Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers

Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.

Ad fontes: divergence-time estimation and the age of angiosperms

Accurate divergence times are essential for interpreting and understanding the context in which lineages have evolved. Over the past several decades, debates have surrounded the discrepancies between the inferred molecular ages of crown angiosperms, often estimated from the Late Jurassic into the Permian, and the fossil record, placing angiosperms in the Early Cretaceous. That crown angiosperms could have emerged as early as the Permian or even the Triassic would have major implications for the paleoecological context of the origin of one of the most consequential clades in the tree of life. Here, we argue, and demonstrate through simulations, that the older ages inferred from molecular data and relaxed-clock models are misled by lineage-specific rate heterogeneity resulting from life history changes that occurred several times throughout the evolution of vascular plants. To overcome persistent discrepancies in age estimates, more biologically informed and realistic models should be developed, and our results should be considered in the context of their biological implications before we accept inferences that are a major departure from our strongest evidence.

Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.

Evolution, divergence, and convergence in the mandibles of opossums (Didelphidae, Didelphimorphia)

Didelphid marsupials are considered a morphologically unspecialized group with a generalist diet that includes vertebrates, invertebrates, and plant matter. While cranium and scapula variation has already been examined within Didelphidae, variation in mandible shape, usually associated with diet or phylogeny in other mammalian groups, has not yet been properly assessed in the family. We evaluated the variation in mandible shape and size of didelphids (2470 specimens belonging to 94 species) using 2D geometric morphometrics. We classified the diet of the didelphids into four broad categories to assess whether morphospace ordination relates to dietary habits. We also provided the most comprehensive phylogeny for the family (123 out of the 126 living species) using 10 nuclear and mitochondrial genes. We then mapped mandible size and shape onto that phylogeny for 93 selected taxa and ancestral size and shapes were reconstructed by parsimony. We found phylogenetically structured variation in mandible morphology between didelphid groups, and our results indicate that they have a significant phylogenetic signal. The main axis of shape variation is poorly related to size, but the second is strongly allometric, indicating that allometry is not the main factor in shaping morphological diversity on their mandibles. Our results indicate that the shape and size of the ancestral mandible of didelphids would be similar to that of the current species of the genus Marmosa.

Nudiviruses in free-living and parasitic arthropods: evolutionary taxonomy

The nudiviruses (family: Nudiviridae) are large double-stranded DNA (dsDNA) viruses that infect insects and crustaceans, and have most recently been identified from ectoparasitic members (fleas and lice). This virus family was created in 2014 and has since been expanded via the discovery of multiple novel viral candidates or accepted members, sparking the need for a new taxonomic and evolutionary overview. Using current information (including data from public databases), we construct a new comprehensive phylogeny, encompassing 49 different nudiviruses. We use this novel phylogeny to propose a new taxonomic structure of the Nudiviridae by suggesting two new viral genera (Zetanudivirus and Etanudivirus), from ectoparasitic lice. We detail novel emerging relationships between nudiviruses and their hosts, considering their evolutionary history and ecological role.

Integrating Phylogenies with Chronology to Assemble the Tree of Life

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey of published literature shows that individual phylogenies are frequently restricted to specific taxonomic groups due to the expertise of investigators and molecular evolutionary considerations, resulting in any given species present in a minuscule fraction of phylogenies. We present a novel approach, called the chronological supertree algorithm (Chrono-STA), that can build a supertree of species from such data by using node ages in published molecular phylogenies scaled to time. Chrono-STA builds a supertree of organisms by integrating chronological data from molecular timetrees. It fundamentally differs from existing approaches that generate consensus phylogenies from gene trees with missing taxa, as Chrono-STA does not impute nodal distances, use a guide tree as a backbone, or reduce phylogenies to quartets. Analyses of simulated and empirical datasets show that Chrono-STA can combine taxonomically restricted timetrees with extremely limited species overlap. For such data, approaches that impute missing distances or assemble phylogenetic quartets did not perform well. We conclude that integrating phylogenies via temporal dimension enhances the accuracy of reconstructed supertrees that are also scaled to time.

Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis

In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.

