among infections caused by Enterobacterales also because of its intrinsic and acquired resistance to last-resort antibiotics. However, despite having been known and studied for over 50 years, genomics and taxonomy of the Providencia genus are currently undergoing a deep rearrangement. In this study we aim to outline and characterized the P. stuartii species. Methods: We retrieved from the GenBank database all genomes labelled as Providencia and performed a comprehensive genome-based species definition founded on average nucleotide identity (ANI) and on alignment-free approaches. Results: After defining the genomes assuredly identifiable as P. stuartii , we devised a MultiLocus Sequence Typing (MLST) and a core-genome MLST (cgMLST) schemes, based on 7 and 2,296 loci respectively. Discussion: This work hence provides a framework for understanding the role of P. stuartii and of other members of this genus, which should be considered as emerging multidrug-resistant pathogens. [ABSTRACT FROM AUTHOR]

In recent years, new wasp species and genera of Cynipidae have been described, and their species delimitation and evolutionary relationships have been supported using molecular markers. However, few studies have included comprehensive and extensive sampling of specimens across the complete distribution of a single genus. In this study, we analysed the phylogenetic relationships of the genus Amphibolips throughout its range using ultraconserved elements (UCEs). We collected 520 adult wasps from 401 sites in various geographic locations, predominantly in Mexico, and used 78 wasps for UCE analysis. Our results demonstrate that Amphibolips forms a monophyletic clade. Amphibolips can be further subdivided into four genetically well‐differentiated clades. Each clade had morphological traits that could be collectively characterised. Species delimitation using molecular sequencing highlights the taxonomic complexity involved in separating and assigning species using exclusively morphological criteria. This approach offers an opportunity to refine current morphological taxonomic criteria or propose new criteria to establish more accurate classifications. The rich diversity of host species and geographic regions in Mexico represents a biodiversity hotspot for Amphibolips. The number of undescribed species remains high. This study facilitates the determination of appropriate boundaries for putative new Amphibolips species. [ABSTRACT FROM AUTHOR]

Background: Astilbe, consisting of about 18 species, is distributed throughout East Asia and Northeastern America, and most Astilbe species are widely cultivated as ornamental plants. A total of four species of Astilbe have been confirmed to be distributed throughout Korea, two of which are endemic to Korea. Methods: In this study, we sequenced and assembled the complete chloroplast genomes of two endemic Korean plants using Illumina sequencing technology, identified simple sequence repeats (SSRs) and repetitive sequences, and compared them with three previously reported chloroplast genomes. Results: The chloroplast genomes of the two species were 156,968 and 57,142 bp in length and had a four-part circular structure. They consisted of a large single-copy region of 87,223 and 87,272 bp and a small single-copy region of 18,167 and 18,138 bp, separated by a pair of inverted repeats (IRa and IRb, 25,789 and 25,866 bp). The genomes contained 130 genes, 49 SSRs, and 49 long repetitive sequences. Comparative analysis with the chloroplast genomes of five Astilbe species indicated that A. uljinensis was closely related to A. chinensis and A. taquetii to A. koreana. Conclusions: This study provides valuable references for the identification of two endemic Korean Astilbe species and contributes to a deeper understanding of the phylogeny and evolution of the genus Astilbe. [ABSTRACT FROM AUTHOR]

Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node‐dating (ND) based on plastomes of all eight extant species and tip‐dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for Pterocarya fraxinifolia and Pterocarya stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change. [ABSTRACT FROM AUTHOR]

Neogastropoda is a large order of predominantly marine gastropod molluscs, typically predatory or parasitic on other animals. It includes over 16,000 species representing a large post‐Cretaceous radiation, but the internal phylogenetic relationships of contained taxa are far from resolved, with inconsistent results from nuclear genes, mitogenomes, and morphology. One major issue in reconstructing the molecular phylogeny is the lack of high‐quality sequences for early‐diverging families and superfamilies such as Volutidae (Volutoidea). Here, we examine the superfamily‐level phylogenetic relationships in Neogastropoda, aided by newly sequenced draft genome and mitogenome of the volutid snail Fulgoraria chinoi from the deep sea off Japan. The genome of F. chinoi is relatively large at 1.54 Gb but exhibits low genome heterozygosity; over 54% of this genome constitutes of repeat contents, and we find evidence for active insertion of transposable elements, particularly LINEs and SINEs. A total of 50,792 protein‐coding genes (PCGs) were predicted from the nuclear genome, and a circular mitogenome was also assembled and annotated. Our phylogenetic analyses using mitogenomes recovered each neogastropod superfamily as monophyletic, though also revealed inconsistent phylogenetic signals within superfamilies. Phylogenetic reconstructions using the PCGs resulted in a robust tree from different models and data matrices, recovering Volutoidea as the earliest diverging superfamily (among those for which comparable data is available) within a monophyletic Neogastropoda. Dated phylogenetic analysis revealed an early Cretaceous radiation of Neogastropoda, congruent with the fossil record. Our study provides a robust internal evolutionary framework for the speciose but genomically undersampled Neogastropoda, and expands the available genomic resources for this order. Genomic data for key missing lineages such as Mitroidea, Olivoidea, and Cancellariidae are much sought in the future for a full understanding of Neogastropoda evolution. [ABSTRACT FROM AUTHOR]

Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon‐capture probe set targeting toxin‐coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from ~1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost‐effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes. [ABSTRACT FROM AUTHOR]

Bioinformatics sequence data mining can reveal hidden microbial symbionts that might normally be filtered and removed as contaminants. Data mining can be helpful to detect Wolbachia, a widespread bacterial endosymbiont in insects and filarial nematodes whose distribution in plant-parasitic nematodes (PPNs) remains underexplored. To date, Wolbachia has only been reported a few PPNs, yet nematode-infecting Wolbachia may have been widespread in the evolutionary history of the phylum based on evidence of horizontal gene transfers, suggesting there may be undiscovered Wolbachia infections in PPNs. The goal of this study was to more broadly sample PPN Wolbachia strains in tylenchid nematodes to enable further comparative genomic analyses that may reveal Wolbachia's role and identify targets for biocontrol. Published whole-genome shotgun assemblies and their raw sequence data from 33 Meloidogyne spp. assemblies, seven Globodera spp. assemblies, and seven Heterodera spp. assemblies were analyzed to look for Wolbachia. No Wolbachia was found in Meloidogyne spp. and Globodera spp., but among seven genome assemblies for Heterodera spp., an H. schachtii assembly from the Netherlands was found to have a large Wolbachia-like sequence that, when re-assembled from reads, formed a complete, circular genome. Detailed analyses comparing read coverage, GC content, pseudogenes, and phylogenomic patterns clearly demonstrated that the H. schachtii Wolbachia represented a novel strain (hereafter, denoted wHet). Phylogenomic tree construction with PhyloBayes showed wHet was most closely related to another PPN Wolbachia, wTex, while 16S rRNA gene analysis showed it clustered with other Heterodera Wolbachia assembled from sequence databases. Pseudogenes in wHet suggested relatedness to the PPN clade, as did the lack of significantly enriched GO terms compared to PPN Wolbachia strains. It remains unclear whether the lack of Wolbachia in other published H. schachtii isolates represents the true absence of the endosymbiont from some hosts. [ABSTRACT FROM AUTHOR]

Introduction: Since its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across evolutionary scales, and thus employed from population genetics, to historical biogeography as well as deep-time phylogenetics. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and tested beyond decapods in other malacostracan lineages. Methods: Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,384 unique UCE loci. We compiled a dataset across Malacostraca,as well as datasets of a deep-sea squat lobster genus, and an intertidal mangrove crab species, to test the probe set at different phylogenetic levels (i.e., class, order, genus, within species). Results: Final mean UCE recovery from fresh samples across Malacostraca was 568 loci,with up to 847 and 658 loci recovered from decapod and non-decapod species, respectively. Final mean recovery from fresh samples in the genus- and within species-level datasets was 849 and 787 loci, respectively. Up to several hundreds of UCEs were recovered from historicalmuseum specimens (10 to > 150 years old), that were included in all datasets. UCE-based phylogenies largely reflected the known relationships of the included taxa, and we were able to infer population differentiation based on >600 SNPs extracted from the species-level dataset. Discussion: Our results showcase the versatility of this UCE probe set, yielding informative data from phylogenetic as well as population-genetic datasets. They demonstrate once more that UCEs are a promising technique for leveraging museum specimens for genomic studies, and overall highlight the probe set's potential for crustacean evolutionary studies. [ABSTRACT FROM AUTHOR]

