Evolution Of Species Research Articles

Meiosis I causes a high spontaneous mutation rate in a multicellular red alga (Pyropia yezoensis) with a complex life cycle

Mutations are the origin of genetic diversity and are fundamental parameters needed to understand the molecular evolution of species. Estimations of mutation rates have been conducted for many diverse taxa, although rates in several major eukaryotic lineages remain unexplored. Here, the first estimation is reported of the spontaneous mutation rate for the multicellular eukaryote red alga, Pyropia yezoensis, which exhibits a complex life cycle. An estimated mutation rate of 2.97 × 10−8 (95 % CI: 2.16 × 10−8–3.99 × 10−8) per site per generation was generated for the primary life cycle, the sexual cycle, which is the highest sexual mutation rate among published sexual plants. Combined with tetrad analysis, meiosis I was identified as the primary period responsible for the high mutation rate during the complex life cycle of P. yezoensis. This result provides direct evidence for the “meiosis is mutagenic” hypothesis for multicellular organisms. The accurate estimate of the mutation rate of P. yezoensis also informs several immediate applications. Based on the above estimate, the effective population size (Ne) of P. yezoensis was estimated at about 19,000, with extensive haploid phases and asexual reproduction through monospores possibly leading to linked selection that may reduce the genome-wide genetic diversity of P. yezoensis and consequently influence Ne estimation. Lastly, P. yezoensis was estimated to have diverged from P. haitanensis about 4.2 Ma, representing a more recent date than estimates from fossil-calibrated phylogenies. These findings provide valuable new information for understanding the evolution of red algae, in addition to the underlying mechanism of mutations.

RCPedia: a global resource for studying and exploring retrocopies in diverse species.

Gene retrocopies arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species. Here, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtles, lizards, frogs, zebrafish, and Drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology, and transposable elements (TEs). In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species. RCPedia is available at https://www.rcpediadb.org.

Two near-chromosomal-level genomes of globally-distributed Macroascomycete based on single-molecule fluorescence and Hi-C methods

Discinaceae holds significant importance within the Pezizales, representing a prominent group of macroascomycetes distributed globally. However, there is a dearth of genomic studies focusing on this family, resulting in gaps in our understanding of its evolution, development, and ecology. Here we utilized state-of-the-art genome assembly methodologies, incorporating third-generation single-molecule fluorescence and Hi-C-assisted methods, to elucidate the genomic landscapes of Gyromitra esculenta and Paragyromitra xinjiangensis. The genome sizes of two species were determined to be 47.10 Mb and 48.20 Mb, with 23 and 22 scaffolds, respectively. 10,438 and 11,469 coding proteins were identified, with functional annotations encompassing over 96.47% and 94.40%, respectively. Assessment of completeness using BUSCO revealed that 98.71% and 98.89% of the conserved proteins were identified. The application of comparative genomic technology has helped in identifying traits associated with of heterothallic life cycle traits and elucidating unique patterns of chromosomal evolution. Additionally, we identified potential saprotrophic nutritional modes and systematic phylogenetic relationships between the two species. Therefore, this study provides crucial genomic insights into the evolution, nutritional type, and ecological roles of species within the Pezizales.

Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae).

In order to understand the bias and main affecting factors of codon usage in the plastid genome of Diplandrorchis sinica, which is a rare and endangered plant species in the Orchidaceae family, the complete plastid genome sequence of D. sinica was downloaded from the GenBank database and 20 protein-coding sequences that met the analysis requirements were finally selected. The GC content, length of the amino acid (Laa), relative synonymous codon usage (RSCU), and effective number of codon (ENC) of each gene and codon were calculated using the CodonW and EMBOSS online programs. Neutral plot analysis, ENC-plot analysis, PR2-plot analysis, and correspondence analysis were performed using Origin Pro 2024 software, and correlation analysis between various indicators was performed using SPSS 23.0 software. The results showed that the third base of the codon in the plastid genome of D. sinica was rich in A and T, with a GC3 content of 27%, which was lower than that of GC1 (45%) and GC2 (39%). The ENC value ranged from 35 to 57, with an average of 47. The codon usage bias was relatively low, and there was a significant positive correlation between ENC and GC3. There were a total of 32 codons with RSCU values greater than 1, of which 30 ended with either A or U. There were a total of nine optimal codons identified, namely, UCU, UCC, UCA, GCA, UUG, AUA, CGU, CGA, and GGU. This study indicated that the dominant factor affecting codon usage bias in the plastid genome of D. sinica was natural selection pressure, while the impact of base mutations was limited. The codon usage patterns were not closely related to gene types, and the distribution of photosynthetic system genes and ribosomal protein-coding gene loci was relatively scattered, indicating significant differences in the usage patterns of these gene codons. In addition, the codon usage patterns may not be related to whether the plant is a photosynthetic autotrophic or heterotrophic nutritional type. The results of this study could provide scientific references for the genomic evolution and phylogenetic research of plant species in the family Orchidaceae.