A revised phylogeny of Boletaceae using whole genome sequences

The porcini mushroom family Boletaceae is a diverse, widespread group of ectomycorrhizal (ECM) mushroom-forming fungi that so far has eluded intrafamilial phylogenetic resolution based on morphology and multilocus data sets. In this study, we present a genome-wide molecular data set of 1764 single-copy gene families from a global sampling of 418 Boletaceae specimens. The resulting phylogenetic analysis has strong statistical support for most branches of the tree, including the first statistically robust backbone. The enigmatic Phylloboletellus chloephorus from non-ECM Argentinian subtropical forests was recovered as a new subfamily sister to the core Boletaceae. Time-calibrated branch lengths estimate that the family first arose in the early to mid-Cretaceous and underwent a rapid radiation in the Eocene, possibly when the ECM nutritional mode arose with the emergence and diversification of ECM angiosperms. Biogeographic reconstructions reveal a complex history of vicariance and episodic long-distance dispersal correlated with historical geologic events, including Gondwanan origins and inferred vicariance associated with its disarticulation. Together, this study represents the most comprehensively sampled, data-rich molecular phylogeny of the Boletaceae to date, establishing a foundation for future robust inferences of biogeography in the group.

Decoding the genome of bloodsucking midge Forcipomyia taiwana (Diptera: Ceratopogonidae): Insights into odorant receptor expansion

Biting midges, notably those within the Ceratopogonidae family, have long been recognized for their epidemiological significance, both as nuisances and vectors for disease transmission in vertebrates. Despite their impact, genomic insights into these insects, particularly beyond the Culicoides genus, remain limited. In this study, we assembled the Forcipomyia taiwana (Shiraki) genome, comprising 113 scaffolds covering 130.4 Mbps-with the longest scaffold reaching 7.6 Mbps and an N50 value of 2.6 Mbps-marking a pivotal advancement in understanding the genetic architecture of ceratopogonid biting midges. Phylogenomic analyses reveal a shared ancestry between F. taiwana and Culicoides sonorensis Wirth & Jones, dating back approximately 124 million years, and highlight a dynamic history of gene family expansions and contractions within the Ceratopogonidae family. Notably, a substantial expansion of the odorant receptor (OR) gene family was observed, which is crucial for the chemosensory capabilities that govern biting midges' interactions with their environment, including host seeking and oviposition behaviors. The distribution of OR genes across the F. taiwana genome displays notable clusters on scaffolds, indicating localized tandem gene duplication events. Additionally, several collinear regions were identified, hinting at segmental duplications, inversions, and translocations, contributing to the olfactory system's evolutionary complexity. Among the 156 ORs identified in F. taiwana, 134 are biting midge-specific ORs, distributed across three distinct clades, each exhibiting unique motif features that distinguish them from the others. Through weighted gene co-expression network analysis, we correlated distinct gene modules with sex and reproductive status, laying the groundwork for future investigations into the interplay between gene expression and adaptive behaviors in F. taiwana. In conclusion, our study not only highlights the unique olfactory repertoire of ceratopogonid biting midges but also sets the stage for future studies into the genetic underpinnings of their unique biological traits and ecological strategies.

Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding

Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC-psbD region showed the biggest number of diagnostides (diagnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others.

Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies

Lingonberry (Vaccinium vitis-idaea L.) produces tiny red berries that are tart and nutty in flavor. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for 2 subspecies of lingonberry (V. vitis-idaea ssp. minus and ssp. vitis-idaea var. 'Red Candy') were sequenced and de novo assembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (Vaccinium myrtillus) to generate a chromosome-anchored reference genome consisting of 12 chromosomes each with a total length of 548.07 Mb [contig N50 = 1.17 Mb, BUSCO (C%) = 96.5%] for ssp. vitis-idaea and 518.70 Mb [contig N50 = 1.40 Mb, BUSCO (C%) = 96.9%] for ssp. minus. RNA-seq-based gene annotation identified 27,243 and 25,718 genes on the respective assembly, and transposable element detection methods found that 45.82 and 44.58% of the genome were repeats. Phylogenetic analysis confirmed that lingonberry was most closely related to bilberry and was more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1-3 MYA, possibly due to the impacts of repeated glacial cycles during the Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry-relevant genes (e.g. anthocyanin production), infer phylogeny, and call sequence-level variants (e.g. SNPs) in future research.

Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast

The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.

Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus

Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1-bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31-bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole-genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome-level gap-less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex-types: NRRL Y-1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838).

Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes

Nitrogen is essential for all organisms, but biological nitrogen fixation (BNF) occurs only in a small fraction of prokaryotes. Previous studies divided nitrogenase-gene-carrying prokaryotes into Groups I to IV and provided evidence that BNF first evolved in bacteria. This study constructed a timetree of the evolution of nitrogen-fixation genes and estimated that archaea evolved BNF much later than bacteria and that nitrogen-fixing cyanobacteria evolved later than 1,900 MYA, considerably younger than the previous estimate of 2,200 MYA. Moreover, Groups III and II/I diverged ∼2,280 MYA, after the Kenorland supercontinent breakup (∼2,500-2,100 MYA) and the Great Oxidation Event (∼2,400-2,100 MYA); Groups III and Vnf/Anf diverged ∼2,086 MYA, after the Yarrabubba impact (∼2,229 MYA); and Groups II and I diverged ∼1,920 MYA, after the Vredefort impact (∼2,023 MYA). In summary, this study provided a timescale of BNF events and discussed the possible effects of geological events on BNF evolution.

Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth

Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites

Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.

Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion

A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.

Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment

BACKGROUND

The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking.

RESULTS

In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways.

CONCLUSIONS

One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.

Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution

We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolution journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue will be accompanied by a perspective that highlights the historic and contemporary contributions of our journals to a specific topic in molecular evolution. This perspective, the first in the series, presents an account of the broad array of methods that have been published in the Society for Molecular Biology and Evolution journals, including methods to infer phylogenies, to test hypotheses in a phylogenetic framework, and to infer population genetic processes. We also mention many of the software implementations that make methods tractable for empiricists. In short, the Society for Molecular Biology and Evolution community has much to celebrate after four decades of publishing high-quality science including numerous important inferential methods.

Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

BACKGROUND

Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.

RESULTS

Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.

CONCLUSIONS

These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.

Unravelling the genome of the brackish water malaria vector Anopheles aquasalis

Malaria is a severe public health problem in several developing tropical and subtropical countries. Anopheles aquasalis is the primary coastal malaria vector in Central and South America and the Caribbean Islands, and it has the peculiar feature of living in water with large changes in salinity. Recent research has recognised An. aquasalis as an important model for studying the interactions of murine and human Plasmodium parasites. This study presents the complete genome of An. aquasalis and offers insights into its evolution and physiology. The genome is similar in size and gene content to other Neotropical anophelines, with 162 Mb and 12,446 protein-coding genes. There are 1387 single-copy orthologs at the Diptera level (eg. An. gambiae, An. darlingi and Drosophila melanogaster). An. aquasalis diverged from An. darlingi, the primary malaria vector in inland South America, nearly 20 million years ago. Proteins related to ion transport and metabolism belong to the most abundant gene families with 660 genes. We identified gene families relevant to osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases, and carbonic anhydrases). Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in insecticide resistance and immunity-related genes for all known classical pathways. The data provided by this study offers candidate genes for further studies of parasite-vector interactions and for studies on how anophelines of brackish water deal with the high fluctuation in water salinity. We also established data and insights supporting An. aquasalis as an emerging Neotropical malaria vector model for genetic and molecular studies.

Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.

A Review of Resistance to Polymyxins and Evolving Mobile Colistin Resistance Gene (mcr) among Pathogens of Clinical Significance

The global rise in antibiotic resistance in bacteria poses a major challenge in treating infectious diseases. Polymyxins (e.g., polymyxin B and colistin) are last-resort antibiotics against resistant Gram-negative bacteria, but the effectiveness of polymyxins is decreasing due to widespread resistance among clinical isolates. The aim of this literature review was to decipher the evolving mechanisms of resistance to polymyxins among pathogens of clinical significance. We deciphered the molecular determinants of polymyxin resistance, including distinct intrinsic molecular pathways of resistance as well as evolutionary characteristics of mobile colistin resistance. Among clinical isolates, Acinetobacter stains represent a diversified evolution of resistance, with distinct molecular mechanisms of intrinsic resistance including naxD, lpxACD, and stkR gene deletion. On the other hand, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa are usually resistant via the PhoP-PhoQ and PmrA-PmrB pathways. Molecular evolutionary analysis of mcr genes was undertaken to show relative relatedness across the ten main lineages. Understanding the molecular determinants of resistance to polymyxins may help develop suitable and effective methods for detecting polymyxin resistance determinants and the development of novel antimicrobial molecules.

