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BACKGROUND: Monitoring genotypes of HIV infections in blood donors may provide insights into infection trends in the general population. METHODS: HIV RNA was extracted from plasma samples of blood donors confirmed as HIV positive by blood screening nucleic acid and antibody tests. HIV genome target regions were amplified using nested real time-polymerase chain reaction followed by next-generation sequencing. Sequences were compared to those in the Los Alamos National Laboratory (LANL) database. Sequences were also assessed for drug resistance mutations (DRM) using the Stanford HIV DRM Database. RESULTS: From available HIV-positive donations collected between 1 September 2015 and 31 December 2020, 563 of 743 (75.8%) were successfully sequenced; 4 were subtype A, 543 subtype B, 5 subtype C, 1 subtype G, 5 circulating recombinant forms (CRF), and 2 were subtype B and D recombinants. Overall, no significant differences between blood donor and available LANL genotypes were found, and the genotypes of newly acquired versus prevalent HIV infections in donors were similar. The proportion of non-B subtypes and CRF remained a small fraction, with no other subtype or CRF representing more than 1% of the total. DRM were identified in 122 (21.6%) samples with protease inhibitor, nucleoside reverse transcriptase inhibitor and non-nucleoside reverse transcriptase inhibitor DRMs identified in 4.9%, 4.6% and 14.0% of samples, respectively. CONCLUSIONS: HIV genetic diversity and DRM in blood donors appear representative of circulating HIV infections in the US general population and may provide more information on infection diversity than sequences reported to LANL, particularly for recently transmitted infections.

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC) run explores the space of phylogenetic trees. In this paper, we investigate the Monte Carlo error of phylogenies, focusing on high-dimensional summaries of the posterior distribution, including variability in estimated edge/branch (known in phylogenetics as split) probabilities and tree probabilities, and variability in the estimated summary tree. Specifically, we ask if there is any measure of effective sample size (ESS) applicable to phylogenetic trees which is capable of capturing the Monte Carlo error of these three summary measures. We find that there are some ESS measures capable of capturing the error inherent in using MCMC samples to approximate the posterior distributions on phylogenies. We term these tree ESS measures, and identify a set of three which are useful in practice for assessing the Monte Carlo error. Lastly, we present visualization tools that can improve comparisons between multiple independent MCMC runs by accounting for the Monte Carlo error present in each chain. Our results indicate that common post-MCMC workflows are insufficient to capture the inherent Monte Carlo error of the tree, and highlight the need for both within-chain mixing and between-chain convergence assessments.

The disparate global range of Plethodontid salamanders in the Batrachoseps subgenus Plethopsis is unique, and implicates perplexing historical biogeographic scenarios.  Using uncorrelated relaxed molecular clock methods and fossil-calibrated divergence estimates from Shen et al. (2016), we present a time-scaled phylogeny for the genus Batrachoseps in order to test hypotheses concerning the diversification of the subgenus Plethopsis.  Our estimated divergence time intervals detract support from a hypothesis that Batrachoseps robustus diverged as the flow of the Owens river changed course at ca. 3.2 Ma, as evidenced by sediment deposits at Searles Lake (Phillips, 2008).  Instead, our estimates support that diversification of the known Plethopsis species began earlier, in the late Miocene to early Pliocene, as extensional activity formed the proto-Owens Valley and led to ensuing hydrological and climatic changes, driving vicariance between populations in the proto-southern Sierra Nevada and Inyo Mountains.  Moreover, our estimates support a scenario wherein B. campi and B. wrighti diverged in the Pliocene as ancestral populations of B. wrighti expanded northward to Oregon via a corridor of relatively mesic habitat in the western Great Basin.

BackgroundHIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data.MethodsWe simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively.ResultsConsensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network.ConclusionSource attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.

With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine-learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.

SUMMARY: Cytochrome P450 monooxygenases of the CYP79 family catalyze conversion of specific amino acids into oximes feeding into a variety of metabolic plant pathways. Here we present an extensive phylogenetic tree of the CYP79 family built on carefully curated sequences collected across the entire plant kingdom. Based on a monophyletic origin of the P450s, a set of evolutionarily distinct branches was identified. Founded on the functionally characterized CYP79 sequences, sequence features of the individual substrate recognition sites (SRSs) were analyzed. Co‐evolving amino acid residues were identified using co‐evolutionary sequence analysis. SRS4 possesses a specific sequence pattern when tyrosine is a substrate. Except for the CYP79Cs and CYP79Fs, substrate preferences toward specific amino acids could not be assigned to specific subfamilies. The highly diversified CYP79 tree, reflecting recurrent independent evolution of CYP79s, may relate to the different roles of oximes in different plant species. The sequence differences across individual CYP79 subfamilies may facilitate the in vivo orchestration of channeled metabolic pathways based on altered surface charge domains of the CYP79 protein. Alternatively, they may serve to optimize dynamic interactions with oxime metabolizing enzymes to enable optimal ecological interactions. The outlined detailed curation of the CYP79 sequences used for building the phylogenetic tree made it appropriate to make a conservative phylogenetic tree‐based revision of the naming of the sequences within this highly complex cytochrome P450 family. The same approach may be used in other complex P450 subfamilies. The detailed phylogeny of the CYP79 family will enable further exploration of the evolution of function in these enzymes. Significance Statement: An extensive phylogenetic tree of the CYP79 family, built on 1531 carefully curated sequences, identified evolutionarily distinct branches reflecting the diversified uses of the oximes produced by CYP79 in plants and necessitated a conservative phylogenetic tree‐based revision of the naming of sequences within this highly complex cytochrome P450 family. The detailed phylogeny of the CYP79 family will guide further exploration of the evolutionary functions of these enzymes in plant resilience. [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]

ABSTRACT Low coverage ‘genome‐skims’ are often used to assemble organelle genomes and ribosomal gene sequences for cost‐effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction‐based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome‐skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low‐coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet. [ABSTRACT FROM AUTHOR]

