All tangled up: Unraveling phylogenetics and reticulate evolution in the vining ferns, Lygodium (Schizaeales).

PREMISE: Reticulate evolution, often accompanied by polyploidy, is prevalent in plants, and particularly in the ferns. Resolving the resulting non-bifurcating histories remains a major challenge for plant phylogenetics. Here, we present a phylogenomic investigation into the complex evolutionary history of the vining ferns, Lygodium (Lygodiaceae, Schizaeales). METHODS: Using a targeted enrichment approach with the GoFlag 408 flagellate land plant probe set, we generated large nuclear and plastid sequence datasets for nearly all taxa in the genus and constructed the most comprehensive phylogeny of the family to date using concatenated maximum likelihood and coalescence approaches. We integrated this phylogeny with cytological and spore data to explore karyotype evolution and generate hypotheses about the origins of putative polyploids and hybrids. RESULTS: Our data and analyses support the origins of several putative allopolyploids (e.g., L. cubense, L. heterodoxum) and hybrids (e.g., L. ×fayae) and also highlight the potential prevalence of autopolyploidy in this clade (e.g., L. articulatum, L. flexuosum, and L. longifolium). CONCLUSIONS: Our robust phylogenetic framework provides valuable insights into dynamic reticulate evolution in this clade and demonstrates the utility of target-capture data for resolving these complex relationships.

The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae.

PREMISE: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape. METHODS: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework. RESULTS: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other. CONCLUSIONS: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.

Biosorption of pb(II) from aqueous solution by citrus reticulate: adsorption studies, and modeling.

Removing toxic Pb(II) ions from aqueous solution by the peels of citrus reticulate (mandarin orange), a fruit industry waste, presents suitable scale-up possibilities. The Scanning Electron Microscope (SEM) and Brunauer-Emmett-Teller (BET) studies reflected that the mandarin orange peel powder had a porous surface area (32.46 m2g-1), average pore size and pore volume was 38.6 Å and 0.402 cm3g-1, respectively, favorable for binding Pb(II) ions. Fourier-transform infrared spectroscopy (FTIR) showed C-Br stretching, primary alcohol (C-O), phenolic O-H, and carbodimide N = C = N bands primarily helped to bind Pb(II) ions. The study evaluated and optimized the parametric influences of pH, adsorbate and biosorbent concentration, contact time and temperature on the removal efficiency of Pb(II) ions. A maximum of 97.08% Pb(II) was removed from 20 mg L-1 solution when 2.5 g L-1 adsorbent was present. The reaction obeyed the pseudo-second-order kinetic model. The intra-particle diffusion was involved in lead sorption. The Langmuir isotherm model resulted in an adsorption capacity of 23.04 mg g-1. 35.28% Pb(II) was removed in the 3rd adsorption-desorption cycle with 0.4 M HCl. The adsorption process was natural, impulsive and endothermic. The statistical investigation used Multiple Polynomial Regression (MPR) and Genetic Algorithm (GA). The analysis effectively forecasted the percentage removal at the optimized condition.

The results of toxic Pb(II) ion removal from aqueous solution by the peels of citrus reticulate (mandarin orange), a food industry waste, are reported. The maximum Pb(II) adsorption capacity of 23.04 mg/g. This work provides a new way to realize good adsorption capacity of Pb(II) by orange peel and accelerates to utilize for small and medium-sized industries in rural areas of 3^rd World Countries.

Species delimitation 4.0: integrative taxonomy meets artificial intelligence.

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

Interspecific transfer of genetic information through polyploid bridges.

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

Clinical Overlaps in Reticulate Pigmentary Disorders: A Study of Three Cases.

Reticulate pigmentary disorders are autosomal dominant pigmentary disorders caused by abnormalities in the keratin 5 and keratin 14 genes. Here, we report three cases of reticulate hyperpigmentation disorders with clinical overlaps of the reticulate acropigmentation of Kitamura, Dowling-Degos disease (DDD), and dyschromatosis symmetrica hereditaria (DSH), all three having limited treatment options.

Evolutionary characteristics of the mitochondrial NADH dehydrogenase subunit 6 gene in some populations of four sympatric Mustela species (Mustelidae, Mammalia) from central Europe.

