Evolutionary Divergence Research Articles

Clinicopathological characteristics and genomic profiling in patients with transformed lymphoma: a monocentric retrospective study

Background Transformed lymphoma occurs when indolent lymphoma transforms into more aggressive lymphoma usually associated with poor prognosis. Methods In this study, we analysed the immunophenotypes, prognostic factors and outcomes of 35 patients with transformed lymphoma from among 306 marginal zone lymphoma (MZL), 544 follicular lymphoma (FL) and 871 chronic lymphocytic leukaemia/small lymphocytic lymphoma (CLL/SLL) cases. In addition, we performed whole-exome sequencing study of seven transformed MZL (tMZL) cases. Results Our results demonstrate that the median time from indolent lymphoma diagnosis to transformed DLBCL was 35 months (range, 14–53 months). The 5-year overall survival (OS) and progression-free survival (PFS) rates after histological transformation (HT) were 50% and 26%, respectively. Kaplan–Meier survival analysis revealed that asynchronous HT and transformed CLL/SLL (tCLL/SLL) were significant adverse prognostic factors for OS after DLBCL HT. We identified mutations involvement in chromatin remodelling (CREBBP and EP300) and regulators of NF-κB signalling (TNFAIP3, BCL10, MYD88, CD79B and CARD11) were affected in tMZL. Conclusion Whole-exome sequencing and copy-number analysis revealed that tMZL derives from the divergent evolution of an ancestral common progenitor clone (CPC). Collectively, this study provides clinicopathological characteristics of three common types of transformed lymphomas and the genetic profile of tMZL with diagnostic and therapeutic implications.

Recent and recurrent autopolyploidization fueled diversification of snow carp on the Tibetan Plateau

Abstract Whole-genome duplication (WGD), or polyploidization, is a major contributor to biodiversity. However, the establishment and survival of WGDs are often considered to be stochastic, since elucidating the processes of WGD establishment remains challenging. In the current study, we explored the processes leading to polyploidy establishment in snow carp (Cyprinidae: Schizothoracinae), a predominant component of the ichthyofauna of the Tibetan Plateau and its surrounding areas. Using large-scale genomic data from isoform sequencing, we analyzed ohnolog genealogies and divergence in hundreds to thousands of gene families across major snow carp lineages. Our findings demonstrated that independent autopolyploidization subsequent to speciation was prevalent, while autopolyploidization followed by speciation also occurred in the diversification of snow carp. This was further supported by matrilineal divergence and drainage evolution evidence. Contrary to the long-standing hypothesis that ancient polyploidization preceded the diversification of snow carp, we determined that polyploidy in extant snow carp was established by recurrent autopolyploidization events during the Pleistocene. These findings indicate that the diversification of extant snow carp resembles a coordinated duet: first, the uplift of the Tibetan Plateau orchestrated the biogeography and diversification of their diploid progenitors; then, the extensive Pliocene-Pleistocene climate changes acted as relay runners, further fueling diversification through recurrent autopolyploidization. Overall, this study not only reveals a hitherto unrecognized recent WGD lineage in vertebrates but also advances current understanding of WGD processes, emphasizing that WGD establishment is a non-stochastic event, emerging from numerous adaptations to environmental challenges and recurring throughout evolutionary history rather than merely in plants.

Development of a humanized mouse model with functional human materno-fetal interface immunity.

Materno-fetal immunity possesses specialized characteristics to ensure pathogen clearance while maintaining tolerance to the semiallogeneic fetus. Most of our understanding on human materno-fetal immunity is based on conventional rodent models that may not precisely represent human immunological processes owing to the huge evolutionary divergence. Herein, we developed a pregnant human immune system (HIS) mouse model through busulfan preconditioning, which hosts multilineage human immune subset reconstitution at the materno-fetal interface. Human materno-fetal immunity exhibits a tolerogenic feature at the midgestation stage (embryonic day [E] 14.5), and human immune regulatory subsets were detected in the decidua. However, the immune system switches to an inflammatory profile at the late gestation stage (E19). A cell-cell interaction network contributing to the alternations in the human materno-fetal immune atmosphere was revealed based on single-cell RNA-Seq analysis, wherein human macrophages played crucial roles by secreting several immune regulatory mediators. Furthermore, depletion of Treg cells at E2.5 and E5.5 resulted in severe inflammation and fetus rejection. Collectively, these results demonstrate that the pregnant HIS mouse model permits the development of functional human materno-fetal immunity and offers a tool for human materno-fetal immunity investigation to facilitate drug discovery for reproductive disorders.