Introduction: Neisseria gonorrhoeae (Ng) has successively developed resistance to all previously recommended antimicrobial therapies, with ceftriaxone being the last option for monotherapy of gonorrhea. Global emergence and international spread of the FC428 clone derived mosaic penA-60 allele, associated with highlevel ceftriaxone minimum inhibitory concentrations (MICs) in non FC428 clone Ng lineages, has become an increasing concern. The penA60 allele carrying Ng was first identified in the U.S. in Las Vegas, Nevada (2019; GCWGS-102723), with a multi-locus sequence type (MLST)-1901 strain, in a non FC428 clone Ng lineage, which is associated with a historically ceftriaxone susceptible core genogroup. Later in 2022, an allele genetically similar to penA-60, mosaic penA-237, was identified in the UK (H22-722) and France (F92) with high-level ceftriaxone MICs and both belonged to MLST-1901. Methods: In this study, we assessed phylogenomic relatedness and antimicrobial resistance (AMR) determinant profiles of these three isolates with high-level ceftriaxone MICs among a global collection of 2,104 genomes belonging to the MLST-1901 core genome cluster group 31, which includes strains separated by a locus threshold of 200 or fewer differences (Ng_cgc_200). Recombination events in and around the penA coding region were catalogued and potential sources of inter species recombinant DNA were also inferred. Results: The global population structure of MLST-1901 core genogroup falls into 4 major lineages. Isolates GCWGS-10723, F92, and H22-722 clustered within Lineage 1, which was dominated by non-mosaic penA-5 alleles. These three isolates formed a clade within Lineage 1 that consisted of isolates from North America and southeast Asia. Neisseria subflava and Neisseria sicca were identified as likely progenitors of two independent recombination events that may have led to the generation of mosaic penA-60 and penA-237, within a possible non-mosaic penA-5 background. Discussions: Our study suggests that there are multiple evolutionary pathways that could generate concerning mosaic penA alleles via homologous recombination of historically susceptible Ng lineages with Neisseria commensals. Enhanced surveillance of gonococcal strains and Neisseria commensals is crucial for understanding of the evolution of AMR, particularly in less-studied regions (e.g., Asia), where high-level ceftriaxone MICs and multi-drug resistance are more prevalent. [ABSTRACT FROM AUTHOR]

Summary Large‐scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs in the terrestrialization and diversification of bryophytes, the second most species‐rich group of land plants, remains largely elusive due to limited sampling in bryophytes. Employing the most extensive nuclear gene dataset in bryophytes to date, we reconstructed a time‐calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, for phylogenomic analyses of LSGDs and diversification. We newly identified two ancient LSGDs: one in the most recent common ancestor (MRCA) of extant bryophytes and another in the MRCA of the majority of Jungermanniales s. lato. Duplicated genes from these two LSGDs show significant enrichment in photosynthesis‐related processes and structures. Rhizoid‐responsive ROOTHAIR DEFECTIVE SIX‐LIKE (RSL) genes from ancient LSGDs are present in rhizoidless bryophytes, challenging assumptions about rhizoid absence mechanisms. We highlighted four major diversification rate upshifts, two of which slightly postdated LSGDs, potentially linked to the flourishing of gymnosperms and angiosperms and explaining over 80% of bryophyte diversity. Our findings, supported by extensive bryophyte sampling, highlight the significance of LSGDs in the early terrestrialization and diversification of bryophytes, offering new insights into land plant evolution. [ABSTRACT FROM AUTHOR]

Recent phylogenetic analyses of anchored‐hybrid, transcriptomic and morphological data have consistently recovered a clade comprising the three previously recognized families of treehoppers (Hemiptera), Aetalionidae, Melizoderidae and Membracidae, as well as two groups traditionally included in the leafhopper family Cicadellidae as subfamilies Megophthalminae and Ulopinae. To reconstruct the phylogeny of these two groups of treehopper‐like leafhoppers, maximum likelihood and multi‐species coalescent analyses were performed on a molecular DNA dataset consisting of ~700 anchored hybrid loci representing 84 terminal taxa. Analyses based on different dataset subsets and approaches yielded largely congruent topologies, although the relationships among Megophthalminae, Ulopinae and treehoppers are still unstable. The monophyly of both subfamilies is strongly supported, but several tribes, including Agalliini, Cephalelini, Megophthalmini and Ulopini, are recovered as non‐monophyletic. The origin of Megophthalminae and Ulopinae was estimated as early Cretaceous (~140 million years ago), and the divergence within each subfamily began in the mid‐Cretaceous. Continental‐scale biogeographic structure is evident in these two groups, with genera occurring on the same continent tending to group together regardless of tribal placement, suggesting that extensive morphological convergence occurred among faunas inhabiting different regions. Ancestral microhabitat reconstruction suggested that megophthalmine and ulopine leafhoppers originally lived on trees or shrubs and later several groups evolved independently to inhabit leaf litter and soil. Convergent modifications of the ocelli, forewings and hindwings accompanied changes in microhabitat preference. [ABSTRACT FROM AUTHOR]