BACKGROUND: Selection on or reticulate evolution of mtDNA is documented in various mammalian taxa and could lead to misleading phylogenetic conclusions if not recognized. We sequenced the MT-ND6 gene of four sympatric Mustelid species of the genus Mustela from some central European populations. We hypothesised positive selection on MT-ND6, given its functional importance and the different body sizes and life histories of the species, even though climatic differences may be unimportant for adaptation in sympatry. METHODS AND RESULTS: MT-ND6 genes were sequenced in 187 sympatric specimens of weasels, Mustela nivalis, stoats, M. erminea, polecats, M. putorius, and steppe polecats, M. eversmannii, from eastern Austria and of fourteen allopatric polecats from eastern-central Germany. Median joining networks, neighbour joining and maximum likelihood analyses as well as Bayesian inference grouped all species according to earlier published phylogenetic models. However, polecats and steppe polecats, two very closely related species, shared the same two haplotypes. We found only negative selection within the Mustela sequences, including 131 downloaded ones covering thirteen species. Positive selection was observed on three MT-ND6 codons of other mustelid genera retrieved from GenBank. CONCLUSIONS: Negative selection for MT-ND6 within the genus Mustela suggests absence of both environmental and species-specific effects of cellular energy metabolism despite large species-specific differences in body size. The presently found shared polymorphism in European polecats and steppe polecats may result from ancestral polymorphism before speciation and historical or recent introgressive hybridization; it may indicate mtDNA capture of steppe polecats by M. putorius in Europe.

Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.

Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Effect of life cycle and venation pattern on the coordination between stomatal and vein densities of herbs.

Life cycle (annual vs perennial) and leaf venation pattern (parallel and reticular) are known to be related to water use strategies in herb species and critical adaptation to certain climatic conditions. However, the effect of these two traits and how they influence the coordination between vein density (vein length per area, VLA) and stomatal density (SD) remains unclear. In this study, we examined the leaves of 53 herb species from a subtropical botanical garden in Guangdong Province, China, including herbs with different life cycles and leaf venation patterns. We assessed 21 leaf water-related functional traits for all species, including leaf area (LA), major and minor VLA, major and minor vein diameter (VD), SD and stomatal length (SL). The results showed no significant differences in mean SD and SL between either functional group (parallel venation vs reticular venation and annual vs perennial). However, parallel vein herbs and perennial herbs displayed a significantly higher mean LA and minor VD, and lower minor VLA compared to reticular vein herbs and annual herbs, respectively. There was a linear correlation between total VLA and SD in perennial and reticular vein herbs, but this kind of correlation was not found in annual and parallel vein herbs. The major VLA and minor VD were significantly affected by the interaction between life cycle and leaf venation pattern. Our findings suggested that VLA, rather than SD, may serve as a more adaptable structure regulated by herbaceous plants to support the coordination between leaf water supply and demand in the context of different life cycles and leaf venation patterns. The results of the present study provide mechanistic understandings of functional advantages of different leaf types, which may involve in species fitness in community assembly and divergent responses to climate changes.

Identification of Philaster apodigitiformis in aquaculture and functional characterization of its ß-PKA gene and expression analysis of infected Poecilia reticulata.

Cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) is a distinctive member of the serine­threonine protein AGC kinase family and an effective kinase for cAMP signal transduction. In recent years, scuticociliate has caused a lot of losses in domestic fishery farming, therefore, we have carried out morphological and molecular biological studies. In this study, diseased guppies (Poecilia reticulata) were collected from an ornamental fish market, and scuticociliate Philaster apodigitiformis Miao et al., 2009 was isolated. In our prior transcriptome sequencing research, we discovered significant expression of the ß-PKA gene in P. apodigitiformis during its infection process, leading us to speculate its involvement in pathogenesis. A complete sequence of the ß-PKA gene was cloned, and quantified by quantitative reverse transcription-polymerase chain reaction to analyse or to evaluate the functional characteristics of the ß-PKA gene. Morphological identification and phylogenetic analysis based on small subunit rRNA sequence, infection experiments and haematoxylin­eosin staining method were also carried out, in order to study the pathological characteristics and infection mechanism of scuticociliate. The present results showed that: (1) our results revealed that ß-PKA is a crucial gene involved in P. apodigitiformis infection in guppies, and the findings provide valuable insights for future studies on scuticociliatosis; (2) we characterized a complete gene, ß-PKA, that is generally expressed in parasitic organisms during infection stage and (3) the present study indicates that PKA plays a critical role in scuticociliate when infection occurs by controlling essential steps such as cell growth, development and regulating the activity of the sensory body structures and the irritability system.

Preliminary evaluation of fish cartilage as a promising biomaterial in cartilage tissue engineering.