Summary While flowering plants have diversified in virtually every terrestrial clime, climate constrains the distribution of individual lineages. Overcoming climatic constraints may be associated with diverse evolutionary phenomena including whole genome duplication (WGD), gene‐tree conflict, and life‐history changes. Climatic shifts may also have facilitated increases in flowering plant diversification rates. We investigate climatic shifts in the flowering plant order Ericales, which consists of c. 14 000 species with diverse climatic tolerances. We estimate phylogenetic trees from transcriptomic data, 64 chloroplast loci, and Angiosperms353 nuclear loci that, respectively, incorporate 147, 4508, and 2870 Ericales species. We use these phylogenetic trees to analyse how climatic shifts are associated with WGD, gene‐tree conflict, life‐history, and diversification rates. Early branches in the phylogenetic trees are extremely short, and have high levels of gene‐tree conflict and at least one WGD. On lineages descended from these early branches, there is a significant association between climatic shifts (primarily out of tropical climates), further WGDs, and life‐history. Extremely short early branches, and their associated gene‐tree conflict and WGDs, appear to underpin the explosive origin of numerous species rich Ericales clades. The evolution of diverse climatic tolerances in these species rich clades is tightly associated with WGD and life‐history. [ABSTRACT FROM AUTHOR]

Morchella helvetica, sp. nov. (Morchella sect. Distantes) is a new species of true morels discovered in Switzerland. It is formally described in the present study using an integrative approach based on micro- and macromorphological characteristics, multilocus phylogenetics, and a brief description of its habitat. Molecular analyses clearly indicated that Morchella helvetica is a sister species to M. eximioides, M. angusticeps, and M. confusa. It can be distinguished by the two phylogenetic markers RNA polymerase II subunit 2 (RPB2) and translation elongation factor-1 alpha (TEF1-α). In addition, M. helvetica exhibits particular morphological features, notably the presence of pale hairs on the pileus, a mealy stipe, and darkening ridges when aging. [ABSTRACT FROM AUTHOR]

Introduction: Throughout domestication, crop plants have gone through strong genetic bottlenecks, dramatically reducing the genetic diversity in today's available germplasm. This has also reduced the diversity in traits necessary for breeders to develop improved varieties. Many strategies have been developed to improve both genetic and trait diversity in crops, from backcrossing with wild relatives, to chemical/radiation mutagenesis, to genetic engineering. However, even with recent advances in genetic engineering we still face the rate limiting step of identifying which genes and mutations we should target to generate diversity in specific traits. Methods: Here, we apply a comparative evolutionary approach, pairing phylogenetic and expression analyses to identify potential candidate genes for diversifying soybean (Glycine max) canopy cover development via the nuclear auxin signaling gene families, while minimizing pleiotropic effects in other tissues. In soybean, rapid canopy cover development is correlated with yield and also suppresses weeds in organic cultivation. Results and discussion: We identified genes most specifically expressed during early canopy development from the TIR1/AFB auxin receptor, Aux/IAA auxin coreceptor, and ARF auxin response factor gene families in soybean, using principal component analysis. We defined Arabidopsis thaliana and model legume species orthologs for each soybean gene in these families allowing us to speculate potential soybean phenotypes based on well-characterized mutants in these model species. In future work, we aim to connect genetic and functional diversity in these candidate genes with phenotypic diversity in planta allowing for improvements in soybean rapid canopy cover, yield, and weed suppression. Further development of this and similar algorithms for defining and quantifying tissue- and phenotype-specificity in gene expression may allow expansion of diversity in valuable phenotypes in important crops. [ABSTRACT FROM AUTHOR]

Background Men and women with a migration background comprise an increasing proportion of incident human immunodeficiency virus (HIV) cases across Western Europe. Methods To characterize sources of transmission in local transmission chains, we used partial HIV consensus sequences with linked demographic and clinical data from the opt-out AIDS Therapy Evaluation in the Netherlands (ATHENA) cohort of people with HIV in the Netherlands and identified phylogenetically and epidemiologically possible HIV transmission pairs in Amsterdam. We interpreted these in the context of estimated infection dates, and quantified population-level sources of transmission to foreign-born and Dutch-born Amsterdam men who have sex with men (MSM) within Amsterdam transmission chains. Results We estimate that Dutch-born MSM were the predominant sources of infections among all Amsterdam MSM who acquired their infection locally in 2010–2021, and among almost all foreign-born Amsterdam MSM subpopulations. Stratifying by 2-year intervals indicated time trends in transmission dynamics, with a majority of infections originating from foreign-born MSM since 2016, although uncertainty ranges remained wide. Conclusions Native-born MSM have predominantly driven HIV transmissions in Amsterdam in 2010–2021. However, in the context of rapidly declining incidence in Amsterdam, the contribution from foreign-born MSM living in Amsterdam is increasing, with some evidence that most local transmissions have been from foreign-born Amsterdam MSM since 2016. [ABSTRACT FROM AUTHOR]

The colonization of land by plants approximately 450–500 million years ago (Mya) is one of the most important events in the history of life on Earth. Land plants, hereafter referred to as “embryophytes,” comprise the foundation of every terrestrial biome, making them an essential lineage for the origin and maintenance of biodiversity. The embryophytes form a monophyletic clade within one of the two major phyla of the green algae (Viridiplantae), the Streptophyta. Estimates from fossil data and molecular clock analyses suggest the Streptophyte algae (Charophytes) diverged from the other main phylum of green algae, the Chlorophyta, as much as 1500 Mya. Here we present a phylogenetic analysis using transcriptomic and genomic data of 62 green algae and embryophyte operational taxonomic units, 31 of which were assembled de novo for this project. We have focused on identifying the charophyte lineage that is sister to embryophytes, and show that the Zygnematophyceae have the strongest support, followed by the Charophyceae. Furthermore, we have examined amino acid and codon usage across the tree and determined these data broadly follow the phylogenetic tree. We concluded by searching the data set for protein domains and gene families known to be important in embryophytes. Many of these domains and genes have homologous sequences in the charophyte lineages, giving insight into the processes that underlay the colonization of the land by plants. This provides new insights into green algal diversification, identifies previously unknown attributes of genome evolution within the group, and shows how functional mechanisms have evolved over time. [ABSTRACT FROM AUTHOR]