Ciliophora are one of the most diverse phyla of unicellular eukaryotes. Members of this group are widely distributed and have been found in several environments including those that are anaerobic. However, the paucity of sufficient omics data for the major classes of the phylum Ciliophora, especially the anaerobic ciliate lineages, has been a serious impediment to research thus far. In this study, omics data were expanded to include representatives of 16 ciliate classes (excluding Cariacotrichea and Copemetopea) using single‐cell sequencing techniques. Using omics data of 57 ciliates and two apicomplexans, we conducted a comparative genomics study. Phylogenomic analysis based on 156 orthologous genes showed that: there are two superclades within the subphylum Intramacronucleata, i.e., Colpodea + Oligohymenophorea + Nassophorea + Plagiopylea + Prostomatea + Phyllopharyngea (CONThreeP), and Spirotrichea + Armophorea + Litostomatea + Odontostomatea + Muranotrichea + Parablepharismea (SALOMP); with the exception of Armophorea, all ciliate classes are monophyletic; neither Metopus nor Plagiopyla is monophyletic; Paraspathidium has a close affiliation with prostomateans. The results of the divergence time estimations indicated that: the radiation of Ciliophora occurred ca. 1067 million years ago (Mya); the SALOMP and CONThreeP lineages diverged from the intramacronucleatean common ancestor ca. 892 Mya and 851 Mya, respectively; the split between Muranotrichea and Parablepharismea occurred ca. 712 Mya; Odontostomatea are the youngest class, with a crown age estimated at ca. 19 Mya. In addition, we profiled stop codon usage and programmed ribosomal frameshifting (PRF) events. Our analyses revealed that: most of the species investigated use either TAA or TGA as the biased stop codon; stop codon usage in Paraspathidium sp. resembles that of Prostomatea; almost all ciliates included in the analyses have prevalent +1 and −1 PRF events. Finally, through GO enrichment analysis for group‐shared orthogroups of five anaerobic ciliate classes, we successfully identified the biological process and molecular function GO terms that were related to the adaptation of this particular group of ciliates to anaerobic environments. Together, these findings provide new insights into the evolutionary history of the Ciliophora and deepen our understanding of the adaptation of anaerobic ciliate groups to anaerobic environments from an evolutionary perspective. [ABSTRACT FROM AUTHOR]

The AP2/ERF family constitutes one of the largest groups of transcription factors in the Solanaceae. AP2/ERF contributes to various plant biological processes, including growth, development, and responses to various stresses. The origins and functional diversification of AP2/ERF within the Solanaceae family remain poorly understood, primarily because of the complex interactions between whole-genome duplications (WGDs) and tandem duplications. In this study, a total of 1282 AP2/ERF proteins are identified from 7 Solanaceae genomes. The amplification of AP2/ERF genes was driven not only by WGDs but also by the presence of clusters of tandem duplicated genes. The conservation of synteny across different chromosomes provides compelling evidence for the impact of the WGD event on the distribution pattern of AP2/ERF genes. Distinct expression patterns suggest that the multiple copies of AP2/ERF genes evolved in different functional directions, catalyzing the diversification of roles among the duplicated genes, which was of great significance for the adaptability of Solanaceae. Gene silencing and overexpression assays suggest that ERF-1 members' role in regulating the timing of floral initiation in C. annuum. Our findings provide insights into the genomic origins, duplication events, and function divergence of the Solanaceae AP2/ERF. [ABSTRACT FROM AUTHOR]

Yersinia is an important genus comprising foodborne, zoonotic and pathogenic bacteria. On the other hand, species of the so-called group Yersinia enterocolitica-like are understudied and mostly characterized as non-pathogenic, despite of some reports of human infections. The present study aimed to provide genomic insights of Yersinia frederiksenii (YF), Yersinia intermedia (YI) and Yersinia kristensenii (YK) isolated worldwide. A total of 22 YF, 20 YI and 14 YK genomes were searched for antimicrobial resistance genes, plasmids, prophages, and virulence factors. Their phylogenomic relatedness was analyzed by Gegenees and core-genome multi-locus sequence typing. Beta-lactam resistance gene blaTEM-116 and five plasmids replicons (pYE854, ColRNAI, ColE10, Col(pHAD28) and IncN3) were detected in less than five genomes. A total of 59 prophages, 106 virulence markers of the Yersinia genus, associated to adherence, antiphagocytosis, exoenzymes, invasion, iron uptake, proteases, secretion systems and the O-antigen, and virulence factors associated to other 20 bacterial genera were detected. Phylogenomic analysis revealed high inter-species distinction and four highly diverse YF clusters. In conclusion, the results obtained through the analyses of YF, YI and YK genomes suggest the virulence potential of these strains due to the broad diversity and high frequency of prophages and virulence factors found. Phylogenetic analyses were able to correctly distinguish these closely related species and show the presence of different genetic subgroups. These data contributed for a better understanding of YF, YI and YK virulence-associated features and global genetic diversity, and reinforced the need for better characterization of these Y. enterocolitica-like species considered non-pathogenic. [ABSTRACT FROM AUTHOR]

The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72–73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health. [ABSTRACT FROM AUTHOR]