The Himalayan uplift and evolution of aquatic biodiversity across Asia: Snowtrout (Cyprininae: Schizothorax) as a test case

Global biodiversity hotspots are often remote, tectonically active areas undergoing climatic fluctuations, such as the Himalaya Mountains and neighboring Qinghai-Tibetan Plateau (QTP). They provide biogeographic templates upon which endemic biodiversity can be mapped to infer diversification scenarios. Yet, this process can be somewhat opaque for the Himalaya, given substantial data gaps separating eastern and western regions. To help clarify, we evaluated phylogeographic and phylogenetic hypotheses for a widespread fish (Snowtrout: Cyprininae; Schizothorax) by sequencing 1,140 base pair of mtDNA cytochrome-b (cytb) from Central Himalaya samples (Nepal: N = 53; Bhutan: N = 19), augmented with 68 GenBank sequences (N = 60 Schizothorax/N = 8 outgroups). Genealogical relationships (N = 132) were analyzed via maximum likelihood (ML), Bayesian (BA), and haplotype network clustering, with clade divergence estimated via TimeTree. Snowtrout seemingly originated in Central Asia, dispersed across the QTP, then into Bhutan via southward-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). Headwaters of five large Asian rivers provided dispersal corridors from Central into eastern/southeastern Asia. South of the Himalaya, the YLTR transitions into the Brahmaputra River, facilitating successive westward colonization of Himalayan drainages first in Bhutan, then Nepal, followed by far-western drainages subsequently captured by the (now) westward-flowing Indus River. Two distinct Bhutanese phylogenetic groups were recovered: Bhutan-1 (with three subclades) seemingly represents southward dispersal from the QTP; Bhutan-2 apparently illustrates northward colonization from the Lower Brahmaputra. The close phylogenetic/phylogeographic relationships between the Indus River (Pakistan) and western tributaries of the Upper Ganges (India/Nepal) potentially implicate an historic, now disjunct connection. Greater species-divergences occurred across rather than within-basins, suggesting vicariance as a driver. The Himalaya is a component of the Earth's largest glacial reservoir (i.e., the "third-pole") separate from the Arctic/Antarctic. Its unique aquatic biodiversity must be defined and conserved through broad, trans-national collaborations. Our study provides an initial baseline for this process.

The Genome of the Korean Island-Originated Perilla citriodora 'Jeju17' Sheds Light on Its Environmental Adaptation and Fatty Acid and Lipid Production Pathways

Perilla is a key component of Korean food. It contains several plant-specialized metabolites that provide medical benefits. In response to an increased interest in healthy supplement food from the public, people are focusing on the properties of Perilla. Nevertheless, unlike rice and soybeans, there are few studies based on molecular genetics on Perilla, so it is difficult to systematically study the molecular breed. The wild Perilla, Perilla citriodora 'Jeju17', was identified a decade ago on the Korean island of Jeju. Using short-reads, long-reads, and Hi-C, a chromosome-scale genome spanning 676 Mbp, with high contiguity, was assembled. Aligning the 'Jeju17' genome to the 'PC002' Chinese species revealed significant collinearity with respect to the total length. A total of 31,769 coding sequences were predicted, among which 3331 were 'Jeju17'-specific. Gene enrichment of the species-specific gene repertoire highlighted environment adaptation, fatty acid metabolism, and plant-specialized metabolite biosynthesis. Using a homology-based approach, genes involved in fatty acid and lipid triacylglycerol biosynthesis were identified. A total of 22 fatty acid desaturases were found and comprehensively characterized. Expression of the FAD genes in 'Jeju17' was examined at the seed level, and hormone signaling factors were identified. The results showed that the expression of FAD genes in 'Jeju17' at the seed level was high 25 days after flowering, and their responses of hormones and stress were mainly associated with hormone signal transduction and abiotic stress via cis-elements patterns. This study presents a chromosome-level genome assembly of P. citriodora 'Jeju17', the first wild Perilla to be sequenced from the Korean island of Jeju. The analyses provided can be useful in designing ALA-enhanced Perilla genotypes in the future.

Genomic analyses indicate the North American Ap-ha variant of the tick-vectored bacterium Anaplasma phagocytophilum was introduced from Europe

BACKGROUND

Anaplasma phagocytophilum is a tick-vectored, obligately intracellular bacterium that infects a diversity of vertebrate hosts. In North America, the Ap-ha variant of A. phagocytophilum can cause dangerous infections in humans, whereas symptomatic human infections in Europe are rare. Conversely, the European host-generalist ecotype of A. phagocytophilum frequently causes illness in domestic ruminants while no comparable infections have been recorded from North America. Despite these differences in pathogenicity, the Ap-ha variant is closely aligned phylogenetically with the European host-generalist ecotype. Furthermore, North American populations of A. phagocytophilum are less genetically diverse than those in Europe. Taken together, these observations suggest that the North American Ap-ha variant may represent an introduced population of this bacterium.

METHODS

Data from publicly available whole genomes of A. phagocytophilum were used to compare phylogeographic patterns and the extent of genetic divergence between the North American Ap-ha variant and the European host-generalist ecotype.

