Analysis Of Molecular Data Research Articles

Phenotypic and Molecular Diversity of Wild Populations of Acca sellowiana (Berg.) Burret in the Southern Area of Natural Distribution

Acca sellowiana is a subtropical tree in the myrtle family (Myrtaceae) native to southern Brazil and northeastern Uruguay. It is recognized for its value as a fruit-bearing, ornamental, and medicinal species. Based on distinctive characteristics of fruits, seeds, and leaves, as well as its geographical distribution pattern, two variants of the species are distinguished: the “Brazilian type” and the “Uruguayan type”. The objective of this study was to characterize, for the first time, the diversity of 202 individuals from four wild populations in Uruguay, representative of the species’ most southern natural distribution. Twenty-three morphological descriptors (leaf, flower, and fruit) and 204 RAPD (Random Amplified Polymorphic DNA) markers were used. The morphological data collected validated the main criteria that distinguish “Uruguayan type” populations from “Brazilian type” populations, such as lower seed weight and fruit size, thin and slightly rough skin, high pulp percentage, and hairy white abaxial leaf surfaces. Analyses of both morphological and molecular data indicated wide diversity and strong population structuring, which is relevant information for designing conservation plans, sustainable utilization, and genetic improvement of the plant genetic resources of this species.

Five new species of Pseudosperma (Inocybaceae, Agaricales) from Benin and Turkey based on morphological characteristics and phylogenetic evidence

Species of Pseudosperma (Inocybaceae) are widely distributed from temperate to tropical regions. In this study, we describe and illustrate five new species of Pseudosperma: P. beninense, P. cremeo-ochraceum, P. squarrosofulvum, P. stramineum, and P. tiliae, based on comprehensive analyses of morphological and molecular data derived from specimens collected in Benin (West Africa) and Turkey (Western Eurasia). These new species have been found in forests with Isoberlinia spp. and other ectomycorrhizal tree species in Benin and in association with Tilia platyphyllos in Turkey. The phylogenetic relationships of the new species were inferred through analyses of nuclear rDNA sequences, encompassing the internal transcribed spacer (ITS), 28S rDNA, and RNA polymerase II second largest subunit (RPB2) region. Phylogenetic analyses revealed that P. beninense, P. cremeo-ochraceum, P. squarrosofulvum, and P. stramineum from Benin cluster with species from Australia, China, and India within a clade formed exclusively by species known from the palaeotropics and Australia, whereas P. tiliae from Turkey clustered with P. mediterraneum from Italy. Detailed descriptions are provided, supplemented by illustrations and line drawings of key micromorphological features. In addition, a comparative analysis with morphologically similar and phylogenetically closely related species is presented and discussed in detail.

Simulation of Full HIV Cluster Networks in a Nationally Representative Model Indicates Intervention Opportunities.

Clusters of rapid HIV transmission in the United States are increasingly recognized through analysis of HIV molecular sequence data reported to the National HIV Surveillance System. Understanding the full extent of cluster networks is important to assess intervention opportunities. However, full cluster networks include undiagnosed and other infections that cannot be systematically observed in real life. We replicated HIV molecular cluster networks during 2015-2017 in the United States using a stochastic dynamic network simulation model of sexual transmission of HIV. Clusters were defined at the 0.5% genetic distance threshold. Ongoing priority clusters had growth of ≥3 diagnoses/year in multiple years; new priority clusters first had ≥3 diagnoses/year in 2017. We assessed the full extent, composition, and transmission rates of new and ongoing priority clusters. Full clusters were 3-9 times larger than detected clusters, with median detected cluster sizes in new and ongoing priority clusters of 4 (range 3-9) and 11 (range 3-33), respectively, corresponding to full cluster sizes with a median of 14 (3-74) and 94 (7-318), respectively. A median of 36.3% (range 11.1%-72.6%) of infections in the full new priority clusters were undiagnosed. HIV transmission rates in these clusters were >4 times the overall rate observed in the entire simulation. Priority clusters reflect networks with rapid HIV transmission. The substantially larger full extent of these clusters, high proportion of undiagnosed infections, and high transmission rates indicate opportunities for public health intervention and impact.

Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution

Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.