Background: Chironomidae occupy a pivotal position within global aquatic ecosystems. The unique structural attributes of the mitochondrial genome provide profound insights and compelling evidence, underpinning the morphological classification of organisms and substantially advancing our understanding of the phylogenetic relationships within Chironomidae. Results: We have meticulously sequenced, assembled, and annotated the mitogenomes of Tanypus chinensis (Wang, 1994) and Tanypus kraatzi (Kieffer, 1912), incorporating an additional 25 previously published mitogenomes into our comprehensive analysis. This extensive dataset enables us to delve deeper into the intricate characteristics and nuances of these mitogenomes, facilitating a more nuanced understanding of their genetic makeup. Conclusions: The genomic nucleotide composition of T. kraatzi was 39.10% A, 36.51% T, 14.33% C, and 10.06% G, with a total length of 1508 bp. The genomic nucleotide composition of T. chinensis was 39.61% A, 36.27% T, 14.55% C, and 9.57% G, with a total length of 1503 bp. This significant enrichment of the chironomid mitogenome library establishes a novel foundation for further exploration in the realm of phylogenetics. [ABSTRACT FROM AUTHOR]

Bacterial spot disease of cucurbits, caused by Xanthomonas cucurbitae, is a major problem in cucurbit‐growing areas worldwide. In the Midwestern region of the United States, pumpkin and squash fields can have greater than 90% infected fruits, leading to high yield losses. While reference genomes are available for this bacterial species, the genetic diversity between different strains and populations is unknown. After performing restriction‐site associated DNA sequencing (RAD‐seq) analysis of X. cucurbitae isolates collected from the Midwestern region, we selected five representative isolates for further characterization, which included whole‐genome sequencing and in vitro enzyme and in planta virulence assays. Our results suggest that minimal genetic diversity exists between these isolates, and that the isolates have differential virulence on different cucurbit host plants. This study contributes to our understanding of X. cucurbitae population dynamics in the Midwestern region and may assist with developing additional management strategies for controlling bacterial spot disease of cucurbits. [ABSTRACT FROM AUTHOR]

The genus Carabus (Coleoptera: Carabidae: Carabinae) is a group of predacious ground beetles found throughout Holarctic temperate zones. The diversification of this group is attributed not only to allopatric speciation but also to diversification in life-history traits and morphological traits that are involved in ecological adaptation and reproductive isolation. Precise phylogenetic reconstruction of Carabus is important to understanding the factors associated with species' divergence in relation to such character divergence. Here, we analyse the phylogeny of Carabus among higher taxonomic groups and among species of the subgenus Apotomopterus , a hyper-diverse group endemic to East Asia. We used genome-wide sequence data from ultraconserved elements for phylogenetic reconstruction via maximum-likelihood and species-tree reconstruction methods. With regard to the relationships among higher taxonomic groups, the obtained phylogenetic trees resolved two structures with previously unresolved divergence. The subgenus Apotomopterus contained three lineages, i.e. the Vitalisi, Prodigus, and Sauteri groups. It showed diversification of the spinula, a sclerotized male genital structure, and variation in the female elytral notch (preapical emargination). These morphological traits may be involved in copulatory behaviour and potentially affect reproductive isolation, and their character state divergence may have facilitated species divergence of Apotomopterus. [ABSTRACT FROM AUTHOR]

The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models. [ABSTRACT FROM AUTHOR]

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1 , a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1. [ABSTRACT FROM AUTHOR]

The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying the early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1,726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus —first in a widely distributed Eurasian clade and then in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also reveal several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes. [ABSTRACT FROM AUTHOR]

The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and time‐calibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing, and explored the evolutionary trends of habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae, Racemobambosinae s.l. (comprising Dinochloinae, Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l. (comprising Bambusinae s.str. plus Holttumochloinae). The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research. [ABSTRACT FROM AUTHOR]

Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command‐line applications. We develop an ultrafast and memory‐efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command‐line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited. see also the Perspective by Kin Onn Chan [ABSTRACT FROM AUTHOR]

Summary: The genomes of ectomycorrhizal (ECM) fungi have a reduced number of genes encoding Carbohydrate‐Active EnZymes (CAZymes), expansions in transposable elements (TEs) and small secreted proteins (SSPs) compared with saprotrophs. Fewer genes for specific peptidases and lipases in ECM fungi are also reported. It is unclear whether these changes occur at the shift to the ECM habit or are more gradual throughout the evolution of ECM lineages.We generated a genomic dataset of 20 species in the ECM lineage Inocybaceae and compared them with six saprotrophic species.Inocybaceae genomes have fewer CAZymes, peptidases, lipases, secondary metabolite clusters and SSPs and higher TE content than their saprotrophic relatives. There was an increase in the rate of gene family evolution along the branch with the transition to the ECM lifestyle. This branch had very high rate of evolution in CAZymes and had the largest number of contractions. Other significant changes along this branch included expansions in transporters, transposons‐related genes and communication genes such as fungal kinases.There is a high concentration of changes in proximity to the transition to the ECM lifestyle, which correspond to the identified key changes for the gain of this lifestyle. [ABSTRACT FROM AUTHOR]