Variation in coat color is a prominent feature in carnivores, thought to be shaped by environmental factors. As new traits could allow populations to occupy novel niches and habitats, color polymorphism may be maintained by balancing selection. Consequently, color polymorphic species may speciate more rapidly and can give rise to monomorphic daughter species. We thus predicted that, within the Carnivora, (i) speciation rate is higher in polymorphic lineages, (ii) divergence between color polymorphic lineages is more recent, and (iii) within closely related groups, polymorphic lineages are ancestral and monomorphic lineages derived. We also tested whether accelerated speciation rates relate to niche breadth, measured by the number of occupied habitats and range size. We collected data of 48 polymorphic and 192 monomorphic carnivore species, and assessed speciation rates using phylogenetic comparative methods. We found that polymorphic carnivores had higher speciation rates (λ1 = 0.29, SD = 0.13) than monomorphic species (λ0 = 0.053, SD = 0.044). Hidden and quantitative state speciation and extinction models inferred that color polymorphism was the main contributing factor, and that niche breadth was not of influence. Therefore, other selective forces than spatial niche segregation, such as predator-prey coevolution, may contribute to color polymorphism in wild carnivores. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions Ferns are globally distributed, yet the number of studies examining the historical evolution of African taxa is relatively low. Investigation of the evolution of African fern diversity is critical in order to understand patterns and processes that have global relevance (e.g., the pantropical diversity disparity [PDD] pattern). This study aims to examine when and from where a globally distributed fern lineage arrived in sub‐Saharan Africa, to obtain a better understanding of potential processes contributing to patterns of diversity across the region.Global, sub‐Saharan Africa.Asplenium (Aspleniaceae).We analysed five loci from 537 Asplenium taxa using a maximum likelihood (IQ‐Tree) phylogenetic framework. For age estimation, we performed penalised likelihood as implemented in treePL, and executed a Bayesian analysis using BEAST. Biogeographical analyses were carried out using BioGeoBEARS.Most dispersals into Africa occurred within the last ~55 myr, with the highest diversity of sub‐Saharan African taxa concentrated in two clades, each of which descended from an Asian ancestor. Additional dispersals to sub‐Saharan Africa can be found throughout the phylogeny. Lastly, potential cryptic species diversity exists within Asplenium as evidenced by several polyphyletic taxa.We recover multiple dispersals of Asplenium to sub‐Saharan Africa, with two major lineages likely diversifying after arrival. [ABSTRACT FROM AUTHOR]

ABSTRACT In silico characterization of the Gretchen Hagen3 (GH3) gene family is required for understanding phytohormone regulation and stress responses in Brassica rapa to develop the improved stress‐tolerant cultivars. The main objective of this research was to identify the key BrGH3 genes under different abiotic stresses. Using bioinformatics tools, a total of 27 BrGH3 genes were identified in B. rapa for which phylogenetic relationship, syntenic pairing, conserved motifs, miRNA regulation, and cis‐regulatory elements of BrGH3s were also studied. BrGH3 gene expression has been examined in numerous tissues and under various abiotic and phytohormone stressors. Phylogenetic studies separated BrGH3 genes into three major classes and nine subclasses based on gene functional evolution. Collinearity analysis demonstrated that all BrGH3 genes had syntenic linkage with AtGH3, BnaGH3, and BolGH3, indicating that genome duplication mechanisms were crucial to BrGH3 gene evolution. The expression dynamics of BrGH3 under diverse phytohormonal stresses methyl jasmonate (MeJA), auxin (IAA), abscisic acid (ABA), gibberellic acid (GA), and salicylic acid (SA) at different time intervals suggest that BrGH3‐5.1 has a consistently greater expression than other BrGH3 genes. Under salt, drought, and low temperature stress, BrGH3‐1 and BrGH3‐4 genes expressed comparatively higher. The findings suggest that five genes (BrGH3‐5.1, BrGH3‐5.2, BrGH3‐15, BrGH3‐17.2, and BrGH3‐19) have a key role in inducing broad stress resilience. These results can be beneficial in developing stress‐tolerant varieties of Chinese cabbage. [ABSTRACT FROM AUTHOR]

Background: The phylum Nematoda is incredibly diverse and includes many parasites of humans, livestock, and plants. Peptide-activated G protein-coupled receptors (GPCRs) are central to the regulation of physiology and numerous behaviors, and they represent appealing pharmacological targets for parasite control. Efforts are ongoing to characterize the functions and define the ligands of nematode GPCRs, with already most peptide GPCRs known or predicted in Caenorhabditis elegans. However, comparative analyses of peptide GPCR conservation between C. elegans and other nematode species are limited, and many nematode GPCRs remain orphan. A phylum-wide perspective on peptide GPCR profiles will benefit functional and applied studies of nematode peptide GPCRs. Results: We constructed a pan-phylum resource of C. elegans peptide GPCR orthologs in 125 nematode species using a semi-automated pipeline for analysis of predicted proteome datasets. The peptide GPCR profile varies between nematode species of different phylogenetic clades and multiple C. elegans peptide GPCRs have orthologs across the phylum Nematoda. We identified peptide ligands for two highly conserved orphan receptors, NPR-9 and NPR-16, that belong to the bilaterian galanin/allatostatin A (Gal/AstA) and somatostatin/allatostatin C (SST/AstC) receptor families. The AstA-like NLP-1 peptides activate NPR-9 in cultured cells and are cognate ligands of this receptor in vivo. In addition, we discovered an AstC-type peptide, NLP-99, that activates the AstC-type receptor NPR-16. In our pan-phylum resource, the phylum-wide representation of NPR-9 and NPR-16 resembles that of their cognate ligands more than those of allatostatin-like peptides that do not activate these receptors. Conclusions: The repertoire of C. elegans peptide GPCR orthologs varies across phylogenetic clades and several peptide GPCRs show broad conservation in the phylum Nematoda. Our work functionally characterizes the conserved receptors NPR-9 and NPR-16 as the respective GPCRs for the AstA-like NLP-1 peptides and the AstC-related peptide NLP-99. NLP-1 and NLP-99 are widely conserved in nematodes and their representation matches that of their receptor in most species. These findings demonstrate the conservation of a functional Gal/AstA and SST/AstC signaling system in nematodes. Our dataset of C. elegans peptide GPCR orthologs also lays a foundation for further functional studies of peptide GPCRs in the widely diverse nematode phylum. [ABSTRACT FROM AUTHOR]