Abstract 2270: UALCAN Mobile, An app for cancer gene expression data analysis

Abstract Cancer is a complex disease effecting different organs and a major cause of death and a burden on the society. Multiple molecular alteration occur during cancer initiation and disease progression and metastasis. Recent advances in technology led to generation of large amount of molecular data including transcriptome. These large datasets can be used to analyze and identify sub-class specific cancer biomarkers and targets. However, there is a need for the development user friendly tools for its analysis and dissemination of the large scale cancer molecular data. Earlier, we had developed and upgraded web based comprehensive proteogenomic platform UALCAN (ualcan.path.uab.edu), which allows users to analyze and integrate the disparate data to better understand the gene, proteins, and pathways perturbed in cancer and make discoveries. UALCAN web platform enables intuitive analysis and discovery by cancer research community. In the current study, we describe the development of UALCAN Mobile application (App) that will provide cancer transcriptomic data obtained from The Cancer Genome Atlas (TCGA) project, to evaluate protein-coding gene expression based on various stratification including stage, grade, race, gender and molecular-subtypes across over 30 types of cancers. The UALCAN Mobile app aims at providing large cancer dataset on the go. In order to find causative gene expression changes, identify biomarkers and therapeutic targets, UALCAN Mobile will assist as the data will be easily mobile and transportable with this App. Here, we describe the development of UALCAN Mobile and its utility to the cancer research community. UALCAN Mobile App can be found at both iOS/Apple and Android play store and is free to download and use. Citation Format: Sooryanarayana Varambally, Darshan Shimoga Chandrashekar, Gopi Chand Puli, Santhosh Kumar Karthikeyan, Upender Manne, Chad J. Creighton, Sidarth Kumar. UALCAN Mobile, An app for cancer gene expression data analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2270.

Abstract 7175: Web-based cross-database exploration of molecular pharmacology data from cancer cell lines and patient genomics

Abstract CellMiner Cross-Database (CellMinerCDB, discover.nci.nih.gov/cellminercdb) allows integration and analysis of molecular and pharmacological data within and across cancer cell line datasets from the National Cancer Institute (NCI), Broad Institute, Sanger/MGH, MD Anderson Cancer Center (MDACC), and the National Center for Advancing Translational Sciences (NCATS, discover.nci.nih.gov/rsconnect/cellminercdb_ncats/). Altogether, our database spans over 1,700 distinct cell lines, over 1,000 clinically relevant drugs, ~25,000 experimental compounds, and molecular profiling data, such as gene/protein expression, molecular signatures including epithelial mesenchymal transition (EMT), replication stress (RepStress), neuroendocrine evaluation (NE), DNA copy, methylation, mutational status, and gene dependencies (Broad DepMap). This rich and growing set of cell lines and tested drugs allows for novel avenues for response determinant discovery and clinical translation that is facilitated by 1) common annotations (e.g., tissues of origin and matched drug names) across pharmacogenomic datasets and 2) various univariate and multivariate analyses tools. A major challenge to clinical translation occurs in relating pre-clinical models to patient samples. As part of this work, we show how the CellMinerCDB infrastructure additionally supports annotated patient multi-omics data to aid researchers to relate findings from cancer cell lines with patient data; we use data from small cell lung cancer (SCLC) and neuroendocrine tumors as illustrative examples. This work provides significant pharmacogenomic integration that allows exploration within a comprehensive dataset of cancer cell lines and to inter-relationships with patient-derived datasets; this is being developed to display and mine patient samples as part of the complementary web-based tool (PatientTumorMiner). Citation Format: William C. Reinhold, Augustin Luna, Fathi Elloumi, Sudhir Varma, Daiki Taniyama, Makito Mizunuma, Jaydira del Rivero, Anish Thomas, Karyyne Reilly, Karel Pacak, Mirit Aladjem, Yves Pommier. Web-based cross-database exploration of molecular pharmacology data from cancer cell lines and patient genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7175.

Evolutionary history of an Irano-Turanian cushion-forming legume (Onobrychis cornuta).