Increased evolutionary rate in the Z-chromosome of sympatric and allopatric species of Morpho butterflies.

Divergent evolution of genomes among closely related species is shaped by both neutral processes and ecological forces, such as local adaptation and reinforcement. These factors can drive accelerated evolution of sex chromosomes relative to autosomes. Comparative genomic analyses between allopatric and sympatric species with overlapping or divergent ecological niches offer insights into reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species coexist in sympatry, with specialization across forest strata and temporal niches. We analyzed the genomes of eight Morpho species, along with previously published genomes of three others, to compare chromosomal rearrangements and signs of positive selection in the Z chromosome vs autosomes. We found extensive chromosomal rearrangements in Z chromosome, particularly in sympatric species with similar ecological niches, suggesting a role for inversions in restricting gene flow at a postzygotic level. Z-linked genes also exhibited significantly higher dN/dS ratios than autosomal genes across the genus, with pronounced differences in closely related species living in sympatry. Additionally, we examined the evolution of eight circadian clock genes, detecting positive selection in Period, located on the Z chromosome. Our findings suggest that the Z chromosome evolves more rapidly than autosomes, particularly among closely related species, raising questions about its role in pre- and post-zygotic isolation mechanisms.

Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades

Torpor encompasses diverse adaptations to extreme environmental stressors such as hibernation, aestivation, brumation, and daily torpor. Here we introduce StrokeofGenus, an analytic pipeline that identifies distinct transcriptomic states and shared gene expression patterns across studies, tissues, and species. We use StrokeofGenus to study multiple and diverse forms of torpor from publicly-available RNA-seq datasets that span eight species and two classes. We identify three transcriptionally distinct states during the cycle of heterothermia: euthermia, torpor, and interbout arousal. We also identify torpor-specific gene expression patterns that are shared both across tissues and between species with over three hundred million years of evolutionary divergence. We further demonstrate the general sharing of gene expression patterns in multiple forms of torpor, implying a common evolutionary origin for this process. Although here we apply StrokeofGenus to analysis of torpor, it can be used to interrogate any other complex physiological processes defined by transient transcriptomic states.

Re-appraising the evidence for the source, regulation and function of p53-family isoforms.

The p53 family of proteins evolved from a common ancestor into three separate genes encoding proteins that act as transcription factors with distinct cellular roles. Isoforms of each member that lack specific regions or domains are suggested to result from alternative transcription start sites, alternative splicing or alternative translation initiation, and have the potential to exponentially increase the functional repertoire of each gene. However, evidence supporting the presence of individual protein variants at functional levels is often limited and is inferred by mRNA detection using highly sensitive amplification techniques. We provide a critical appraisal of the current evidence for the origins, expression, functions and regulation of p53-family isoforms. We conclude that despite the wealth of publications, several putative isoforms remain poorly established. Future research with improved technical approaches and the generation of isoform-specific protein detection reagents is required to establish the physiological relevance of p53-family isoforms in health and disease. In addition, our analyses suggest that p53-family variants evolved partly through convergent rather than divergent evolution from the ancestral gene.

Description of Ixodeslanigeri sp. nov., a new hard tick species (Acari, Ixodidae) collected from mouse-eared bats (Vespertilionidae, Myotis) in Vietnam.