The multigene family of the major histocompatibility complex (MHC) codes for the key antigen-presenting molecules of the vertebrate immune system. In birds, duplicated MHC class II (MHC-II) genes are highly homogenized by concerted evolution, and thus, identification of their orthologous relationships across long evolutionary timescales remains challenging. Relatively low evolutionary rate of avian MHC class IIA genes has been expected to provide a promising avenue to allow such inferences, but availability of MHC-IIA sequences in nonmodel bird species has been limited until recently. Here, taking advantage from accumulating genomic resources, we identified and analyzed MHC-IIA sequences from the most basal lineage of extant birds (Palaeognathae). Conserved region of the MHC-IIA membrane-proximal domain was used to search for orthologous relationships between palaeognath birds and nonavian reptiles. First, analyses of palaeognath sequences revealed the presence of a separate MHC-IIA gene lineage (DAA3) in kiwis, which did not cluster with previously described avian MHC-IIA lineages (DAA1 and DAA2). Next, phylogenetic reconstruction showed that kiwi DAA3 sequences form a single well-supported cluster with turtle MHC-IIA. High similarity of these sequences most likely reflects their remarkable evolutionary conservation and retention of ancient orthologous relationships, which can be traced back to basal archosauromorphs ca. 250 million years ago. Our analyses offer novel insights into macroevolutionary history of the MHC and reinforce the view that rapid accumulation of high-quality genome assemblies across divergent nonmodel species can substantially advance our understanding of gene evolution. [ABSTRACT FROM AUTHOR]

Brassinosteroid (BR) signaling is regulated by BRI1-EMS SUPPRESSOR 1 (BES1) transcription factors, which are crucial for plant growth, development, and stress responses. Despite their importance, BES1 gene studies in Medicago sativa L. are limited, hindering our understanding of the BR signaling in this species. This study identified four BES1 genes in M. sativa; characterized their properties, conserved motifs, cis-regulatory elements, and chromosomal location; and explored their functions in development and stress responses. A phylogenetic analysis grouped these genes into two subfamilies. Transcript profiling showed widespread and tissue-specific expression patterns. A qRT-PCR analysis unveiled that most MsBESI genes were upregulated under salt and drought treatments, except MsG0280009980, which was suppressed. This research lays the groundwork for enhancing M. sativa stress resistance and understanding the BES1 gene family's function. [ABSTRACT FROM AUTHOR]

Premise: The wheat tribe, Triticeae, has been the subject of molecular phylogenetic analyses for nearly three decades, and extensive phylogenetic conflict has been apparent from the earliest comparisons among DNA‐based data sets. While most previous analyses focused primarily on nuclear vs. chloroplast DNA conflict, the present analysis provides a broader picture of conflict among nuclear loci throughout the tribe. Methods: Exon data were generated from over 1000 nuclear loci using targeted sequence capture with custom baits, and nearly complete chloroplast genome sequences were recovered. Phylogenetic conflict was assessed among the trees from the chloroplast genomes, the concatenated nuclear loci, and a series of nuclear‐locus subsets guided by Hordeum chromosome gene maps. Results: At the intergeneric level, the analyses collectively revealed a few broadly consistent relationships. However, the prevailing pattern was one of extensive phylogenetic conflict throughout the tribe, among both deep and shallow branches, and with the extent of the conflict varying among data subsets. Conclusions: The results suggest continual introgression or lineage sorting within and among the named lineages of the Triticeae, shaping both deep and shallow relationships in the tribe. [ABSTRACT FROM AUTHOR]

Accurate taxonomic species identification is essential to the study of mammals. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for noninvasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a polymerase chain reaction (PCR)-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from 9 mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS barcoding of noninvasive samples. By mapping to the entire National Center for Biotechnology Information mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all fecal samples. Eight of 9 species identifications matched previous PCR or animal/fecal appearance-based identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications—particularly in field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts cause changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies. [ABSTRACT FROM AUTHOR]

Despite tropical species comprising nearly 60% of Psocidae species, previous studies examining the Psocidae phylogeny have undersampled tropical diversity (<40% species in trees). Here we discuss the systematics of the Psocidae based on the most comprehensive species-level sampling of the Psocidae. We infer the phylogenetic position of 43 previously unsampled Neotropical species in the Psocidae phylogeny. We find that Neotropical psocids are generally not closely related to morphologically similar taxa in the Holarctic region. Consequently, the monophyletic status for the major groups within Psocidae (subfamilies and tribes) is recovered only when Holarctic groups are sampled (7–10 of 11 higher-level groups are monophyletic) but violated when Neotropical species are also sampled in the tree (1 of 11 higher-level groups are monophyletic). Our study pinpoints at the downfalls of simply extending taxonomic knowledge from lineages of a certain area (i.e. Holarctic) to inform diversity and evolution of lineages in other regions (i.e. Neotropics). [ABSTRACT FROM AUTHOR]

Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5'UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases. [ABSTRACT FROM AUTHOR]

In this study, the complete mitochondrial genome of Triplophysa erythraea was determined for the first time. Results showed the mitogenome was 16 565 bp, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 2 non-coding regions. The overall base composition of its mitochondrial genome was 28.9% A, 25.2% T, 28.7% C and 17.2% G. Phylogenetic tree revealed that Triplophysa erythraea had the closest relationship with Triplophysa xiangxiensis, which was also found in Xiangxi Tujia and Miao Nationality Autonomous Prefecture, Hunan province. In general, this study provided valuable information for conservation genetics analyses of Triplophysa erythraea and further displayed the evolution of species within the genus Triplophysa. [ABSTRACT FROM AUTHOR]