The Irano-Turanian region is one of the largest floristic regions in the world and harbors a high percentage of endemics, including cushion-like and dwarf-shrubby taxa. Onobrychis cornuta is an important cushion-forming element of the subalpine/alpine flora of the Irano-Turanian floristic region. To specify the genetic diversity among the populations of this species (including individuals of O. elymaitica), we employed nrDNA ITS and two noncoding regions of plastid DNA (rpl32-trnL(UAG) and trnT(UGU)-trnL(UAA)). The most striking feature of O. cornuta assemblages was the unexpectedly high nucleotide diversity in both the nDNA and cpDNA dataset. In the analyses of nuclear and plastid regions, 25 ribotypes and 42 haplotypes were found among 77 and 59 accessions, respectively, from Iran, Turkey, and Afghanistan. Network analysis of the datasets demonstrated geographic differentiation within the species. Phylogenetic analyses of all dataset retrieved O. cornuta as a non-monophyletic species due to the inclusion of O. elymaitica, comprising four distinct lineages. In addition, our analyses showed cytonuclear discordance between both nuclear and plastid topologies regarding the position of some O. cornuta individuals. The underlying causes of this inconsistency remain unclear. However, we speculate that chloroplast capture, incomplete lineage sorting, and introgression were the main reasons for this event. Furthermore, molecular dating analysis indicated that O. cornuta originated in the early Pliocene (around 4.8 Mya) and started to diversify throughout the Pliocene and in particular the Pleistocene. Moreover, O. elymaitica was reduced to a subspecific rank within the species.

Plastid phylogenomics provides new insights into the systematics, diversification, and biogeography of Cymbidium (Orchidaceae)

Cymbidium (Orchidaceae: Epidendroideae), with around 60 species, is widely-distributed across Southeast Asia, providing a nice system for studying the processes that underlie patterns of biodiversity in the region. However, phylogenetic relationships of Cymbidium have not been well resolved, hampering investigations of species diversification and the biogeographical history of this genus. In this study, we construct a plastome phylogeny of 56 Cymbidium species, with four well-resolved major clades, which provides a framework for biogeographical and diversification rate analyses. Molecular dating and biogeographical analyses show that Cymbidium likely originated in the region spanning northern Indo-Burma to the eastern Himalayas during the early Miocene (∼21.10 Ma). It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle Miocene. Cymbidium spp. migration to the adjacent regions (Borneo, Philippines, and Sulawesi) primarily occurred during the Pliocene-Pleistocene period. Our analyses indicate that the net diversification rate of Cymbidium has decreased since its origin, and is positively associated with changes in temperature and monsoon intensity. Favorable hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification, after which the net diversification rate was reduced with the cooling climate after the middle Miocene. The transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches, yet without a significant effect on diversification rates. This study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.

Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales.

The reversible unfolding and refolding of proteins is a regulatory mechanism of tissue elasticity and signalling used by cells to sense and adapt to extracellular and intracellular mechanical forces. However, most of these proteins exhibit low mechanical stability, posing technical challenges to the characterization of their conformational dynamics under force. Here, we detail step-by-step instructions for conducting single-protein nanomechanical experiments using ultra-stable magnetic tweezers, which enable the measurement of the equilibrium conformational dynamics of single proteins under physiologically relevant low forces applied over biologically relevant timescales. We report the basic principles determining the functioning of the magnetic tweezer instrument, review the protein design strategy and the fluid chamber preparation and detail the procedure to acquire and analyze the unfolding and refolding trajectories of individual proteins under force. This technique adds to the toolbox of single-molecule nanomechanical techniques and will be of particular interest to those interested in proteins involved in mechanosensing and mechanotransduction. The procedure takes 4 d to complete, plus an additional 6 d for protein cloning and production, requiring basic expertise in molecular biology, surface chemistry and data analysis.

Total-evidence phylogeny of the subfamily Cylapinae and the divergence dates for its subgroupings (Insecta: Heteroptera: Miridae)