Fish cartilage is known as a valuable source of natural biomaterials due to its unique composition and properties. It contains a variety of bioactive components that contribute to its potential applications in different domains such as tissue engineering. The present work aimed to consider the properties of backbone cartilage from fish with a cartilaginous skeleton, including elasmobranch (reticulate whipray: Himantura uarnak and milk shark: Rhizoprionodon acutus) and sturgeon (beluga: Huso huso). The histomorphometric findings showed that the number of chondrocytes was significantly higher in reticulate whipray and milk shark compared to beluga (p < 0.05). The highest GAGs content was recorded in reticulate whipray cartilage compared to the other two species (p < 0.05). The cartilage from reticulate whipray and beluga showed higher collagen content than milk shark cartilage (p < 0.05), and the immunohistochemical assay for type II collagen (Col II) showed higher amounts of this component in reticulate whipray compared to the other two species. Young's modulus of the cartilage from reticulate whipray was significantly higher than that of milk shark and beluga (p < 0.05), while no significant difference was recorded between Young's modulus of the cartilage from milk shark and beluga. The gene expression of ACAN, Col II, and Sox9 showed that the cartilage-ECM from three species was able to induce chondrocyte differentiation from human adipose tissue-derived stem cells (hASCs). From these results, it can be concluded that the cartilage from three species, especially reticulate whipray, enjoys the appropriate biological properties and provides a basis for promoting its applications in the field of cartilage tissue engineering.

Scanning electron microscopic exploration of intricate pollen morphology and antimicrobial potentials of gourd family.

This study employs scanning electron microscopy (SEM) to delve into the intricate pollen morphology of Cucurbitaceae (Gourd Family) species, unraveling the nuanced details of their structural features. Concurrently, the research investigates the antimicrobial potentials encoded within these pollen grains, shedding light on their possible applications in the realm of natural antimicrobial agents. Cucurbitaceae plants showcases significant antibacterial and antifungal potentials, underscoring its potential as a source for novel antimicrobial compounds. This research endeavors to provide a comprehensive analysis of pollen morphometry in 12 Cucurbitaceous species, with the primary goal of identifying pollen morpho-types to enrich the taxonomic understanding of the Cucurbitaceae. Following the Erdtman protocol, the study involved processing, measuring, and capturing pollen grains using SEM techniques. Qualitative data were analyzed to evaluate the variations in pollen types, size, and exine stratified sculptured layering. The pollen grains exhibit characteristics of being monads, ranging in size from medium to very large, with the prevailing shape being prolate-spheroidal in six species. Notably, the maximum polar axis diameter was recorded for Cucurbita pepo (106.3 µm), while the minimum was observed in Zehneria anomala (32.6 µm). The grains of Cucurbitaceae exhibit diverse surface patterns, including reticulate columellae, reticulate, verrucate-scabrate, verrucate-gemmate, echinate baculate, reticulate-perforate, and micro-reticulate. This SEM investigation illuminates the intricacies of Cucurbitaceae pollen morphology while concurrently highlighting their noteworthy antimicrobial potentials. HIGHLIGHTS: High-resolution imaging reveals complex pollen morphology. Identification of unique antimicrobial structures on Cucurbitaceae pollen (gourd family). Exploring medicinal potential: Antimicrobial properties of cucurbitaceae species.

Optimizing BP neural network algorithm for Pericarpium Citri Reticulatae (Chenpi) origin traceability based on computer vision and ultra-fast gas-phase electronic nose data fusion.

This study utilized computer vision to extract color and texture features of Pericarpium Citri Reticulatae (PCR). The ultra-fast gas-phase electronic nose (UF-GC-E-nose) technique successfully identified 98 volatile components, including olefins, alcohols, and esters, which significantly contribute to the flavor profile of PCR. Multivariate statistical Analysis was applied to the appearance traits of PCR, identifying 57 potential marker-trait factors (VIP > 1 and P < 0.05) from the 118 trait factors that can distinguish PCR from different origins. These factors include color, texture, and odor traits. By integrating multivariate statistical Analysis with the BP neural network algorithm, a novel artificial intelligence algorithm was developed and optimized for traceability of PCR origin. This algorithm achieved a 100% discrimination rate in differentiating PCR samples from various origins. This study offers a valuable reference and data support for developing intelligent algorithms that utilize data fusion from multiple intelligent sensory technologies to achieve rapid traceability of food origins.

Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region.

Polygonatum is the largest genus of tribe Polygonateae (Asparagaceae) and is widely distributed in the temperate Northern Hemisphere, especially well diversified in southwestern China to northeastern Asia. Phylogenetic relationships of many species are still controversial. Hence it is necessary to clarify their phylogenetic relationships and infer possible reticulate relationships for the genus. In this study, genome-wide data of 43 species from Polygonatum and its closely related taxa were obtained by Hyb-Seq sequencing. The phylogenetic trees constructed from genome-wide nuclear and chloroplast sequences strongly supported the monophyly of Polygonatum with division into three major clades. A high level of incongruence was detected between nuclear and chloroplast trees as well as among gene trees within the genus, but all occurred within each major clade. However, introgression tests and reticulate evolution analyses revealed low level of gene flow and weak introgression events in the genus, suggesting hybridization and introgression were not dominant during the evolutionary diversification of Polygonatum in the Northern Hemisphere. This study provides important insights into reconstructing evolutionary relationships and speciation pattern of taxa from the north temperate flora.