RESULTS

The results confirm that North American Ap-ha samples are phylogenetically nested within the diversity of the European host-generalist ecotype, and that Ap-ha likely radiated within the last 100 years. As expected, the Ap-ha variant also exhibited relatively low genetic diversity levels compared to the European host-generalist ecotype. Finally, North American Ap-ha harbored significantly more derived alleles than the European host-generalist A. phagocytophilum population.

CONCLUSIONS

Collectively, these results support the hypothesis that the Ap-ha variant was recently introduced to North America from Europe and underwent a strong genetic bottleneck during this process (i.e. a 'founder event'). Adaptation to novel vectors may have also played a role in shaping genetic diversity and divergence patterns in these pathogenic bacteria. These findings have implications for future studies aimed at understanding evolutionary patterns and pathogenicity variation within A. phagocytophilum.

Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph

Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.

Deciphering the Origin of DNA Viruses (Replication-Associated Parvo-NS1) That Infect Vertebrates from Invertebrate-Infecting Viruses

DNA replication is a standard and essential function among DNA viruses; however, this functional domain's common ancestor, origin, and evolutionary path in invertebrate- and vertebrate-infecting viruses are not yet fully understood. Here, we present evidence, using a combination of phylogenetic relationships, coevolution, and CLANS (cluster analysis of sequences) analysis, that the parvo-NS1 domain (nonstructural protein NS1, DNA helicase domain) of these DNA viruses that infect vertebrates potentially originated from the invertebrate (Platyhelminthes) parvo-NS1 domain of parvovirus-related sequences (PRSs). Our results suggest that papillomaviruses and the parvovirus subfamilies Densovirinae and Hamaparvovirinae DNA helicase evolved directly from the Platyhelminthes NS1 domain (PRSs). Similarly, the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the PRSs through Hamaparvovirinae. Further, our analysis also clarified that herpesviruses and adenoviruses independently obtained the parvo-NS1 domain from Dependoparvovirus (Parvovirinae). Furthermore, virus-host coevolution analysis revealed that the parvovirus NS1 domain has coevolved with hosts, from flatworms to humans, and it appears that the papillomavirus may have obtained the DNA helicase during the early stages of parvovirus evolution and later led to the development of the DNA helicase of adomavirus and polyomavirus. Finally, herpesviruses and adenoviruses likely inherited the parvo-NS1 domain from Dependoparvovirus in the later stages of evolution. To the best of our knowledge, this is the first evolutionary evidence to suggest that the DNA helicase of viruses that infect vertebrates originated from the invertebrate PRSs. IMPORTANCE DNA replication of DNA viruses is an essential function. This allows DNA replication of viruses to form virus particles. The DNA helicase domain is responsible for this primary function. This domain is present in parvoviruses, papillomaviruses, polyomaviruses, herpesviruses, and adenoviruses. But little is known about the common ancestor, origin, and evolutionary path of DNA helicase in invertebrate- and vertebrate-infecting viruses. Here, we report the possibility of the origin of DNA viruses (DNA helicase) infecting vertebrates from Platyhelminthes (invertebrate) PRSs. Our study established that the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the Platyhelminthes PRSs through Hamaparvovirinae. Furthermore, our study suggests that the papillomavirus DNA helicase may have evolved in the early stages of parvovirus evolution and then led to the development of the adomavirus and polyomavirus. Our study suggests that the herpesviruses and adenoviruses likely inherited the parvo-NS1 domain through gene capture from Dependoparvovirus in the later stages of parvovirus evolution in their hosts.

Molecular timetrees using relaxed clocks and uncertain phylogenies

A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.

Morphology and Mitochondrial Lineage Investigations Corroborate the Systematic Status and Pliocene Colonization of Suncus niger (Mammalia: Eulipotyphla) in the Western Ghats Biodiversity Hotspot of India

