Ancient Group Research Articles

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution.

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]

Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis and overall fitness in Toxoplasma.

Iron-sulfur (Fe-S) clusters are one of the most ancient and ubiquitous prosthetic groups, and they are required by a variety of proteins involved in important metabolic processes. Apicomplexan parasites have inherited different plastidic and mitochondrial Fe-S clusters biosynthesis pathways through endosymbiosis. We have investigated the relative contributions of these pathways to the fitness of Toxoplasma gondii, an apicomplexan parasite causing disease in humans, by generating specific mutants. Phenotypic analysis and quantitative proteomics allowed us to highlight notable differences in these mutants. Both Fe-S cluster synthesis pathways are necessary for optimal parasite growth in vitro, but their disruption leads to markedly different fates: impairment of the plastidic pathway leads to a loss of the organelle and to parasite death, while disruption of the mitochondrial pathway trigger differentiation into a stress resistance stage. This highlights that otherwise similar biochemical pathways hosted by different sub-cellular compartments can have very different contributions to the biology of the parasites, which is something to consider when exploring novel strategies for therapeutic intervention.

Slow and fast evolutionary rates in the history of lepidosaurs

AbstractBiodiversity today is uneven, with equally ancient sister groups containing few or many species. It has often been assumed that high biodiversity indicates fast evolution, and yet in a classic work in 1944 George Simpson suggested that fast evolution might generate instability and extinction, and that slow evolution led to high biodiversity. Here we show that evolutionary rates can vary substantially through the history of a clade and find evidence for Simpson’s claim. In a comparative phylogenetic study deploying Bayesian methods, we find that Squamata, comprising today over 10 000 species of lizards and snakes, showed slow rates of evolution in the first two‐thirds of their history, whereas their sister clade, Rhynchocephalia, comprising just one living species, showed high rates of evolution in the past. Slow and steady won the race for the Mesozoic squamates, and the high‐rate boom and bust existence of rhynchocephalians at that time leaves them with a single survivor. We need to explore other cases where fast evolution can lead to short‐term high diversification, but in the end long‐term low biodiversity.

The inter‐forest line could be the master key to track biocoenotic effects of climate change in a subtropical forest

AbstractAt least three strata of vegetational formations can be recognized in many mountainous ecosystems. For instance, the Andean Yungas exhibits: 1) upper fog grasslands, 2) intermediate montane forest, and 3) lower montane rain forest. The respective delimiters are the treeline and the inter‐forest line. We develop an approach to perform an optimal tripartition of mountainous ecosystems using elevational cutoffs per watershed. This pair of cutoffs allows us to transform heights of a given digital elevation map onto a universal adimensional scale. Normalized elevation facilitates worldwide comparisons and entails synthetic information (e.g., >0 means above treeline and < −1 below inter‐forest line). To test the reliability of delimiting elevation lines, we compare them against the hand‐drawn treeline and we assess the agreement with another tripartition of sampling points, but based on a different set of organisms (i.e., mayflies, an ancient group of insects that mimic ecological patterns found in many other aquatic taxa). The resulting delimiters of strata pass the test successfully. The upper delimiter fits the detailed treeline well. The lower delimiter segregates different types of mayflies on either side. Only the intermediate layer holds a distinctive set of co‐occurring mayfly species. We finally stress the relevance of the inter‐forest line to track the imprints of global change on community composition.Abstract in Spanish is available with online material.

A new species of the iron maiden ant based on an alate female from mid-Cretaceous Burmese amber (Hymenoptera: Formicidae: †Zigrasimecia)

The iron maiden ant, which was first described as †Zigrasimecia Barden & Grimaldi, 2013, received its nickname for bearing a unique mandible and ferocious mouthparts covered by spiky, columnar-shaped denticles. Here, we describe a new species based on an alate female preserved in 99-Ma Kachin amber – †Zigrasimecia goldingot sp. nov. – which displays several diagnostic features shared with the known species of this genus. Such features include the peg-like mandibular setae, setae of the labrum, clypeal denticles, and an omega-shaped head capsule. Our findings suggest a high diversity among †Zigrasimeciinae and support the grouping of this subfamily. Our work adds to the biodiversity of †Zigrasimecia and †Zigrasimeciinae, and explores the morphological and functional aspects, as well as the early appearance of the unique mouthparts in this ancient ant group.