Historically, for more than one and a half centuries, only one so-called "long-legged bat tick" species, i.e., Ixodesvespertilionis Koch was known to science. However, during the past decade, it was recognized on a molecular basis that long-legged ixodid ticks associated with bats may represent at least six species. Of these, until recently, five have been morphologically described. In this study, Ixodes ticks were collected from two Myotis species in southeastern Asia, Vietnam. Based on the morphological and molecular characteristics of the female, nymph and larva, Ixodeslanigeri Hornok, sp. nov. is described here. The male is unknown. Like other members of the Ixodesariadnae complex, I.lanigeri Hornok apparently shows a preference for vesper bats as its typical hosts. In this context, host-association and geographical separation may explain the evolutionary divergence of I.lanigeri Hornok from its closest relative occurring on Murinahilgendorfi Peters in East Asia, Japan, because no Myotis or Murina spp. have overlapping distribution between Vietnam and the main islands of Japan. On the other hand, supposing that (similarly to I.ariadnae) I.lanigeri Hornok probably occurs on other myotine bats and knowing that several Myotis species indigenous in Vietnam have a broad geographical range in southern and southeastern Asia, the new tick species most likely has a widespread distribution in this area.

Oscillatory DeltaC Expression in Neural Progenitors Primes the Prototype of Forebrain Development.

Notch signaling plays a pivotal role in regulating various developmental processes, particularly in controlling the timing of neuronal production within the developing neocortex. Central to this regulatory mechanism is the oscillatory pattern of Delta, which functions as a developmental clock modulator. Its deficiency profoundly impairs mammalian brain formation, highlighting its fundamental role in brain development. However, zebrafish carrying a mutation in the functional ortholog DeltaC (dlc) within their functional ortholog exhibit an intact forebrain structure, implying evolutionary variations in Notch signaling within the forebrain. In this study, we unveil the distinct yet analogous expression profiles of Delta and Her genes in the developing vertebrate forebrain. Specifically, for the first time, we detected the oscillatory expression of the Delta gene dlc in the developing zebrafish forebrain. Although this oscillatory pattern appeared irregular and was not pervasive among the progenitor population, attenuation of the dlc-involved Notch pathway using a γ-secretase inhibitor impaired neuronal differentiation in the developing zebrafish forebrain, revealing the indispensable role of the dlc-involved Notch pathway in regulating early zebrafish neurogenesis. Taken together, our results demonstrate the foundational prototype of dlc-involved Notch signaling in the developing zebrafish forebrains, upon which the intricate patterns of the mammalian neocortex may have been sculpted.

In silico Analysis and Characterization of the F5H Gene Family in Sorghum bicolor and Its Role in Lignin Production

Ferulate 5-hydroxylase (F5H), a cytochrome P450-dependent monooxygenase, catalyzes the hydroxylation of coniferaldehyde, a crucial step in the formation of syringyl lignin monomer (S). However, evolutionary divergence, expression patterns under abiotic stress conditions (ABA, PEG and NaOH) and lignin content-related features of the F5H gene family in Sorghum bicolor have not been explored. This study envisaged mining of Sorghum genomic data leading to the identification of 61 SbF5H genes. Bioinformatics analysis revealed the phylogenetic evolutionary relations, gene structures, conserved motifs, physicochemical properties, and promoter cis-acting elements related to these genes and their encoded proteins. Based on the gene structural and phylogenetic features, these 61 SbF5Hs were grouped into 4 subclasses. The in silico expression analysis revealed higher accumulation of SbF5H1 transcripts in embryo and in root under stress conditions. Similarly, Other SbF5H genes have shown expression in stem and root, thus indicating SbF5H genes involvement in Sorghum lignin biosynthesis. By exploring into the functional aspects of the F5H gene, our study sought to shed light on its significance in influencing not only the chemical makeup of lignin but also the resultant plant phenotypes. This insight into the molecular mechanisms governing lignin biosynthesis can have implications for bioenergy production and crop improvement.

Understanding the genetic landscape of flowering time variation in Brassica juncea (L.) Czern. and its diploid progenitors: unravelling the role of selection and cytoplasmic backgrounds