The Indian highland shrew, Suncus niger (Horsfield, 1851), is the least studied soricid species from its original range distribution in Southern India, with several systematics conundrums. Following its discovery in 1851, the species was synonymized with Suncus montanus (Kelaart, 1850) (endemic to Sri Lanka) and subsequently identified as a separate Indian population. However, the systematic status of S. niger from topotype specimens in Southern India has yet to be determined through an integrated approach. Both taxonomy and mitochondrial genetic data (Cytochrome b and 16S ribosomal RNA) were used to re-examine the systematics of S. niger. The mtCytb gene clearly distinguished topotypic S. niger from other Suncus species, with high genetic divergences varying from 8.49% to 26.29%. Further, the Bayesian and maximum likelihood topologies clearly segregated S. niger from other congeners and corroborated the sister relationship with S. stoliczkanus with expected divergence in the late Pliocene (2.62 MYA). The TimeTree analysis also exhibits a strong matrilineal affinity of S. dayi (endemic to India) toward the African species. The current study hypothesizes that the ancestor of the soricids evolved in Africa and that genetic lineages were subsequently shifted by plate tectonic events that subsequently colonized different continents as distinct species during the late Miocene (Tortonian) to the Holocene era. In addition to the new range expansion and elevation records of S. niger in the Central Western Ghats, we propose that additional sampling across its distribution, as well as the use of multiple genetic markers, may be useful in determining the genetic diversity and population structure of this endemic species. The present study also recommends that more molecular data on the Soricomorphs lineages, and estimates of their divergence times, will shed light on the evolution of these small mammals on Earth.

Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey

Two strains of fission yeast were isolated from honey. They differ from the type strain of Schizosaccharomyces octosporus by three substitutions in the D1/D2 domain of the nuclear 26S large subunit ribosomal RNA (rRNA) gene sequence, resulting in a 99.5% identity. In the internal transcribed spacer (ITS) region (consisting of ITS1, 5.8S rDNA, and ITS2), the strains differ from S. octosporus by 16 gaps and 91 substitutions, which is equivalent to an identity of 88.1%. Genome sequencing on one of the new strains revealed that the average nucleotide identity (ANI) between its genome and the reference genome of S. octosporus is 90.43% and there exist major genome rearrangements between the two genomes. Mating analysis revealed that S. octosporus and one of the new strains are completely reproductively separated. A strong prezygotic barrier exists and the few mating products consist of diploid hybrids that do not form recombinant ascospores. In the new strains, asci are either zygotic, arising from conjugation, or they develop without conjugation from asexual cells (azygotic). Compared to the currently recognized Schizosaccharomyces species, the spectrum of nutrients that are assimilated by the new strains is restricted. Of the 43 carbohydrates that were included in the physiological standard tests, only 7 were assimilated. According to the results of the genome sequence analysis, the mating trials, and the phenotypic characterization, the new species Schizosaccharomyces lindneri is described to accommodate the two strains (holotype: CBS 18203^T  and ex-type: MUCL 58363; MycoBank no.: MB 847838).

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials

BACKGROUND AND AIMS

Southwestern Asia is a significant centre of biodiversity and a cradle of diversification for many plant groups, especially xerophytic elements. In contrast, little is known about the evolution and diversification of its hygrophytic flora. To fill this gap, we focus on Cardamine (Brassicaceae) species that grow in wetlands over a wide altitudinal range. We aimed to elucidate their evolution, assess the extent of presumed historical gene flow between species, and draw inferences about intraspecific structure.

METHODS

We applied the phylogenomic Hyb-Seq approach, ecological niche analyses and multivariate morphometrics to a total of 85 Cardamine populations from the target region of Anatolia-Caucasus, usually treated as four to six species, and supplemented them with close relatives from Europe.

KEY RESULTS

Five diploids are recognized in the focus area, three of which occur in regions adjacent to the Black and/or Caspian Sea (C. penzesii, C. tenera, C. lazica), one species widely distributed from the Caucasus to Lebanon and Iran (C. uliginosa), and one western Anatolian entity (provisionally C. cf. uliginosa). Phylogenomic data suggest recent speciation during the Pleistocene, likely driven by both geographic separation (allopatry) and ecological divergence. With the exception of a single hybrid (allotetraploid) speciation event proven for C. wiedemanniana, an endemic of southern Turkey, no significant traces of past or present interspecific gene flow were observed. Genetic variation within the studied species is spatially structured, suggesting reduced gene flow due to geographic and ecological barriers, but also glacial survival in different refugia.

CONCLUSIONS

This study highlights the importance of the refugial regions of the Black and Caspian Seas for both harbouring and generating hygrophytic species diversity in Southwestern Asia. It also supports the significance of evolutionary links between Anatolia and the Balkan Peninsula. Reticulation and polyploidization played a minor evolutionary role here in contrast to the European relatives.

Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama

Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03523-0.