Expression of Urocortin 3 mRNA in the Central Nervous System of the Sea Lamprey Petromyzon marinus.

Simple SummaryNeuropeptides are small proteins produced and released by neurons. Neuropeptides are key mediators in the communication between neurons. Urocortin 3 is an important neuropeptide that is involved in stress-related behaviors. In this study, our aim was to determine in which regions of the lamprey brain urocortin 3 is expressed. The study of the distribution of neuroregulatory peptides in lamprey species helps in understanding their early evolution of neuropeptidergic systems in vertebrates because lampreys are one of the most ancient vertebrate groups. The sea lamprey life cycle lasts between five and nine years, and it includes a long larval stage and a transformation to the adult stage. We analyzed the organization of urocortin 3-expressing neuronal populations in the brain of larval and adult sea lampreys to establish whether this neuropeptide is expressed differentially in these two widely different phases of the sea lamprey life cycle. Our results revealed important differences between larval and adult stages. Moreover, comparing our results with the distribution of urocortin 3 reported in other vertebrate groups also revealed a poor evolutionary conservation of urocortin 3 expression in vertebrates. Our work sheds light on the evolution and role of urocortin 3 in vertebrates.In this study, we analyzed the organization of urocortin 3 (Ucn3)-expressing neuronal populations in the brain of the adult sea lamprey by means of in situ hybridization. We also studied the brain of larval sea lampreys to establish whether this prosocial neuropeptide is expressed differentially in two widely different phases of the sea lamprey life cycle. In adult sea lampreys, Ucn3 transcript expression was observed in neurons of the striatum, prethalamus, nucleus of the medial longitudinal fascicle, torus semicircularis, isthmic reticular formation, interpeduncular nucleus, posterior rhombencephalic reticular formation and nucleus of the solitary tract. Interestingly, in larval sea lampreys, only three regions showed Ucn3 expression, namely the prethalamus, the nucleus of the medial longitudinal fascicle and the posterior rhombencephalic reticular formation. A comparison with distributions of Ucn3 in other vertebrates revealed poor conservation of Ucn3 expression during vertebrate evolution. The large qualitative differences in Ucn3 expression observed between larval and adult phases suggest that the maturation of neuroregulatory circuits in the striatum, torus semicircularis and hindbrain chemosensory systems is closely related to profound life-style changes occurring after the transformation from larval to adult life.

Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Echinoderms: Structure and Possible Functions.

Echinoderms are one of the most ancient groups of invertebrates. The study of their genomes has made it possible to conclude that these animals have a wide variety of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). The phylogenetic analysis shows that the MMPs and TIMPs underwent repeated duplication and active divergence after the separation of Ambulacraria (Echinodermata+Hemichordata) from the Chordata. In this regard the homology of the proteinases and their inhibitors between these groups of animals cannot be established. However, the MMPs of echinoderms and vertebrates have a similar domain structure. Echinoderm proteinases can be structurally divided into three groups—archetypal MMPs, matrilysins, and furin-activatable MMPs. Gelatinases homologous to those of vertebrates were not found in genomes of studied species and are probably absent in echinoderms. The MMPs of echinoderms possess lytic activity toward collagen type I and gelatin and play an important role in the mechanisms of development, asexual reproduction and regeneration. Echinoderms have a large number of genes encoding TIMPs and TIMP-like proteins. TIMPs of these animals, with a few exceptions, have a structure typical for this class of proteins. They contain an NTR domain and 10–12 conservatively located cysteine residues. Repeated duplication and divergence of TIMP genes of echinoderms was probably associated with an increase in the functional importance of the proteins encoded by them in the physiology of the animals.