Abstract Representatives of the subfamily Cylapinae (Insecta: Heteroptera: Miridae) mostly inhabit the subtropics and tropics. The group currently comprises five tribes: Bothriomirini, Cylapini, Fulviini, Rhinomirini, and Vanniini. Additionally, the Psallopinae are sometimes included in this subfamily as a tribe. The interrelationships within Cylapinae are unknown, the monophyly is doubtful, and a phylogenetic study focusing on the entire subfamily has never been published. The molecular and fossil data analyses show that Miridae occurred at least in the Jurassic. The divergence dates for Cyalpinae tribes are unknown. We performed the phylogenetic analysis of Cylapinae based on molecular and morphological data, in addition to a combined dataset. We calibrated the molecular trees with fossil data. The results suggested non-monophyly of Cylapinae. The monophyly of Bothriomirini was confirmed. Cylapini were rendered as non-monophyletic. The Cylapus complex formed a clade with Vanniini, and the monophyly of Vanniini was doubtful. Fulviini were recovered as non-monophyletic, and the representatives fell into two separate well-supported clades. Dating analyses showed that the groups of the suprageneric level distributed across different continents diverged near the boarder between Mesosoic and Cenosoic, that was also true for the Asian suprageneric groups and the South American Cylapus complex. Australian groups of genera diverged in the Cenozoic.

Distribution, diversity and diversification from DNA barcoding perspective: The case of Gammarus radiation in the ancient Lake Ohrid

AbstractAimA detailed, comparative DNA‐barcoding and morphospecies‐based overview of the vertical and horizontal distribution of Lake Ohrid's endemic Gammarus species flock is provided. Re‐evaluation of the time frame for the onset of the species flock and identification of events that putatively influenced diversification processes.LocationLake Ohrid, Balkan Peninsula, Europe.TaxonGammarus species flock (Amphipoda, Crustacea).MethodsExtensive sampling and DNA barcoding of 600 individuals was carried out. DNA sequences were analysed using species delimitation methods, haplotype network reconstructions, Bayesian molecular dating and demographic analyses. The COI‐based species delimitation results were validated with nuclear 28S RNA data.ResultsThe species flock distribution has a weak horizontal but clear vertical structure. The diversity along bathymetric gradients correlates with temperature and salinity; and the highest diversity is observed in sublittoral and springs on the lake's shore. Two new molecular units representing putatively new species are revealed and supported also by the nuclear marker. The onset of flock radiation overlaps with the time of lake formation. The COI gene shows signs of positive selection and an acceleration in substitution rate. The demographic changes within the flock happened during the last thousands years.Main ConclusionsDistribution of the Gammarus species flock is vertically structured, reflecting habitat zonation. Parapatric speciation is one of the possible mechanisms behind the flock's diversification. Detection of new MOTUs suggests that the flock's diversity is still not fully revealed. Simultaneously, failure to collect three previously known MOTUs suggests a loss of gammarid diversity in the lake. This represents, together with the current threats to the lake ecosystem (i.e. climate changes, development of tourism), a clear call for conservation efforts. The speciation events and demographic changes within the flock relate presumably to glacial and postglacial water level changes and to the colonisation of new depth ranges and the associated springs.

Three new species in Russula subsection Xerampelinae supported by genealogical and phenotypic coherence

ABSTRACT Xerampelinae is a subsection composed of species of ectomycorrhizal fungi belonging to the hyperdiverse and cosmopolitan genus Russula (Russulales). Species of Xerampelinae are recognized by their fishy or shrimp odor, browning context, and a green reaction to iron sulfate. However, species delimitation has traditionally relied on morphology and analysis of limited molecular data. Prior taxonomic work in Xerampelinae has led to the description of as many as 59 taxa in Europe and 19 in North America. Here we provide the first multilocus phylogeny of European and North American members based on two nrDNA loci and two protein-coding genes. The resulting phylogeny supports the recognition of 17 species-rank Xerampelinae clades; however, higher species richness (~23) is suggested by a more inclusive nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) analysis. Phylogenetic and morphological analyses support three new species with restricted geographic distributions: R. lapponica, R. neopascua, and R. olympiana. We confirm that the European species R. subrubens is present in North America and the North American species R. serissima (previously known as R. favrei) is present in Europe. Most other Xerampelinae appear restricted to either North America or Eurasia, which indicates a high degree of regional endemism; this includes R. xerampelina, a name widely applied to North American taxa, but a species restricted to Eurasia.