Characterization, genome analysis and antibiofilm efficacy of lytic Proteus phages RP6 and RP7 isolated from university hospital sewage

The crystalline formation of biofilms by Proteus blocks the urine flow which often complicates the health care of catheterized patients. Bacteriophages has been highlighted as a promising tool to control biofilm-mediated bacterial infections. Here, we isolated and characterized two newly isolated lytic phages capable of infecting clinical isolates of P. mirabilis and P. vulgaris. Moreover, insights regarding the biological and molecular characterization were analysed. Both RP6 and RP7 phages showed a Proteus-genus-specific profile, administering no lytic activity against other family of Enterobacteriaceae. The optimal MOI value of the RP6 and RP7 phages were determined as 0.1 and 0.01, respectively. The one-step growth curve showed that RP6 and RP7 phages have a short latent period of 20 min and large burst size of 220-371 PFU/ML per infected host cell. Bacteria growth was reduced immediately after the phages were added, which is shown by the optical density (OD) measurement after 24 hr. Proteus phage RP6 and RP7 were found to eradicate both the planktonic and mature biofilms produced by the Proteus isolates tested. Genome sequence of Proteus phage RP6 was found to be 58,619 bp, and a G-C content of 47%. Also, Proteus phage RP7 genome size was 103,593 bp with G-C ratio of 38.45%. A total of 70 and 172 open reading frame (ORF) was encoded in RP6 and RP7 phage genomes, respectively. Interestingly, there were no tRNA encoded by Proteus phage RP6 genome even though there is a significant G-C content difference between the phage and its host. Additionally, the exhibition of highly lytic activity and absence of virulence and antibiotic-resistant genes in both Proteus RP6 and RP7 phages emphasized that this newly isolated phages are promising for potential therapeutic phages.

A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni

BACKGROUND

Biomphalaria pfeifferi is the world's most widely distributed and commonly implicated vector snail species for the causative agent of human intestinal schistosomiasis, Schistosoma mansoni. In efforts to control S. mansoni transmission, chemotherapy alone has proven insufficient. New approaches to snail control offer a way forward, and possible genetic manipulations of snail vectors will require new tools. Towards this end, we here offer a diverse set of genomic resources for the important African schistosome vector, B. pfeifferi.

METHODOLOGY/PRINCIPAL FINDINGS

Based largely on PacBio High-Fidelity long reads, we report a genome assembly size of 772 Mb for B. pfeifferi (Kenya), smaller in size than known genomes of other planorbid schistosome vectors. In a total of 505 scaffolds (N50 = 3.2Mb), 430 were assigned to 18 large linkage groups inferred to represent the 18 known chromosomes, based on whole genome comparisons with Biomphalaria glabrata. The annotated B. pfeifferi genome reveals a divergence time of 3.01 million years with B. glabrata, a South American species believed to be similar to the progenitors of B. pfeifferi which undertook a trans-Atlantic colonization < five million years ago.

CONCLUSIONS/SIGNIFICANCE

The genome for this preferentially self-crossing species is less heterozygous than related species known to be preferential out-crossers; its smaller genome relative to congeners may similarly reflect its preference for selfing. Expansions of gene families with immune relevance are noted, including the FReD gene family which is far more similar in its composition to B. glabrata than to Bulinus truncatus, a vector for Schistosoma haematobium. Provision of this annotated genome will help better understand the dependencies of trematodes on snails, enable broader comparative insights regarding factors contributing to susceptibility/ resistance of snails to schistosome infections, and provide an invaluable resource with respect to identifying and manipulating snail genes as potential targets for more specific snail control programs.

Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.

Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae)

Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories.

Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches

Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.

The profile of HSPA1A gene expression and its association with heat tolerance in crossbred cattle and the tropically adapted dwarf Vechur and Kasaragod

Certain livestock breeds are adapted to hot and humid environments, and these breeds have genetics that could be useful in a changing climate. The expression of several genes has been identified as a useful biomarker for heat stress. In this study, the responses to heat exposure of heat-tolerant Vechur and Kasaragod cattle found in Kerala state in India (also known as dwarf Bos taurus indicus) were compared to crossbred cattle (crosses of Bos t. taurus with Bos t. indicus). At various time points during heat exposure, rectal temperature and the expression of HSPA1A were determined, and the relationship between them was characterized. We characterized HSPA1A mRNA in Vechur cattle and performed molecular clock analysis. The expression of HSPA1A between the lineages and at different temperature humidity index (THI) was significant. There were significant differences between the expression profiles of HSPA1A in Kasaragod and crossbred (p < 0.01) and Vechur and crossbred (p < 0.01) cattle, but no significant difference in expression was observed between Vechur and Kasaragod cattle. The genetic distance between Vechur, B. grunniens, B. t. taurus, and B. t. indicus was 0.0233, 0.0059, and 0.007, respectively. The genetic distance between Vechur and the Indian dwarf breed Malnad Gidda was 0.0081. A molecular clock analysis revealed divergent adaptive evolution of Vechur cattle to B. t. taurus, with adaptations to the high temperatures and humidity that are prevalent in their breeding tract in Kerala, India. These results could also prove useful in selecting heat-tolerant animals using HSPA1A as a marker.