On subfamily structure of the Cupedidae (Coleoptera, Archostemata): data from paleontology and an approach to solving conflicting classifications

This paper demonstrates some of main differences between the systematic constructions based mostly on paleontological research and constructions involving the other approaches. Some reasons for these differences are discussed, together with an approach to solve contradictions between the conflicting hypotheses. The multiple (multidimensional) parallelism gives a possibility to solve many problems of phylogenetic interrelations due to reconstructions based on coincidence of patterns of changes (series of interconnected facts) traced in different aspects of evolutionary processes. This principle originates in the ideas by Jean Agassiz and Ernst Haeckel defined as the principle of triple parallelism. Other aspects of the evolution can be added to the morphology, embryology, and paleontology, initially included in this method. The molecular method is one of such aspects. It is shown that the potential resolution of the morphological and molecular approaches in some cases could be rather restricted, particularly applying ancient groups with main evolutionary transformations passed far in the past. The infraorder Cupediformia and suborder Archostemata in general are examples of such cases. It is advisable in the current research period that has followed the previous interpretation of the systematic structure of the family Cupedidae recognizing three subfamilies with not quite distinct hiatus between them (Cupedinae, Ommatinae and Triadocupedinae). Some recent morphological and molecular approaches proposed to divide the Cupedidae into two separate families on the basis of incomplete information accessible after study of only modern representatives, as most events in the family evolution occurred during the Palaeozoic and Mesozoic, and these events are scarcely possible to trace without considering fossils. As the principle of multiple parallelism cannot be currently used for archostematans to the full extent of its power, it is necessary to choose the paleontological method of phylogenetic reconstruction as crucial. This approach is preferable for groups that are well-documented through very diverse fossils, and for which only few of its remnants of the past diversity reached the modern epoque.

Dissecting the genetic history of the Roman Catholic populations of West Coast India.

Migration and admixture history of populations have always been curious and an interesting theme. The West Coast of India harbours a rich diversity, bestowing various ethno-linguistic groups, with many of them having well-documented history of migrations. The Roman Catholic is one such distinct group, whose origin was much debated. While some historians and anthropologists relating them to ancient group of Gaud Saraswat Brahmins, others relating them for being members of the Jews Lost Tribes in the first Century migration to India. Historical records suggests that this community was later forcibly converted to Christianity by the Portuguese in Goa during the Sixteenth Century. Till date, no genetic study was done on this group to infer their origin and genetic affinity. Hence, we analysed 110 Roman Catholics from three different locations of West Coast of India including Goa, Kumta and Mangalore using both uniparental and autosomal markers to understand their genetic history. We found that the Roman Catholics have close affinity with the Indo-European linguistic groups, particularly Brahmins. Additionally, we detected genetic signal of Jews in the linkage disequilibrium-based admixture analysis, which was absent in other Indo-European populations, who are inhabited in the same geographical regions. Haplotype-based analysis suggests that the Roman Catholics consist of South Asian-specific ancestry and showed high drift. Ancestry-specific historical population size estimation points to a possible bottleneck around the time of Goan inquisition (fifteenth century). Analysis of the Roman Catholics data along with ancient DNA data of Neolithic and bronze age revealed that the Roman Catholics fits well in a basic model of ancient ancestral composition, typical of most of the Indo-European caste groups of India. Mitochondrial DNA (mtDNA) analysis suggests that most of the Roman Catholics have aboriginal Indian maternal genetic ancestry; while the Y chromosomal DNA analysis indicates high frequency of R1a lineage, which is predominant in groups with higher ancestral North Indian (ANI) component. Therefore, we conclude that the Roman Catholics of Goa, Kumta and Mangalore regions are the remnants of very early lineages of Brahmin community of India, having Indo-Europeans genetic affinity along with cryptic Jewish admixture, which needs to be explored further.

Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China

The Yi is one of fifty-six ethnic populations and one of the most ancient ethnic groups in China. The Liangshan Yi Autonomous Prefecture (LYAP) in Sichuan Province has the single largest Yi community in China. To establish a Yi population database in the LYAP of Sichuan in China, a Goldeneye™ DNA Identification System 20A Kit with 19 autosomal STRs (short tandem repeats) was used. As a result, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for these STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8–22 alleles for each locus were found. The allelic frequencies ranged from 0.0005 to 0.5084. The forensic parameter averages of these STRs were as follows: observed heterozygosity (Hobs) of 78.44%, expected heterozygosity (Hexp) of 79.89%, discrimination power (DP) of 92.66%, and probability of exclusion (PE) of 57.68%. Penta E presented the highest levels of Hobs and DP, whereas TPOX showed the lowest Hobs and DP values. Nei’s standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056). Altogether, we first reported the forensic parameters and allele frequencies of 19 autosomal STRs of the Yi group in Liangshan. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.

TICK SALIVA TOXINS, HOST IMMUNE RESPONSES AND ITS BIOLOGICAL EFFECTS

Ticks are the most important ancient group of obligate blood-sucking ectoparasites of terrestrial vertebrates mainly of livestock. These small-sized animals are found in tropical and sub-tropical regions of the world. These act as vectors and transmit a wide range of protozoa, bacteria and viruses tick-borne diseases. These attach to host skin for blood-sucking and transmit disease pathogens through saliva. Ticks withdraw large volumes of blood from livestock and make them anemic and do significant weight loss. Ticks cause severe economic losses in livestock directly through blood-feeding and indirectly by transmitting protozoan, rickettsial and viral diseases This article highlights toxins/proteins secreted in tick saliva, and its important biological effects like anti-inflammatory, immunosuppressant peptide, and immunomodulatory and anti-chemokine activities. The present article clears host-pathogen interactions and invasion of a host by ticks, biological effects of tick saliva toxins and its host immune responses. These toxins could be used as immunoreactive proteins as a prerequisite for the development of specific and sensitive immunoassays for the determination of tick-borne illness. The authors suggest important management strategies for successful control of cattle, bird and canine ticks. This article also suggests tick control methods such as physical, chemical, hormonal and including prophylactic use of antibody and vaccine immune therapy.

Ceramic Traditions in the Forest-Steppe Zone of Eastern Europe

Abstract Early pottery on the territory from the Eastern Caspian Sea and Aral Sea to Denmark reveals a certain typological similarity. It is represented by egg-shaped vessels with an S-shaped profile of the upper part and a pointed bottom. The vessels are not ornamented or decorated with incised lines, organized often in a net. This type of pottery was spread within hunter-gatherer ancient groups. The forest-steppe Volga region is one of the earliest centers of pottery production in Eastern Europe. The first pottery is recorded here in the last quarter of the seventh millennium BC. Its appearance is associated with the bearers of the Elshanskaya cultural tradition. The most likely source of its formation is the territory of Central Asia. Later, due to aridization, these ceramic traditions distributed further westward to the forest-steppe Don region. During the first half of the sixth millennium BC, groups associated with the bearers of the Elshanskaya cultural tradition moved westward. Significant similarities with the ceramic complexes of the Elshanskaya culture are found in materials from a number of early pottery cultures of Central Europe and the Baltic (Narva, Neman, and Ertebølle).

Biogeographic status of the steppe plains and foothills of the northern and western Caspian lowland

The discussion focuses on the zonal nature of the Caspian steppe and the status of the local biota, which in its spatial-temporal organization and regional succession system has preserved the pool of biodiversity of dry-steppe and desert complexes. Each of them represents a set of ancient systematic groups of organisms that migrated here along both the Eastern (Turan) and Western (Caucasus, Mediterranean) coasts of the Caspian Sea, forming “young” lowland ecosystems. There is a weak significance in the Genesis of the biota of the xerophilic foothills of the Eastern Caucasus (Daghestan) and the southern Urals, which, apparently, only at the early stages of formation during periods of major sea transgressions served as refugia. The phylocenogenetically determined polyclimax and the predominance of pasqual and climatogenic subclimaxes in the region are manifested due to constant impact of cyclical short-term (hundreds of years) destabilizing factors.