Xanthium is a genus of annual herbaceous plants that stands out within Asteraceae for being wind‐pollinated, diclinous monoecious, and bearing solitary pistillate flowers in peculiar spiny structures (burs). Xanthium sect. Acanthoxanthium is native to South America and characterized by the presence of trifurcate spines at the base of the leaves. Past taxonomic treatments of the section have been contradictory, some recognising up to six species, others reducing all to a single polymorphic species. Altogether, 42 samples of X. sect. Acanthoxanthium were analysed, the vast majority taken from herbarium specimens between 20 and 160 years old. We sampled multiple specimens of X. spinosum from throughout its broad range as well as those taxa with narrower distributions, covering the whole range of morphological variation in the section. When possible, we included types and original material. We used Hyb‐Seq techniques to obtain information from about 1000 single‐copy nuclear genes and complete plastomes. Phylogenomic data were submitted to coalescent‐based species delimitation approaches (SPEEDEMON). Additionally, we performed geometric morphometric analysis of leaf outlines. The results strongly support the identification of four lineages in the section favouring the acceptance of four of the hitherto described species, i.e., X. ambrosioides, X. argenteum, X. catharticum, and X. spinosum. These results were to some extent corroborated by morphometric analyses. While X. ambrosioides was well distinct from X. spinosum based on leaf morphology, such difference was not observed between X. spinosum and X. catharticum. However, X. catharticum differs from X. spinosum in its ecological requirements, being a species rather adapted to high‐mountain environments of the Neotropics. Intriguingly, X. argenteum – a taxon described from a single herbarium collection – was also inferred as a species. [ABSTRACT FROM AUTHOR]

Background: The Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo. Methods: Muscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene. Results: The complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species. [ABSTRACT FROM AUTHOR]

The biota of cave habitats faces heightened conservation risks, due to geographic isolation and high levels of endemism. Molecular datasets, in tandem with ecological surveys, have the potential to precisely delimit the nature of cave endemism and identify conservation priorities for microendemic species. Here, we sequenced ultraconserved elements of Tegenaria within, and at the entrances of, 25 cave sites to test phylogenetic relationships, combined with an unsupervised machine learning approach for detecting species. Our analyses identified clear and well-supported genetic breaks in the dataset that accorded closely with morphologically diagnosable units. Through these analyses, we also detected some previously unidentified, potential cryptic morphospecies. We then performed conservation assessments for seven troglobitic Israeli species of this genus and determined five of these to be critically endangered. [ABSTRACT FROM AUTHOR]

Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time‐scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time‐consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often times chosen arbitrarily. Progress towards building robust biological timescales necessitates the development of better methods to visualize and quantify the sensitivity of results to these decisions.Here, we present an R package that assists in this endeavour through the use of chronospaces, that is, graphical representations summarizing variation in the node ages contained in time‐calibrated trees. We further test this approach by estimating divergence times for three empirical datasets—spanning widely differing evolutionary timeframes—using the software PhyloBayes.Our results reveal large differences in the impact of many common methodological decisions, with the choice of clock (uncorrelated vs autocorrelated) and loci having strong effects on inferred ages. Other decisions have comparatively minor consequences, including the use of the computationally intensive site‐heterogeneous model CAT‐GTR, whose effect might only be discernible for exceedingly old divergences (e.g. the deepest eukaryote nodes).The package chronospace implements a range of graphical and analytical tools that assist in the exploration of sensitivity and the prioritization of computational resources in the inference of divergence times. [ABSTRACT FROM AUTHOR]

Abstract The Pleidae, or pygmy backswimmers, is a family of aquatic bugs (Hemiptera, Heteroptera, Nepomorpha) containing four genera. Here, we describe Plea cryptica sp. nov. and redescribe its sister species, Plea minutissima Leach, 1817. Whereas the morphological distinction of these closely related species is only possible for males, molecular data clearly separate them. As part of our taxonomic study, we provide comprehensive molecular data including more than 200 DNA barcodes from all over Europe, complete nuclear ribosomal DNA, full mitochondrial genome data, and 3D scans for both species. Furthermore, the same molecular markers are also presented for Neoplea striola (Fieber, 1844). We used Maximum Likelihood (ML) analyses to reconstruct the phylogeny of the Pleidae and Notonectoidea based on available mitogenomic data. Our study represents a successful implementation of the proposed concept of taxonomics, using data from high-throughput sequencing technologies for integrative taxonomic studies, and allowing high confidence for both biodiversity and ecological research.