The present study aimed to analyze the cladistics and population structure analysis of Rhipicephalus microplus ticks infesting buffaloes in Haryana, India, as well as the assessment of the anti-tick efficacy of the ethanolic extracts of Cassia fistula (bark, pod pulp, and flowers) against R. microplus larvae. The molecular characterization and population structure analysis were performed by targeting the amplification of the partial mitochondrial cytochrome C oxidase subunit 1 (cox1) gene, whereas anti-tick efficacy was evaluated using a larval packet test. The sequences generated herein revealed a homology of 98.26–100% to the GenBank-archived R. microplus sequences. In population structure analysis, high haplotype (0.500 ± 0.265) and low nucleotide (0.002 ± 0.001) diversities were recorded for the sequences generated in this study. Significantly negative neutrality indices were recorded for the overall dataset. The extracts were found to significantly affect mortality rates in a dose-dependent manner, and the ethanolic extracts of the bark, pod pulp, and flowers of C. fistula exhibited median lethal concentration (LC50) values of 27.989, 40.457, and 49.43 mg/mL, respectively. The LC50 value recorded for the combination of the ethanolic extracts of the bark, flower, and pod pulp of C. fistula was 19.724 mg/mL, whereas the synthetic acaricide ivermectin had an LC50 value of 351.56 mg/mL. In conclusion, R. microplus populations infesting cattle and buffalo hosts in India exhibited negligible genetic differentiation and high gene flow between them. Additionally, the combination of all C. fistula extracts could serve as a potential substitute for the synthetic acaricide. [ABSTRACT FROM AUTHOR]

There are substantial gaps in our empirical knowledge of the effects of chemical exposure on aquatic life that are unlikely to be filled by traditional laboratory toxicity testing alone. One possible alternative of generating new toxicity data is cross-species extrapolation (CSE), a statistical approach in which existing data are used to predict the effect of a chemical on untested species. Some CSE models use relatedness as a predictor of chemical sensitivity, but relatively little is known about how strongly shared evolutionary history influences sensitivity across all chemicals. To address this question, we conducted a survey of phylogenetic signal in the toxicity data from aquatic animal species for a large set of chemicals using a phylogeny inferred from taxonomy. Strong phylogenetic signal was present in just nine of thirty-six toxicity datasets, and there were no clear shared properties among those datasets with strong signal. Strong signal was rare even among chemicals specifically developed to target insects, meaning that these chemicals may be equally lethal to non-target taxa, including chordates. When signal was strong, distinct patterns of sensitivity were evident in the data, which may be informative when assembling toxicity datasets for regulatory use. Although strong signal does not appear to manifest in aquatic toxicity data for most chemicals, we encourage additional phylogenetic evaluations of toxicity data in order to guide the selection of CSE tools and as a means to explore the patterns of chemical sensitivity across the broad diversity of life. [ABSTRACT FROM AUTHOR]

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. Highlights: • Expanding the taxon sampling of phylogenomic analyses for diplomonads by sequencing transcriptomes of 13 free-living isolates and one endobiotic isolate. • Constructing a well-resolved evolutionary framework for exploring lifestyle adaptation in diplomonads using a phylogenomic approach. • Identifying genetic signatures of parasitic ancestry (variant-specific surface proteins, virulence factors) in free-living diplomonads. [ABSTRACT FROM AUTHOR]

The diagnosis of drug‐resistant tuberculosis (TB) by molecular testing of Mycobacterium tuberculosis drug resistance genes is becoming increasingly common clinically. However, M. bovis, as an uncommon pathogen of human TB, may interfere with the test results. A comprehensive understanding of phylogenetically informative mutations in the drug resistance genes of M. bovis is required to distinguish true resistance‐conferring mutations. We analyzed 53 drug resistance genes in 165 M. bovis isolated from humans using whole‐genome sequencing data and found that 98.2% (162/165) of isolates have pyrazinamide intrinsic genotypic resistance, owing to the H57D mutation in the pncA gene. 12.1% (20/165) of M. bovis isolates were resistant to drugs other than pyrazinamide. Furthermore, we discovered 18 phylogenetically informative mutations that differed between M. bovis and the major lineages 1–4 of M. tuberculosis. Additionally, we reported false‐positive ethambutol resistance caused by M. bovis infection due to the phylogenetically informative mutation embB E378A. This study is crucial for gaining insights into the genetic characterization and drug resistance of M. bovis prevalent in humans, as well as contributing to the development of more accurate molecular diagnostic methods and detection tools for drug resistance. [ABSTRACT FROM AUTHOR]

The taxonomy of the Parachela–Oxygaster–Macrochirichthys clade of Xenocyprididae has been confused since the original descriptions of Parachela oxygastroides and Parachela hypophthalmus in the mid‐19th century. The confusion seems attributable to the substantial intraspecific variation in color and other morphological characteristics of species of Oxygaster and Parachela. Morphological data on 401 specimens from throughout the range of Parachela and molecular phylogenetic analyses indicate that six available species names for Parachela are valid: Parachela cyanea, P. hypophthalmus, Parachela ingerkongi, Parachela johorensis (removed from the synonymy of P. oxygastroides), P. oxygastroides, and Parachela williaminae. In addition, two new species of Parachela, Parachela melanosticta and Parachela microlepis, are described. Chela pointoni is a synonym of P. oxygastroides, not a valid species of Oxygaster as previously hypothesized, and Parachela maculicauda is a synonym of Parachela johorensis. Considerable morphological and genetic variation is present in all well‐sampled species of Parachela. [ABSTRACT FROM AUTHOR]

AbstractApomixis, the reproduction via asexually formed seed, is taxonomically scattered in angiosperms. Here we review the major developmental pathways to apomixis and the occurrences on the level of orders and families. We provide surveys of large families for which occurrences and evolutionary pathways of apomixis are well documented (Poaceae, Ranunculaceae, Plumbaginaceae, Rosaceae, Brassicaceae, Rutaceae, and Asteraceae). Molecular phylogenetic, phylogenomic, and cytogenetic studies have confirmed that apomixis frequently arises in hybrids, with or without polyploidy. Multiple origins, different developmental pathways, and genetic/epigenetic control mechanisms confirm that apomixis is a derived trait. Pollen functions are in many taxa maintained for fertilization of polar nuclei and proper endosperm development, which allows also for maintenance of facultative sexuality and further intercrossing of lineages. This way, apomixis often results in huge and dynamic complexes of numerous hybrid genotypes and phenotypes with highly reticulate relationships. Such complexes are successful to establish in various habitats and geographical regions. Expression of apomixis appears to be in some genera influenced by environmental conditions. The diversity of evolutionary pathways is reflected in various, genus-wise taxonomic treatments. Future research is needed to understand the short-term evolutionary dynamics, the functional background for apomixis, and the long-term evolutionary fates of apomictic lineages. [ABSTRACT FROM AUTHOR]