Context Brassica juncea germplasm exhibits significant variations in flowering timing and vernalisation requirements. However, knowledge gaps exist with respect to variations in expression and the divergent evolution of flowering genes in B. juncea subgenomes. Aims This study aims to examine the role of flowering genes in defining trait variation and to identify indications of directional selection on these genes. Methods Employing a combination of genome-wide association studies, functional genomics and population genetic assays, we explored the genetic architecture underlying flowering time variation within expansive germplasm collections of this allopolyploid and its progenitor species. Key results Genome-wide association studies aided in predicting 17 and 34 candidate genes in B. rapa and B. juncea, respectively. Seven of these (FT, FLC, BAG4, ELF4-L2, EFM, SEP4, and LSH6) were predicted in both B. juncea and B. rapa. Some genes, GA20OX3, NF-YA1, PI, MMP, RPS10B, CRY2, AGL72, LFY, TOC1, ELF5, EFM, FLC and TFL1 exhibited directional selection as inferred from negative Tajima’s D and Fu’s Fs statistics. Conclusions Common predicted genes are known influencers of flowering time and phenological changes between species as well as across zones of adaptation. An analysis of gene expression patterns indicates that the gene expression bias in resynthesised B. juncea could be influenced by the cytoplasmic background. Most expression variants are found in B genome copies. Some genes lacked expression variation in their diploid progenitors, whereas these genes exhibit expression variation in polyploid species. Implications This study highlights that integrating genome-wide association studies with molecular signals of natural selection can effectively contribute to our understanding of the ecological genetics of adaptive evolution.

Evolutionary divergence of facial muscle physiology between domestic dogs and wolves.

Domestic dogs (Canis familiaris) are descended from gray wolf (Canis lupus) populations that inhabited Western Europe and Siberia. The specific timing of dog domestication is debated, but archeological and genetic evidence suggest that it was a multi-phase process that began at least 15,000 years ago. There are many morphological differences between dogs and wolves, including marked divergence in facial muscle morphology, but we know little about the comparative physiology of these muscles. A better understanding of comparative facial muscle physiology between domestic dogs and gray wolves would improve our conceptual framework for the processual mechanisms in dog domestication. To address these issues, we assessed the myosin profiles (type I and type II) from the zygomaticus and orbicularis oris muscles of 6 domestic dogs and 4 gray wolves. Due to small sample sizes, statistical analyses were not done. Results reveal that sampled domestic dogs have almost 100% fast-twitch (type II) muscle fibers while gray wolves have less than 50%, meaning that dog faces can contract fast while wolf faces are able to sustain facial muscle contraction. Sample sizes are limited but the present study indicates that dog domestication is associated with not only a change in facial muscle morphology but a concomitant change in how these muscles function physiologically. Selective pressures in the development of communication between dogs and humans using facial expression may have influenced this evolutionary divergence, but the paedomorphic retention of barking in adult dogs may have also played a role.

Genetic and evolutionary divergence of harbour seals (Phoca vitulina) in Iliamna Lake, Alaska.

Freshwater populations of typically marine species present unique opportunities to investigate biodiversity, evolutionary divergence, and the adaptive potential and niche width of species. A few pinniped species have populations that reside solely in freshwater. The harbour seals inhabiting Iliamna Lake, Alaska constitute one such population. Their remoteness, however, has long hindered scientific inquiry. We used DNA from seal scat and tissue samples provided by Indigenous hunters to screen for mitochondrial DNA and microsatellite variation within Iliamna Lake and eight regions across the Pacific Ocean. The Iliamna seals (i) were substantially and significantly discrete from all other populations ( [Formula: see text]F st-mtDNA = 0.544, [Formula: see text]Φ st - mtDNA = 0.541, [Formula: see text]F st-microsatellites = 0.308), (ii) formed a discrete genetic cluster separate from all marine populations (modal ∆k = 2, PC1 = 14.8%), had (iii) less genetic diversity (Hd, π, H exp), and (iv) higher inbreeding (F) than marine populations. These findings are both striking and unexpected revealing that Iliamna seals have likely been on a separate evolutionary trajectory for some time and may represent a unique evolutionary legacy for the species. Attention must now be given to the selective processes driving evolutionary divergence from harbour seals in marine habitats and to ensuring the future of the Iliamna seal.

Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye.