Polygonatum gracile P. Y. Li is a perennial rhizomatous medicinal herb endemic to China with recognized medicinal value. Here, the first complete plastid genome of P. gracile is reported and characterized, and the phylogenetic relationships of P. gracile with other Polygonatum species are clarified by phylogenetic inferences based on complete plastid genome sequences. The complete plastid genome of P. gracile is 155,734 bp in length and exhibits the typical quadripartite circular structure consisting of a large single-copy (LSC, 84,385 bp) region, a small single-copy (SSC, 18,519 bp) region, and a pair of inverted repeat regions (IRa/b, 26,415 bp). A total of 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified. Seven protein-coding genes, eight tRNA genes, and four rRNA genes were duplicated in the IR regions. Phylogenetic reconstructions indicated that P. gracile belongs to sect. Verticillata and is most closely related to P. zanlanscianense Pamp. This study provides a basis for further phylogenetic reconstructions, conservation and utilization of Polygonatum species.

Abstract Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time‐scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time‐consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often times chosen arbitrarily. Progress towards building robust biological timescales necessitates the development of better methods to visualize and quantify the sensitivity of results to these decisions. Here, we present an R package that assists in this endeavour through the use of chronospaces, that is, graphical representations summarizing variation in the node ages contained in time‐calibrated trees. We further test this approach by estimating divergence times for three empirical datasets—spanning widely differing evolutionary timeframes—using the software PhyloBayes. Our results reveal large differences in the impact of many common methodological decisions, with the choice of clock (uncorrelated vs autocorrelated) and loci having strong effects on inferred ages. Other decisions have comparatively minor consequences, including the use of the computationally intensive site‐heterogeneous model CAT‐GTR, whose effect might only be discernible for exceedingly old divergences (e.g. the deepest eukaryote nodes). The package chronospace implements a range of graphical and analytical tools that assist in the exploration of sensitivity and the prioritization of computational resources in the inference of divergence times.

Abstract Background Diplomonads are anaerobic flagellates classified within Metamonada. They contain both host-associated commensals and parasites that reside in the intestinal tracts of animals, including humans (e.g., Giardia intestinalis), as well as free-living representatives that inhabit freshwater and marine anoxic sediments (e.g., Hexamita inflata). The evolutionary trajectories within this group are particularly unusual as the free-living taxa appear to be nested within a clade of host-associated species, suggesting a reversal from host-dependence to a secondarily free-living lifestyle. This is thought to be an exceedingly rare event as parasites often lose genes for metabolic pathways that are essential to a free-living life strategy, as they become increasingly reliant on their host for nutrients and metabolites. To revert to a free-living lifestyle would require the reconstruction of numerous metabolic pathways. All previous studies of diplomonad evolution suffered from either low taxon sampling, low gene sampling, or both, especially among free-living diplomonads, which has weakened the phylogenetic resolution and hindered evolutionary insights into this fascinating transition. Results We sequenced transcriptomes from 1 host-associated and 13 free-living diplomonad isolates; expanding the genome scale data sampling for diplomonads by roughly threefold. Phylogenomic analyses clearly show that free-living diplomonads form several branches nested within endobiotic species. Moreover, the phylogenetic distribution of genes related to an endobiotic lifestyle suggest their acquisition at the root of diplomonads, while traces of these genes have been identified in free-living diplomonads as well. Based on these results, we propose an evolutionary scenario of ancestral and derived lifestyle transitions across diplomonads. Conclusions Free-living taxa form several clades nested within endobiotic taxa in our phylogenomic analyses, implying multiple transitions between free-living and endobiotic lifestyles. The evolutionary history of numerous virulence factors corroborates the inference of an endobiotic ancestry of diplomonads, suggesting that there have been several reversals to a free-living lifestyle. Regaining host independence may have been facilitated by a subset of laterally transferred genes. We conclude that the extant diversity of diplomonads has evolved from a non-specialized endobiont, with some taxa becoming highly specialized parasites, others becoming free-living, and some becoming capable of both free-living and endobiotic lifestyles.

Abstract Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.

Abstract Background Hemiptera is the fifth species-rich order of insects and the most species-rich order of hemimetabolous insects, including numerous insect species that are of agricultural or medical significance. Despite much effort and recent advance in inferring the Hemiptera phylogeny, some high-level relationships among superfamilies remain controversial. Results We sequenced the genomes of 64 hemipteran species from 15 superfamilies and the transcriptomes of two additional scale insect species, integrating them with existing genomic and transcriptomic data to conduct a comprehensive phylogenetic analysis of Hemiptera. Our datasets comprise an average of 1625 nuclear loci of 315 species across 27 superfamilies of Hemiptera. Our analyses supported Cicadoidea and Cercopoidea as sister groups, with Membracoidea typically positioned as the sister to Cicadoidea + Cercopoidea. In most analyses, Aleyrodoidea was recovered as the sister group of all other Sternorrhyncha. A sister-group relationship was supported between Coccoidea and Aphidoidea + Phylloxeroidea. These relationships were further supported by four-cluster likelihood mapping analyses across diverse datasets. Our ancestral state reconstruction indicates phytophagy as the primary feeding strategy for Hemiptera as a whole. However, predation likely represents an ancestral state for Heteroptera, with several phytophagous lineages having evolved from predatory ancestors. Certain lineages, like Lygaeoidea, have undergone a reversal transition from phytophagy to predation. Our divergence time estimation placed the diversification of hemipterans to be between 60 and 150 million years ago. Conclusions By expanding phylogenomic taxon sampling, we clarified the superfamily relationships within the infraorder Cicadomorpha. Our phylogenetic analyses supported the sister-group relationship between the superfamilies Cicadoidea and Cercopoidea, and the superfamily Membracoidea as the sister to Cicadoidea + Cercopoidea. Our divergence time estimation supported the close association of hemipteran diversification with the evolutionary success and adaptive radiation of angiosperms during the Cretaceous period.