The ROCO family is a family of GTPases characterized by a central ROC-COR tandem domain. Interest in the structure and function of ROCO proteins has increased with the identification of their important roles in human disease. Nevertheless, the functions of most ROCO proteins are still unknown. In the present study, we characterized the structure, evolution, and expression of ROCOs in four species of brown algae. Brown algae have a larger number of ROCO proteins than other organisms reported to date. Phylogenetic analyses showed that ROCOs have an ancient origin, likely originated in prokaryotes. ROCOs in brown algae clustered into four groups and showed no strong relationship with red algae or green algae. Brown algal ROCOs retain the ancestral LRR-ROC-COR domain arrangement, which is found in prokaryotes, plants and some basal metazoans. Remarkably, individual LRR motifs in ROCO genes are each encoded by separate exons and exhibit intense exon shuffling and diversifying selection. Furthermore, the tandem LRR exons exhibit alternative splicing to generate multiple transcripts. Both exon shuffling and alternative splicing of LRR repeats may be important mechanisms for generating diverse ligand-binding specificities as immune receptors. Besides their potential immune role, expression analysis shows that many ROCO genes are responsive to other stress conditions, suggesting they could participate in multiple signal pathways, not limited to the immune response. Our results substantially enhance our understanding of the structure and function of this mysterious gene family. [ABSTRACT FROM AUTHOR]

Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome. Here, we sequenced, assembled, and annotated the cp genomes of the threatened Quercus marlipoensis (160,995 bp) and Q. kingiana (161,167 bp), and mined these genomes for repeat sequences and codon usage bias. Comparative genomic analyses, phylogenomics, and selection pressure analysis were also performed in these two threatened species along with other species of Quercus. We found that the guanine and cytosine content of the two cp genomes were similar. All 131 annotated genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, had the same order in the two species. A strong A/T bias was detected in the base composition of simple sequence repeats. Among the 59 synonymous codons, the codon usage pattern of the cp genomes in these two species was more inclined toward the A/U ending. Comparative genomic analyses indicated that the cp genomes of Quercus section Ilex are highly conserved. We detected eight highly variable regions that could be used as molecular markers for species identification. The cp genome structure was consistent and different within and among the sections of Quercus. The phylogenetic analysis showed that section Ilex was not monophyletic and was divided into two groups, which were respectively nested with section Cerris and section Cyclobalanopsis. The two threatened species sequenced in this study were grouped into the section Cyclobalanopsis. In conclusion, the analyses of cp genomes of Q. marlipoensis and Q. kingiana promote further study of the taxonomy, phylogeny and evolution of these two threatened species and Quercus. [ABSTRACT FROM AUTHOR]

Metamonads are a large and exclusively anaerobic group of protists. Additionally, they are one of the three clades proposed to ancestrally possess an “excavate” cell morphology, with a conspicuous ventral groove accompanied by a posterior flagellum with a vane. Here, we cultivate and characterize four anaerobic bacterivorous flagellates from hypersaline and alkaline soda lake environments, which represent a novel clade. Small subunit ribosomal RNA (SSU rRNA) gene phylogenies support recent phylogenomic analyses in placing them as the sister of barthelonids, a group that is itself sister to or deeply branching within Fornicata (Metamonada). The new isolates have a distinctive morphology: the hunchbacked cell body is traversed by a narrow ventral groove ending in a large opening to a conspicuous recurrent cytopharynx. The right margin of the groove is defined by a thin “lip.” The posterior flagellum bears a wide ventral‐facing vane. The narrow ventral groove and elongate cytopharynx are shared with barthelonids. We describe one isolate as Skoliomonas litria, gen. et sp. nov. Further investigation of their mitochondrial‐related organelles (MROs) and detailed ultrastructural studies would be important to understanding the adaptation to anaerobic conditions in Metamonads—especially fornicates—as well as the evolution of the “excavate” cell architecture. [ABSTRACT FROM AUTHOR]

The reed snakes of the genus Calamaria Boie, 1827 are one of the largest groups of Asian snakes, distributed from northeast India to the Maluku Islands of east Indonesia. Recent research on the genus in China has revealed that the species diversity of the group was underestimated. In this study, morphological comparisons and mitochondrial DNA analysis revealed that a junior synonym of C. pavimentata Duméril, Bibron & Duméril, 1854 — Calamaria berezowskii Günther, 1896 is valid, hence we redescribed and recovered the validity of C. berezowskii. This species can be distinguished from other congeners by the combination of the following characters: four supralabials; one preocular; rostral shield width larger than height; mental not touching anterior chin shields; eye diameter less than the distance from eye to mouth edge; less than 1/2 of the posterior chin shield meets in the midline; dorsal scales reduced to six rows at tail; indistinct light ring present in the nuchal region or a more or less distinct yellowish collar. Phylogenetically, this species is sister to C. pavimentata, with significant genetic differences (0.190) on mitochondrial gene Cyt b. [ABSTRACT FROM AUTHOR]

Limnebius exhibits uniform external appearance but variable male genitalia: from differently curved rod shapes in the subgenus Bilimneus to up to seven longitudinally separated folds or appendages in Limnebius s.s.. Among nonsexual traits, two subgenera diverge only in the wing. The aedeagal complexity in Limnebius s.s. is associated with the secondary sexual structures on the abdomen and metatibia; larger body size, which forms two clusters; and male-biased sexual dimorphism. To cluster the subdivisions with phylogenetically unresolved relationships, we examined the coincidence of the traits in both sexes, based on the premise of the independent and monophyletic origin of histologically unsimilar elements. The folds and additional appendages on the median lobe, abdominal paired rows of setae, and protuberances show that the L. parvulus and L. nitidus groups have maximum aedeagal complexity in the L. parvulus and L. nitiduloides subgroups, respectively. The L. parvulus group exhibits a gradual increase in the number of elements of the aedeagi. The histology of connections of the parameres and additional appendages to the median lobe, along with that of the flagellum opening, reveal the subgroups' relationship in the L. nitidus group, as well as a decrease in the complexity of the male genitalia in their recent branches. [ABSTRACT FROM AUTHOR]