Reticulate evolution of the tertiary relict Osmanthus.

When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.

[Translated article] Reticulate Skin Lesions: Practical Color-Based Algorithm for Initial Clinical Assessment.

Reticular patterns are observed in a great variety of skin diseases. While these morphologic patterns are often highly distinctive, they are seldom discussed or studied in clinical contexts or recognized as a diagnostic category in their own right. Diseases presenting with reticulate skin lesions have multiple etiologies (tumors, infections, vascular disorders, inflammatory conditions, and metabolic or genetic alterations) and can range from relatively benign conditions to life-threatening ones. We review a selection of these diseases and propose a clinical diagnostic algorithm based on predominant coloring and clinical features to aid in their initial assessment.

Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements.

Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera. This group has undergone various taxonomic changes recently, spurred by investigations using traditional genetic markers. Here we used over 1,000 ultraconserved loci to infer the relationships within Poeciliidae in the first attempt at understanding their diversification based on genome-scale data. We explore gene tree discordance and investigate potential incongruence between concatenation and coalescent inference methods. Our aim is to examine the influence of incomplete lineage sorting and reticulate evolution on the poeciliids' evolutionary history and how these factors contribute to the observed gene tree discordace. Our concatenated and coalescent phylogenomic inferences recovered four major clades within Poeciliidae. Most supra-generic level relationships we inferred were congruent with previous molecular studies, but we found some disagreements; the Middle American taxa Phallichthys and Poecilia (Mollienesia) were recovered as non-monophyletic, and unlike other recent molecular studies, we recovered Brachyrhaphis as monophyletic. Our study is the first to provide signatures of reticulate evolution in Poeciliidae at the family level; however, continued finer-scale investigations are needed to understand the complex evolutionary history of the family along with a much-needed taxonomic re-evaluation.

Reticulate Skin Lesions: Practical Color-Based Algorithm for Initial Clinical Assessment. / Lesiones cutáneas reticulares: algoritmo clínico práctico basado en el color de la lesión para el abordaje inicial.

Reticular patterns are observed in a great variety of skin diseases. While these morphologic patterns are often highly distinctive, they are seldom discussed or studied in clinical contexts or recognized as a diagnostic category in their own right. Diseases presenting with reticulate skin lesions have multiple etiologies (tumors, infections, vascular disorders, inflammatory conditions, and metabolic or genetic alterations) and can range from relatively benign conditions to life-threatening ones. We review a selection of these diseases and propose a clinical diagnostic algorithm based on predominant coloring and clinical features to aid in their initial assessment.

Chlamydia muridarum infection causes bronchointerstitial pneumonia in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice.

The murine bacterial pathogen Chlamydia muridarum (Cm) has been used to study human Chlamydia infections in various mouse models. CD4+ T-cells, natural killer cells, and interferon-gamma (IFN-γ)-mediated immunity are important to control experimentally induced Cm infections. Despite its experimental use, natural infection by Cm has not been documented in laboratory mice since the 1940s. In 2022, the authors reported the discovery of natural Cm infections in numerous academic institutional laboratory mouse colonies around the globe. To evaluate the impact of Cm infection in severely immunocompromised mice, 19 NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice were cohoused with Cm shedding, naturally infected immunocompetent mice and/or their soiled bedding for 4 weeks and subsequently euthanized. Clinical disease, characterized by lethargy, dyspnea, and weight loss, was observed in 11/19 NSG mice, and 16/18 NSG mice had neutrophilia. All mice exhibited multifocal to coalescing histiocytic and neutrophilic bronchointerstitial pneumonia (17/19) or bronchiolitis (2/19) with intraepithelial chlamydial inclusions (CIs). Immunofluorescence showed CIs were often associated with bronchiolar epithelium. CIs were frequently detected by immunohistochemistry in tracheal and bronchiolar epithelium (19/19), as well as throughout the small and large intestinal epithelium without lesions (19/19). In a subset of cases, Cm colonized the surface epithelium in the nasopharynx (16/19), nasal cavity (7/19), and middle ear canal (5/19). Endometritis and salpingitis with intraepithelial CI were identified in a single mouse. These findings demonstrate that Cm infection acquired through direct contact or soiled bedding causes significant pulmonary pathology and widespread intestinal colonization in NSG mice.