Dipterocarpus retusus Blume is an endangered species on the IUCN Red List. In this study, we reported the complete chloroplast (cp) genome of D. retusus (GenBank accession number: OP271853). The cp genome was 154,303 bp long, with a large single-copy (LSC) region of 85,586 bp and a small single-copy (SSC) region of 20,273 bp separated by a pair of inverted repeats (IRs) of 24,222 bp. It encodes 128 genes, including 84 protein-coding genes, 36 tRNA genes, and eight ribosomal RNA genes. We also reconstructed the cp genome phylogeny of Dipterocarpus, which indicated D. retusus was closely related with the sympatric species D. gracilis. This study may contribute valuable information to the phylogenetic relationships within the genus Dipterocarpus.

Dracocephalum is a large genus comprises approximately 80 species of perennial herbs, mainly distributed in high elevation regions of temperate and Central Asia, with about half native to China. Within the genus, D. argunense and D. integrifolium are important herbs with great medicinal value. We sequenced plastomes of these two species for the first time. These plastomes showed a typical quadripartite structure and the length varied from 149,978 bp (D. integrifolium) to 150,802 bp (D. argunense). Plastomes of D. argunense and D. integrifolium included 127 and 133 genes, respectively. Phylogenetic analyses supported the monophyly of the redefined Dracocephalum and systematic relationships within the sampled species were well resolved. Our study added new genetic information about D. argunense and D. integrifolium and has great potential for further diversity studies, phylogenetic studies, and understanding of evolutionary history in Dracocephalum.

Abstract Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda’s recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.

Abstract Cyanobacteria are globally occurring photosynthetic bacteria notable for their contribution to primary production and production of toxins which have detrimental ecosystem impacts. Furthermore, cyanobacteria can form mutualistic symbiotic relationships with a diverse set of eukaryotes, including land plants, aquatic plankton and fungi. Nevertheless, not all cyanobacteria are found in symbiotic associations suggesting symbiotic cyanobacteria have evolved specializations that facilitate host-interactions. Photosynthetic capabilities, nitrogen fixation, and the production of complex biochemicals are key functions provided by host-associated cyanobacterial symbionts. To explore if additional specializations are associated with such lifestyles in cyanobacteria, we have conducted comparative phylogenomics of molecular functions and of biosynthetic gene clusters (BGCs) in 984 cyanobacterial genomes. Cyanobacteria with host-associated and symbiotic lifestyles were concentrated in the family Nostocaceae, where eight monophyletic clades correspond to specific host taxa. In agreement with previous studies, symbionts are likely to provide fixed nitrogen to their eukaryotic partners, through multiple different nitrogen fixation pathways. Additionally, our analyses identified chitin metabolising pathways in cyanobacteria associated with specific host groups, while obligate symbionts had fewer BGCs. The conservation of molecular functions and BGCs between closely related symbiotic and free-living cyanobacteria suggests the potential for additional cyanobacteria to form symbiotic relationships than is currently known.

Abstract The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.

Endemic to Taiwan Province, China, Cotoneaster rosiflorus Kun-Cheng Chang & Fu-Yuan Lu 2011 (Rosaceae) holds significant ecological and ornamental importance. Despite its value, research on its molecular data and phylogenetic position has remained limited. In this study, we addressed this gap by sequencing the genome-skimming data, assembling its plastome, and investigating its phylogenetic position. The plastome, spanning 159,449 bp in length, consisted of a large single-copy (87,433 bp), a small single-copy (19,262 bp), and two inverted repeat regions (26,377 bp). We annotated a total of 128 functional genes, including 84 protein-coding genes, 36 transfer genes, and eight ribosomal RNA genes. The phylogenetic results indicated that C. rosiflorus is closely related to C. dammerii, suggesting that C. rosiflorus might have captured its chloroplast from C. dammerii through hybridization and introgression events. This study offered valuable insights for forthcoming phylogenetic and population genetic investigations of Cotoneaster.