Simple Summary: The mosquito species Culex pipiens, has two ecotypes, pipiens and molestus. The two forms differ in mating behavior and how they manage overwintering, with the molestus form thriving in closed indoor surroundings but without an ability to manage cold winter conditions, and the pipiens form that requiring open spaces for mating and going into diapause during winter. Both ecotypes are important vectors for mosquito-borne viruses. Cx. pipiens mosquitoes often carry endosymbiotic Wolbachia bacteria that are transmitted from the mother to the egg, but this varies frequency of occurrence. The Wolbachia endosymbiont affects the reproductive success of mosquitoes so that only eggs infected with a compatible Wolbachia can be fertilized by an infected male. In artificially infected Aedes mosquitoes, Wolbachia affects whether the mosquito can transmit a virus though bites. We studied how Cx. pipiens mosquitoes from Sweden carried Wolbachia and compared them to mosquitoes from other European countries, and found that all tested Cx. pipiens mosquitoes carried Wolbachia. We characterized the Wolbachia from these mosquitoes and found that Cx. pipiens of the two ecotypes carry different strains of Wolbachia in Sweden and Norway but not in sampled mosquitoes from Italy or England. This highlights the differences between the two ecotypes in northern Europe. The mosquito Culex pipiens occurs in two ecotypes differing in their mating and overwintering behavior: pipiens mate in open environments and diapause, and molestus also mate in small spaces and is active throughout the year. Cx. pipiens carry Wolbachia endosymbionts of the wPip strain, but the frequency of infection differs between studied populations. Wolbachia infection affects the host reproductive success through cytoplasmic incompatibility. wPip Wolbachia is divided into five types, wPip I–V. The type of wPip carried varies among Cx. pipiens populations. In northern European locations different wPip types are found in the two ecotypes, whereas in southern locations, they often carry the same type, indicating differences in hybridization between ecotypes. In this study, Cx. pipiens specimens of both ecotypes were collected from Sweden and compared to specimens from Norway, England, Italy, and the Netherlands, as well as Cx. quinquefasciatus from Mali and Thailand. The abundance varied, but all specimens were infected by Wolbachia, while the tested specimens of other mosquito species were often uninfected. The wPip strains were determined through the sequence analysis of Wolbachia genes ank2 and pk1, showing that Cx. pipiens ecotypes in Scandinavia carry different wPip strains. The observed differences in wPip strains indicate that hybridization is not frequent and may contribute to barriers against hybridization of the ecotypes in Sweden and Norway. [ABSTRACT FROM AUTHOR]

Arthropoda represents the most diverse animal phylum, but clarifying the phylogenetic relationships among arthropod taxa remains challenging given the numerous arthropod lineages that diverged over a short period of time. In order to resolve the most controversial aspects of deep arthropod phylogeny, focusing on the Myriapoda, we conducted phylogenetic analyses based on ten super-matrices comprised of 751 to 1,233 orthologous genes across 64 representative arthropod species, including 28 transcriptomes that were newly generated in this study. Our findings provide unambiguous support for the monophyly of the higher arthropod taxa, Chelicerata, Mandibulata, Myriapoda, Pancrustacea, and Hexapoda, while the Crustacea are paraphyletic, with the class Remipedia supported as the lineage most closely related to hexapods. Within the Hexapoda, our results largely affirm previously proposed phylogenetic relationships among deep hexapod lineages, except that the Paraneoptera (Hemiptera, Thysanoptera, and Psocodea) was recovered as a monophyletic lineage in some analyses. The results corroborated the recently proposed phylogenetic framework of the four myriapod classes, wherein Symphyla and Pauropoda, as well as Chilopoda and Diplopoda, are each proposed to be sister taxa. The findings provide important insights into understanding the phylogeny and evolution of arthropods. [ABSTRACT FROM AUTHOR]

Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of "big data", which has also affected the field of virology. The collaboration between the communities of bioinformaticians and virologists already started a few decades ago and it was strongly enhanced by the recent SARS-CoV-2 pandemics. In this article, which is the first in a series on how bioinformatics can enhance virus research, we show that highly useful information is retrievable from selected general and dedicated databases. Indeed, an enormous amount of information—both in terms of nucleotide/protein sequences and their annotation—is deposited in the general databases of international organisations participating in the International Nucleotide Sequence Database Collaboration (INSDC). However, more and more virus-specific databases have been established and are progressively enriched with the contents and features reported in this article. Since viruses are intracellular obligate parasites, a special focus is given to host-pathogen protein-protein interaction databases. Finally, we illustrate several phylogenetic and phylodynamic tools, combining information on algorithms and features with practical information on how to use them and case studies that validate their usefulness. Databases and tools for functional inference will be covered in the next article of this series: Bioinformatics goes viral: II. Sequence-based and structure-based functional analyses for boosting virus research. [ABSTRACT FROM AUTHOR]

Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their "centre of emergence". We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima's D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility. [ABSTRACT FROM AUTHOR]

Species in Alternaria sections Infectoriae and Pseudoalternaria are commonly isolated from agricultural crops and a variety of other plant hosts. With the increasing appreciation that species from these two sections are often the dominant taxa recovered from important cereal crops, the need for improved understanding of their biodiversity and taxonomy has grown. Given that morphological characteristics and existing molecular markers are not sufficient for distinguishing among species, we expanded the genomic resources for these sections to support research in biosystematics and species diagnostics. Whole genome assemblies for 22 strains were generated, including the first genomes from section Infectoriae or Pseudoalternaria strains sampled from Canada, which significantly increases the number of publicly released genomes, particularly for section Pseudoalternaria. We performed comprehensive phylogenomic analyses of all available genomes (n = 39) and present the first robust phylogeny for these taxa. The segregation of the two sections was strongly supported by genomewide data, and multiple lineages were detected within each section. We then provide an overview of the biosystematics of these groups by analyzing two standard molecular markers from the largest sample of section Infectoriae and Pseudoalternaria strains studied to date. The patterns of relative diversity suggest that, in many cases, multiple species described based on minor morphological differences may actually represent different strains of the same species. A list of candidate loci for development into new informative molecular markers, which are diagnostic for sections and lineages, was created from analyses of phylogenetic signals from individual genes across the entire genome. [ABSTRACT FROM AUTHOR]