The impact of Bayesian optimization on feature selection

Feature selection is an indispensable step for the analysis of high-dimensional molecular data. Despite its importance, consensus is lacking on how to choose the most appropriate feature selection methods, especially when the performance of the feature selection methods itself depends on hyper-parameters. Bayesian optimization has demonstrated its advantages in automatically configuring the settings of hyper-parameters for various models. However, it remains unclear whether Bayesian optimization can benefit feature selection methods. In this research, we conducted extensive simulation studies to compare the performance of various feature selection methods, with a particular focus on the impact of Bayesian optimization on those where hyper-parameters tuning is needed. We further utilized the gene expression data obtained from the Alzheimer's Disease Neuroimaging Initiative to predict various brain imaging-related phenotypes, where various feature selection methods were employed to mine the data. We found through simulation studies that feature selection methods with hyper-parameters tuned using Bayesian optimization often yield better recall rates, and the analysis of transcriptomic data further revealed that Bayesian optimization-guided feature selection can improve the accuracy of disease risk prediction models. In conclusion, Bayesian optimization can facilitate feature selection methods when hyper-parameter tuning is needed and has the potential to substantially benefit downstream tasks.

Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene-Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth's biota.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

BackgroundThe genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution.ResultsIn the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074–86,197 bp), a small single copy region (SSC: 17,047–17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176–26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68–25.28 Ma).ConclusionThe plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

'Out of Africa' origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis.

The staghorn fern genus Platycerium is one of the most commonly grown ornamental ferns, and it evolved to occupy a typical pantropical intercontinental disjunction. However, species-level relationships in the genus have not been well resolved, and the spatiotemporal evolutionary history of the genus also needs to be explored. Plastomes of all the 18 Platycerium species were newly sequenced. Using plastome data, we reconstructed the phylogenetic relationships among Polypodiaceae members with a focus on Platycerium species, and further conducted molecular dating and biogeographical analyses of the genus. The present analyses yielded a robustly supported phylogenetic hypothesis of Platycerium. Molecular dating results showed that Platycerium split from its sister genus Hovenkampia ~35.2 million years ago (Ma) near the Eocene-Oligocene boundary and began to diverge ~26.3 Ma during the late Oligocene, while multiple speciation events within Platycerium occurred during the middle to late Miocene. Biogeographical analysis suggested that Platycerium originated in tropical Africa and then dispersed eastward to southeast Asia-Australasia and westward to neotropical areas. Our analyses using a plastid phylogenomic approach improved our understanding of the species-level relationships within Platycerium. The global climate changes of both the Late Oligocene Warming and the cooling following the mid-Miocene Climate Optimum may have promoted the speciation of Platycerium, and transoceanic long-distance dispersal is the most plausible explanation for the pantropical distribution of the genus today. Our study investigating the biogeographical history of Platycerium provides a case study not only for the formation of the pantropical intercontinental disjunction of this fern genus but also the 'out of Africa' origin of plant lineages.

Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus.

The genus Tripterygium was of great medicinal value and attracted much attention on the taxonomic study using morphological and molecular methods. In this study, we assembled 12 chloroplast genomes of Tripterygium to reveal interspecific difference and intraspecific variation. The sequence length (156,692-157,061 bp) and structure of Tripterygium were conserved. Comparative analyses presented abundant variable regions for further study. Meanwhile, we determined the ndhB gene under positive selection through adaptive evolution analysis. And the phylogenetic analyses based on 15 chloroplast genomes supported the monophyly of Tripterygium hypoglaucum and the potential sister relationship between Tripterygium wilfordii and Tripterygium regelii. Molecular dating analysis indicated that the divergence time within Tripterygium was approximately 5.99 Ma (95% HPD = 3.11-8.68 Ma). The results in our study provided new insights into the taxonomy, evolution process, and phylogenetic construction of Tripterygium using complete plastid genomes.

Unraveling the Phylogenetic Relationships and Taxonomic Status of a Puzzling Freshwater Mussel Genus Inversidens (Bivalvia, Unionidae) through Multilocus Phylogeny and Mitochondrial Phylogenomics