Annuality and perenniality represent two different life-history strategies in plants, and an analysis of genomic differentiation between closely related species of different life histories bears the potential to identify the underlying targets of selection. Additionally, understanding the interactions between patterns of recombination and signatures of natural selection is a central aim in evolutionary biology, because patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Here, our aim was to characterise the landscape of genomic differentiation between weedy annual rye (Secale cereale L.) and wild perennial rye (Secale strictum C. Presl), and explore the extent to which signatures of selection are influenced by recombination rate variation. We used population-level sequence data of annual and perennial rye to analyse population structure and their demographic history. Based on our analyses, annual and perennial rye diverged approximately 26,500 years ago (ya) from an ancestral population size of ~85,000 individuals. We analysed patterns of genetic diversity and genetic differentiation, and found highly differentiated regions located in low-recombination regions, indicative of linked selection. Although all highly differentiated regions, as revealed by F ST-outlier scans, were located in low-recombining regions, not all chromosomes showed this tendency. We therefore performed a gene ontology enrichment analysis, which showed that highly differentiated regions comprise genes involved in photosynthesis. This enrichment was confirmed when F ST outlier scans were performed separately in low- and intermediate-recombining regions, but not in high-recombining regions, suggesting that local recombination rate variation in rye affects outlier scans. Cultivated rye is an annual crop, but the introduction of perenniality may be advantageous in regions with poor soil quality or under low-input farming. Although the resolution of our analysis is limited to a broad-scale, knowledge about the evolutionary divergence between annual and perennial rye might support breeding efforts towards perennial rye cultivation.

Discovery of the first sea turtle adenovirus and turtle associated circoviruses

Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host−virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome b amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus Circovirus, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host–virus interactions.

The U-turn in educational inequality. Why a multidimensional approach matters for measuring social inequalities in tertiary educational attainment.

This study examines the evolution in the association between social origins and tertiary educational attainment in Belgium, from post-World War II to the millennium’s onset. For this, we rely on a multidimensional measurement of social origins that accounts for interaction mechanisms between parental class and educational resources. We analyse 13 803 individuals over four birth cohorts. In contrast to previous studies, we find a decline in social inequalities for cohorts born before 1975, followed by a resurgence among those born afterwards. This U-turn in social inequalities of tertiary educational attainment is only observable when social origins are measured multidimensionally. Additionally, we investigate the interaction effects between parental resources, revealing divergent evolutions in accumulation, and compensation mechanisms. Our findings underscore the renewed importance of combining parental education with parental social class for generations born after 1975.

Genotyping and phylogenetic analysis of human Papillomaviruses from women with genital warts

Background and objectives. The pathophysiology of Human Papillomavirus (HPV) infections is dependent on the genotype of virus, the host immune system and the local environmental conditions. HPV infections are linked to a variety of benign and malignant disorders. Anogenital warts is a Sexually Transmitted Infection (STI) primarily caused by Low-Risk HPV (LR-HPV) genotypes 6 and 11. The aims were to Investigation of the prevalence and genotypic distribution of HPV in women with genital warts in Mosul/Iraq, HPV-DNA sequencing and Phylogenetic analysis including minimum spanning trees of amplified HPV L1 gene comparison the present sequences with similar genotypes in GenBank – National Center Biotechnology Information (NCBI) using mega-7-software. Materials and methods. A total of 150 samples were collected from women with genital wart infections. Polymerase Chain Reaction (PCR) was performed using GP+5/GP+6 and MY09/MY11 consensus primers. Results. About 84.6% prevalence of HPV genotypes. The highest frequency (32% and 28.6%) were observed in the 19-28 and 29-38 age groups. Conclusion. Women in Mosul, Iraq, who have genital warts are more likely to have different genotypes of HPV. HPV 11 type was found to be the most common, followed HPV6 and HPV10 as LR HPV, while HPV 16 and HPV45 were the most common as HR HPV. The analysis of the phylogenetic tree revealed a genetic relationship between our isolates and global isolates ranging from (10-100%) bootstrap ratio this indicating phylogenetic relationships (divergent and convergent evolution) this was meant the diversity in origin of the various genotypes common in Mosul, Iraq.