The Calotes genus presents a challenge due to the complexity of its species. However, research on the cryptic species complex within the Indonesian Calotes genus is still lacking. This study aims to determine the extent of genetic relationships and assess the potential existence of a species complex within the Indonesian genus Calotes (Daudin, 1802) (Squamata, Agamidae) using the partial Cytochrome c Oxidase Subunit 1 (COI) gene sequence as a molecular marker. Samples of the Indonesian Calotes genus in this study were collected from South Lampung (Lampung), Bogor (West Java), and Langkat (North Sumatra). By aligning 582 bp sequence similarities with reference sequences in GenBank, we confirmed that seven out of eight samples analyzed belonged to Calotes vultuosus, while one sample was identified as Calotes versicolor. The identity values ranged from 96 to 100%. The C. vultuosus samples in this study displayed lower genetic distances, ranging from 0 to 3%, with the reference C. vultuosus sequence from Indonesia compared to the reference sequence from India, which ranged from 6 to 9%. Phylogenetic tree reconstruction, utilizing both maximum likelihood with IQ-Tree and Bayesian Inference with BEAST methods, further supports these findings. It reveals distinct groupings between C. vultuosus samples from Indonesia and India. These results suggest the potential occurrence of a species complex within the Indonesian genus Calotes. Furthermore, the inclusion of eight COI gene sequences from two Calotes species in the GenBank database has the potential to confirm the existence of previously undocumented species in Indonesia. [ABSTRACT FROM AUTHOR]

Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units. [ABSTRACT FROM AUTHOR]

Bayesian phylogenetic inference is powerful but computationally intensive. Researchers may find themselves with two phylogenetic posteriors on overlapping data sets and may wish to approximate a combined result without having to re-run potentially expensive Markov chains on the combined data set. This raises the question: given overlapping subsets of a set of taxa (e.g. species or virus samples), and given posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we optimize a probability distribution on phylogenetic tree topologies for the entire taxon set? In this paper we develop a variational approach to this problem and demonstrate its effectiveness. Specifically, we develop an algorithm to find a suitable support of the variational tree topology distribution on the entire taxon set, as well as a gradient-descent algorithm to minimize the divergence from the restrictions of the variational distribution to each of the given per-subset probability distributions, in an effort to approximate the posterior distribution on the entire taxon set. [ABSTRACT FROM AUTHOR]

Maximum likelihood estimation is among the most widely-used methods for inferring phylogenetic trees from sequence data. This paper solves the problem of computing solutions to the maximum likelihood problem for 3-leaf trees under the 2-state symmetric mutation model (CFN model). Our main result is a closed-form solution to the maximum likelihood problem for unrooted 3-leaf trees, given generic data; this result characterizes all of the ways that a maximum likelihood estimate can fail to exist for generic data and provides theoretical validation for predictions made in Parks and Goldman (Syst Biol 63(5):798–811, 2014). Our proof makes use of both classical tools for studying group-based phylogenetic models such as Hadamard conjugation and reparameterization in terms of Fourier coordinates, as well as more recent results concerning the semi-algebraic constraints of the CFN model. To be able to put these into practice, we also give a complete characterization to test genericity. [ABSTRACT FROM AUTHOR]

The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes, hence particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae relative to land plants, but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits, such as intricate signalling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants but were bequeathed from their algal progenitors. [ABSTRACT FROM AUTHOR]

Litter size plays an essential role in mammalian evolution and is one of the most important factors determining whether an organism is deemed to have a 'slow' or 'fast' life history strategy. Humans are distinct in being classified as having slow life history yet bearing singletons who have completed relatively less growth than other ape neonates. Previous work has proposed that the ancestral primate gave birth to singletons. However, primate litter size has not yet been contextualized within a broad phylogenetic assessment of mammalian life history. We performed a comprehensive investigation of primate litter size using life history data for 155 primate species, and litter size data for an additional 791 boreoeutherian mammals. Litter size and life history traits have strong phylogenetic signal in primates (Pagel's lambda: 0.99, p < 0.001; Blomberg's K: 0.6311. p < 0.001), and litter size is significantly negatively correlated with gestation length (p < 0.001). Our data support that the last common ancestors of both primates and Haplorhini gave birth to multiples (litter size 1.7 and 1.6, respectively). We also find that singleton-bearing pregnancies evolved convergently in multiple primate lineages, including tarsiers and other haplorhines. This study contributes significantly to our understanding of life history and litter size in mammals, and we emphasize the utility of a callitrichid model for investigating the evolution of human reproduction. [ABSTRACT FROM AUTHOR]

Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common matrix of exchangeabilities and distinct sets of equilibrium amino acid frequencies known as profiles. Combining the exchangeability matrix with each profile generates the matrix of instantaneous rates of amino acid exchange for that profile. Currently, empirically estimated exchangeability matrices (e.g. the LG matrix) are widely used for phylogenetic inference under profile mixture models. However, these were estimated using a single profile and are unlikely optimal for profile mixture models. Here, we describe the GTRpmix model that allows maximum likelihood estimation of a common exchangeability matrix under any profile mixture model. We show that exchangeability matrices estimated under profile mixture models differ from the LG matrix, dramatically improving model fit and topological estimation accuracy for empirical test cases. Because the GTRpmix model is computationally expensive, we provide two exchangeability matrices estimated from large concatenated phylogenomic-supermatrices to be used for phylogenetic analyses. One, called Eukaryotic Linked Mixture (ELM), is designed for phylogenetic analysis of proteins encoded by nuclear genomes of eukaryotes, and the other, Eukaryotic and Archaeal Linked mixture (EAL), for reconstructing relationships between eukaryotes and Archaea. These matrices, combined with profile mixture models, fit data better and have improved topology estimation relative to the LG matrix combined with the same mixture models. Starting with version 2.3.1, IQ-TREE2 allows users to estimate linked exchangeabilities (i.e. amino acid exchange rates) under profile mixture models. [ABSTRACT FROM AUTHOR]