Accurate phylogenetic reconstructions are crucial for comprehending the evolutionary histories, reproductive traits, and ecological habits of organisms. The subfamily Gonideinae of freshwater mussels is currently thought to include eight tribes. However, due to inadequate taxon sampling and molecular data, the assignment of the freshwater mussel genus Inversidens at the tribe level has been unstable. Additionally, the lack of phylogenetic data has hindered efforts to understand the basic biology and implementation of conservation efforts of Inversidens rentianensis, an endemic species to China. Here, we first present the complete mitochondrial genome of Inversidens rentianensis and offer a detailed description of its anatomical morphology. Based on DNA sequence data from five genes (COI, ND1, 16S rRNA, 18S rRNA, and 28S rRNA) and complete mitochondrial genomes, we investigated the phylogenetic position of Inversidens using various analytical methods. Both the concatenated five-gene and mitogenome datasets strongly supported that Inversidens classified to the tribe Gonideini in Gonideinae and formed a basal clade within the tribe Gonideini. Molecular dating analysis suggested that Inversidens originated during the mid-Cretaceous era (102.73 Mya, 95% highest posterior density HPD=72.22‐137.03 Mya) and underwent diversification in the Late Paleogene era (37.92 Mya, 95% HPD=20.39‐60.59 Mya). Moreover, based on the Quantitative Assessment of Species for Conservation (QASCP), Inversidens rentianensis is ranked as second priority, providing valuable insights for its management and conservation efforts. Taken together, this study provides a comprehensive understanding of the systematic position and evolutionary history of Inversidens within the currently accepted subfamily Gonideinae classification framework. These findings establish a solid foundation for future investigations on the ecology, reproductive behavior patterns, and conservation biology of this taxonomic group.

Photobiomodulation Improves Histological Parameters of Testis and Spermatogenesis in Adult Mice Exposed to Scrotal Hyperthermia in the Prepubertal Phase.

Introduction: Heat stress is one of the environmental causes of damage to the testis, whose effects are less known before puberty. The aim of the present study was to investigate the impact of photobiomodulation (PBM) on the testis of prepubertal mice subjected to hyperthermia. Methods: Twenty-four three-week-old prepubertal male mice were allocated to the following groups: I) control, II) scrotal hyperthermia (Hyp), and III) Hyp+PBM (n=8/each group). In order to induce hyperthermia, the scrotum was placed in water at 43 °C for 20 minutes every other day for a total duration of 10 days. In the Hyp+PBM group, after hyperthermia induction, the testis of the mice was subjected to laser irradiation at a wavelength of 890 nm (0.03 J/cm2 for 30 seconds) for 35 days. After the mice were sacrificed, the testis and epididymis were removed for testing. Results: Compared with those of the Hyp group, the sperm parameters of the laser irradiation group improved notably. In addition, histological examinations revealed that the final number of testis cells and the volume of tissue in the Hyp+PBM group were dramatically greater than those in the Hyp group. The analysis of molecular data revealed an increase in the expression of mitotic genes and testosterone levels and a decrease in the formation of reactive oxygen species (ROS) and the expression of the apoptotic gene in the testis subjected to PBM. Conclusion: Based on the present findings, laser therapy can reduce complications caused by scrotal hyperthermia during prepuberty and ameliorate spermatogenesis during puberty.

Stereocaulon tomentosoides, a new combination for a western North American endemic species with cyanobiont and chemotype polymorphisms

Based on resampling the type locality and surrounding regions, along with phylogenetic analysis of molecular data, we elevate Stereocaulon sasakii var. tomentosoides to the species level, while we treat S. sasakii var. simplex as an environmental modification of S. tomentosoides. We found no phylogenetic evidence that any variety of S. sasakii occurs in North America, so we suggest that the species be removed from the North American list and its North American varieties transferred to S. tomentosoides. Stereocaulon tomentosoides is so far confirmed only from the Pacific Northwest of North America. Furthermore, it is largely allopatric with S. tomentosum, apart from a small region of overlap in northern Idaho and western Montana. While S. tomentosum always contains stictic acid and never lobaric acid as secondary metabolites, S. tomentosoides differs in having a predominant chemotype of lobaric acid as the major substance, with an infrequent chemotype containing both lobaric and stictic acids. While S. tomentosoides usually contains Nostoc in the cephalodia, occasional individuals, especially from old mossy lava flows, contain Stigonema; one specimen was found with both kinds of cephalodia on a single thallus. Phylogenetic analysis of these species and other close relatives revealed an additional species described here, S. cyaneum, so far known only from the Great Lakes region of the United States and Canada and separated from S. tomentosum by its bluish coloration, wet or dry