Tentacle Morphological Variation Coincides with Differential Expression of Toxins in Sea Anemones.

Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple actiniarian species. In this study, we assess whether morphological variants of tentacles are associated with distinct toxin expression profiles and investigate the functional significance of specialised tentacular structures. Using five sea anemone species, we analysed differential expression of toxin-like transcripts and found that expression levels differ significantly across tentacular structures when substantial morphological variation is present. Therefore, the differential expression of toxin genes is associated with morphological variation of tentacular structures in a tissue-specific manner. Furthermore, the unique toxin profile of spherical tentacular structures in families Aliciidae and Thalassianthidae indicate that vesicles and nematospheres may function to protect branched structures that host a large number of photosynthetic symbionts. Thus, hosting zooxanthellae may account for the tentacle-specific toxin expression profiles observed in the current study. Overall, specialised tentacular structures serve unique ecological roles and, in order to fulfil their functions, they possess distinct venom cocktails.

Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety.

Olea europaea ‘Galega vulgar’ variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. ‘Galega vulgar’ is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of ‘Galega vulgar’, 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the ‘Galega vulgar’ intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the ‘Galega vulgar’, with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of ‘Galega vulgar’. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of ‘Galega vulgar’).

Research on the Application of Step-pool System in Ancient Irrigation Engineering

The “step-pool system” is a common river topography in mountain rivers. In the application for Heritage Irrigation Structures in 2020, an artificial “step-pool system” built two thousand years ago was shown to the world, which is located in the 36 Weirs of Baishaxi Stream in Wucheng District, Jinhua City, Zhejiang Province. The creator of this ancient irrigation project used the ideas of “Building weirs by ponds” and “Distributed river development” on the Baishaxi stream, which spans 45 kilometers from the end to the end and has a vertical drop of 168 meters, to build this multifunctional ancient super barrage group project. Their experience and insights coincide with modern engineering theories, which have changed the natural characteristics of the river and made positive changes in the ecological environment of the river basin in a direction that is beneficial to human life.

Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species.

Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of chemicals valuable to humans and as a drug target against pathogens. Understanding the evolution of P450s in a bacterial population is gaining momentum. In this study, we report comprehensive analysis of P450s in the ancient group of the bacterial class Alphaproteobacteria. Genome data mining and annotation of P450s in 599 alphaproteobacterial species belonging to 164 genera revealed the presence of P450s in only 241 species belonging to 82 genera that are grouped into 143 P450 families and 214 P450 subfamilies, including 77 new P450 families. Alphaproteobacterial species have the highest average number of P450s compared to Firmicutes species and cyanobacterial species. The lowest percentage of alphaproteobacterial species P450s (2.4%) was found to be part of secondary metabolite biosynthetic gene clusters (BGCs), compared other bacterial species, indicating that during evolution large numbers of P450s became part of BGCs in other bacterial species. Our study identified that some of the P450 families found in alphaproteobacterial species were passed to other bacterial species. This is the first study to report on the identification of CYP125 P450, cholesterol and cholest-4-en-3-one hydroxylase in alphaproteobacterial species (Phenylobacterium zucineum) and to predict cholesterol side-chain oxidation capability (based on homolog proteins) by P. zucineum.