Reconstructing oral cavity tumor evolution through brush biopsy

Oral potentially malignant disorders (OPMDs) with genomic alterations have a heightened risk of evolving into oral squamous cell carcinoma (OSCC). Currently, genomic data are typically obtained through invasive tissue biopsy. However, brush biopsy is a non-invasive method that has been utilized for identifying dysplastic cells in OPMD but its effectiveness in reflecting the genomic landscape of OPMDs remains uncertain. This pilot study investigates the potential of brush biopsy samples in accurately reconstructing the genomic profile and tumor evolution in a patient with both OPMD and OSCC. We analyzed single nucleotide variants (SNVs), copy number aberrations (CNAs), and subclonal architectures in paired tissue and brush biopsy samples. The results showed that brush biopsy effectively captured 90% of SNVs and had similar CNA profiles as those seen in its paired tissue biopsies in all lesions. It was specific, as normal buccal mucosa did not share these genomic alterations. Interestingly, brush biopsy revealed shared SNVs and CNAs between the distinct OPMD and OSCC lesions from the same patient, indicating a common ancestral origin. Subclonal reconstruction confirmed this shared ancestry, followed by divergent evolution of the lesions. These findings highlight the potential of brush biopsies in accurately representing the genomic profile of OPL and OSCC, proving insight into reconstructing tumor evolution.

Dynamics and Evolution of Donor-derived Cytomegalovirus Infection in 3 Solid Organ Transplant Recipients With the Same Multiorgan Donor.

Cytomegalovirus (CMV) infection poses a significant risk to immunosuppressed transplant recipients, manifesting through primary infection, reinfection, or reactivation. We analyzed the emergence of drug resistance in CMV infection in 3 patients who were later found to have received an allograft from a shared, deceased donor. The seronegative transplant recipients developed symptomatic CMV infections after bowel/pancreas, kidney, or lung transplantation. Prospective Sanger sequencing was used to identify mutations in the viral DNA polymerase (DP) and protein kinase (PK). DP and PK variants were retrospectively quantified by targeted next-generation sequencing. The impact of the novel DP-A505G substitution on drug susceptibility was assessed using a recombinant virus. Whole-genome sequencing of clinical CMV samples was enabled through target DNA enrichment. The DP-A505G substitution was found in all patient samples and could be associated with a natural polymorphism. A subsequent review of the patients' clinical histories revealed that they had all received organs from a single donor. The CMV infection exhibited divergent evolution among the patients: patient 1 developed resistance to ganciclovir and foscarnet because of 2 DP mutations (V715M and V781I), patient 2 showed no genotypic resistance, and patient 3 developed ganciclovir (PK-L595S) and maribavir resistance (PK-T409M). Interpatient variation across the entire CMV genome was minimal, with viral samples clustering in phylogenetic analysis. All 3 transplant recipients were infected with the same donor-derived CMV strain and readily developed different drug susceptibility profiles. This underscores the importance of judicious antiviral drug use and surveillance in preventing antiviral resistance emergence.

Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant

Host specificity is a key factor influencing the ecology and evolutionary diversification of parasitic organisms. Host specialisation and geographic isolation are known to lead to the genetic differentiation of allopatric races in parasitic plants. However, how divergence can co-occur in sympatry remains largely unknown. We investigated phenological and phenotypic differentiation and potential reproductive isolation among three sympatric genetic races of Cytinus hypocistis (Cytinaceae) - an extreme endophytic holoparasite with a high degree of host specialisation. We compared spatio-temporal variations in flowering phenology, flower production, floral longevity, floral rewards, and morphology, and conducted inter-race pollinations among three races parasitising Cistus ladanifer, C. salviifolius, and Halimium halimifolium (Cistaceae) in six co-occurring populations. We found that host-defined genetic races differed significantly across multiple phenotypic and phenological aspects – a phenomenon previously overlooked due to the plants’ cryptic morphology. The race parasitising H. halimifolium showed earlier blooming, higher floral display, longer flowers, and higher pollen production and nectar concentration; the race on C. salviifolius showed later flowering, significantly lower floral display and smaller flowers with lower floral rewards; the race on C. ladanifer had intermediate characteristics. Genetic races were interfertile yet may remain differentiated by restricted gene flow and host-driven selection pressures. Together, our data point to a rare case of sympatric divergent evolution hiding in plain sight: apparently morphologically similar co-occurring parasite races can be genetically, phenotypically, and phenologically distinct. This hitherto unreported example of host-driven sympatric diversification challenges how species concepts are applied to cryptic parasitic plant races.

Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.

Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.