Assessing the relative performance of fast molecular dating methods for phylogenomic data

Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.

Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing

Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.

Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds

Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed’s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.

Phylogeography and colonization pattern of subendemic round-leaved oxeye daisy from the Dinarides to the Carpathians

The Carpathians are an important biodiversity hotspot and a link between mountain ranges on the European continent. This study investigated the phylogeography of one the Carpathian subendemics, Leucanthemum rotundifolium, which is distributed throughout the range and in one isolated population outside it. Range-wide sampling was used to examine phylogeographic patterns by sequencing uniparentally inherited chloroplast markers that exemplify seed dispersal. Reconstruct Ancestral State in Phylogenies (RASP) software, Bayesian binary Markov Chain Monte Carlo (BBM) analysis, and ecological niche modeling based on concatenated results of five algorithms were used to infer migration routes and examine links with other species through phylogeny. The round-leaved oxeye daisy is an example of organisms that reached the Carpathians through a southern "Dacian" migration route, most probably through long-distance dispersal. Dating placed the events in the Pleistocene and supported migrations during cooler periods and stasis/isolation followed by separation in the interglacials. Haplotype diversification indicated that after L. rotundifolium reached the area around the Fagaras Mountains, several migration events occurred leading to colonization of the Southern Carpathians followed by migration to the Apuseni Mountains, the Eastern Carpathians, and finally the Western Carpathians. The results are consistent with previous phylogeographic studies in this region and indicate several novel patterns.

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family

Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper-Temminck's stint (Calidris temminckii), preliminarily named Temminck's stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family-previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)-the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species.

Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.

Construction and Analysis of the Complete Genome Sequence of Leprosy Agent Mycobacterium lepromatosis

Leprosy is caused by Mycobacterium leprae and Mycobacterium lepromatosis. We report construction and analyses of the complete genome sequence of M. lepromatosis FJ924. The genome contained 3,271,694 nucleotides to encode 1,789 functional genes and 1,564 pseudogenes. It shared 1,420 genes and 885 pseudogenes (71.4%) with M. leprae but differed in 1,281 genes and pseudogenes (28.6%). In phylogeny, the leprosy bacilli started from a most recent common ancestor (MRCA) that diverged ~30 million years ago (Mya) from environmental organism Mycobacterium haemophilum. The MRCA then underwent reductive evolution with pseudogenization, gene loss, and chromosomal rearrangements. Analysis of the shared pseudogenes estimated the pseudogenization event ~14 Mya, shortly before species bifurcation. Afterwards, genomic changes occurred to lesser extent in each species. Like M. leprae, four major types of highly repetitive sequences were detected in M. lepromatosis, contributing to chromosomal rearrangements within and after MRCA. Variations in genes and copy numbers were noted, such as three copies of the gene encoding bifunctional diguanylate cyclase/phosphodiesterase in M. lepromatosis, but single copy in M. leprae; 6 genes encoding the TetR family transcriptional regulators in M. lepromatosis, but 11 such genes in M. leprae; presence of hemW gene in M. lepromatosis, but absence in M. leprae; and others. These variations likely aid unique pathogenesis, such as diffuse lepromatous leprosy associated with M. lepromatosis, while the shared genomic features should explain the common pathogenesis of dermatitis and neuritis in leprosy. Together, these findings and the genomic data of M. lepromatosis may facilitate future research and care for leprosy. IMPORTANCE Leprosy is a dreaded infection that still affects millions of people worldwide. Mycobacterium lepromatosis is a recently recognized cause in addition to the well-known Mycobacterium leprae. M. lepromatosis is likely specific for diffuse lepromatous leprosy, a severe form of the infection and endemic in Mexico. This study constructed and annotated the complete genome sequence of M. lepromatosis FJ924 and performed comparative genomic analyses with related mycobacteria. The results afford new and refined insights into the genome size, gene repertoire, pseudogenes, phylogenomic relationship, genome organization and plasticity, process and timing of reductive evolution, and genetic and proteomic basis for pathogenesis. The availability of the complete M. lepromatosis genome may prove to be useful for future research and care for the infection.