Exploration of the potential mechanism of Banxia Xiexin Decoction for the effects on TNBS-induced ulcerative colitis rats with the assistance of network pharmacology analysis

Ethnopharmacological relevanceBanxia Xiexin Decoction (BXD), an ancient TCM prescription originating from Treatise on Febrile Diseases (Shang Han Lun) of the Han Dynasty, has been widely used in modern clinical practice, especially for gastrointestinal diseases, including ulcerative colitis (UC). However, the modern decoction method of BXD differs from that of the original method. Thus, an exploration of the influence of the different decoction methods on the pharmacological effects is interesting and significant. Aim of the studyThis study aimed to systematically compare the pharmacological effects of extracts of BXD on TNBS induce UC rats that were prepared by different methods, the ancient method and the modern method. The findings may provide important information for the further mechanical exploration of the classical prescription, contributing to the rational application and enhancing the understanding of BXD in modern applications or scientific research. MethodsFifty-four SD rats were randomly divided into the following nine groups at n = 6/group: control group; model group; salicylazosulfapyridine group; BXD ancient extraction method's low-dose group (BXD-AED-L, 3.6 g BXD-AED/kg), medium-dose group (BXD-AED-M, 7.2 g BXD-AED/kg), and high-dose group (BXD-AED-H, 14.4 g BXD-AED/kg); and BXD modern extraction method's low-dose group (BXD-MED-L, 1 g BXD-MED/kg), medium-dose group (BXD-MED-M, 2 g BXD-MED/kg), and high-dose group (BXD-MED-H, 4 g BXD-MED/kg). All the groups, except the control group, were rectally injected with 70 mg/kg ethanol solution containing TNBS (2,4,6-trinitrobenzenesulfonic acid) to establish the UC models. The pharmacological evaluations including disease activity index, colon weight index, macroscopic and histological evaluation of colon damage, and inflammatory cytokine levels (IL-4, IL-10, IL-1β, TNF-α, and IL-6)were measured. In the network pharmacology analysis, the “herbs-components-targets-disease” network was constructed and visually analyzed with which the targets with a strong correlation with UC were screened out. ResultsThe results showed that both BXD-AED and BXD-MED might alleviate the severity of UC with different degrees according to the majority of indices that were evaluated. At similar doses, the BXD-AED groups performed better compared with the BXD-MED groups. With the assistance of the network pharmacology analysis, some key active components (quercetin, baicalein, wogonin, and baicalin) related to the anti-UC/inflammation were screened out. The contents of the components in BXD-AED were higher than those in BXD-MED. The joint results of the study indicated that BXD, an ancient TCM compound prescription, is an effective drug candidate for the modern treatment of UC.

Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)

The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.].

Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae

The chlorophyte green algae (Chlorophyta) are species-rich ancient groups ubiquitous in various habitats with high cytological diversity, ranging from microscopic to macroscopic organisms. However, the deep phylogeny within core Chlorophyta remains unresolved, in part due to the relatively sparse taxon and gene sampling in previous studies. Here we contribute new transcriptomic data and reconstruct phylogenetic relationships of core Chlorophyta based on four large data sets up to 2,698 genes of 70 species, representing 80% of extant orders. The impacts of outgroup choice, missing data, bootstrap-support cutoffs, and model misspecification in phylogenetic inference of core Chlorophyta are examined. The species tree topologies of core Chlorophyta from different analyses are highly congruent, with strong supports at many relationships (e.g., the Bryopsidales and the Scotinosphaerales-Dasycladales clade). The monophyly of Chlorophyceae and of Trebouxiophyceae as well as the uncertain placement of Chlorodendrophyceae and Pedinophyceae corroborate results from previous studies. The reconstruction of ancestral scenarios illustrates the evolution of the freshwater-sea and microscopic–macroscopic transition in the Ulvophyceae, and the transformation of unicellular→colonial→multicellular in the chlorophyte green algae. In addition, we provided new evidence that serine is encoded by both canonical codons and noncanonical TAG code in Scotinosphaerales, and stop-to-sense codon reassignment in the Ulvophyceae has originated independently at least three times. Our robust phylogenetic framework of core Chlorophyta unveils the evolutionary history of phycoplast, cyto-morphology, and noncanonical genetic codes in chlorophyte green algae.