A Microcosm Analysis of Species-Specific Responses of Chironomidae on Heavy Metal Pollution in The Nyanza Gulf of Lake Victoria

The Chironomidae family, known as "non-biting midges" in their adult stage and "bloodworms" in their larval stage, consists of diverse dipteran insects inhabiting various global aquatic environments. Despite extensive global research, data on Chironomidae in the polluted Nyanza Gulf of Lake Victoria, Kenya, is scarce, and molecular identification methods have not been explored. This study aimed to quantify heavy metal concentrations in water, sediment, and insect samples and assess their impact on Chironomid species identified using mitochondrial DNA barcoding of the cytochrome oxidase subunit 1 (COI) gene. Analysis of Variance was used to determine if there were any statistically significant differences in heavy metal concentrations across different sample types or locations along the pollution gradient. Chironomids were collected from Nyanza Gulf, focusing on a pollution gradient. Results showed that concentrations of arsenic (As), lead (Pb), and cadmium (Cd) in insect, water, and sediment samples exceeded standard limits, while mercury (Hg) concentrations were within limits. Significant variations (p ≤ 0.05) in Pb levels were observed in water samples, and heavy metal concentrations in sediment samples varied significantly (p ≤ 0.05), with Pb showing the highest variation (p ≤ 0.0001). Insect samples exhibited significant differences (p ≤ 0.0001) in As and Hg contents. Genetic analysis identified two known species: Chironomus transvaalensis at the heavily polluted Kisumu station and Chironomus pseudothummi at the moderately polluted Kendu Bay and Homa Bay stations. Additionally, a unique Chironomus species was found on Ndere Island, a relatively clean site with restricted human activities. Sequence comparisons indicated proximity to global data but also highlighted the evolutionary significance and uniqueness of the identified species. This study demonstrated the potential use of genetic methods in determining Chironomid species diversity, community structure, and abundance in relation to heavy metal concentration. It suggests that heavy metal pollution may act as a selective pressure, driving the evolution of Chironomid species. The study recommends combining genetic approaches with other pollution sources for a comprehensive understanding of using this species in monitoring pollution

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata.

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

Advancing EDGE Zones to identify spatial conservation priorities of tetrapod evolutionary history

The biodiversity crisis is pruning the Tree of Life in a way that threatens billions of years of evolutionary history and there is a need to understand where the greatest losses are predicted to occur. We therefore present threatened evolutionary history mapped for all tetrapod groups and describe patterns of Evolutionarily Distinct and Globally Endangered (EDGE) species. Using a complementarity procedure with uncertainty incorporated for 33,628 species, we identify 25 priority tetrapod EDGE Zones, which are insufficiently protected and disproportionately exposed to high human pressure. Tetrapod EDGE Zones are spread over five continents, 33 countries, and 117 ecoregions. Together, they occupy 0.723% of the world’s surface but harbour one-third of the world’s threatened evolutionary history and EDGE tetrapod species, half of which is endemic. These EDGE Zones highlight areas of immediate concern for researchers, practitioners, policymakers, and communicators looking to safeguard the tetrapod Tree of Life.

Introgression drives adaptation to the plateau environment in a subterranean rodent

BackgroundIntrogression has repeatedly been shown to play an important role in the adaptation of species to extreme environments, yet how introgression enables rodents with specialized subterranean lifestyle to acclimatize to high altitudes is still unclear. Myospalacinae is a group of subterranean rodents, among which the high-altitude plateau zokors (Eospalax baileyi) and the low-altitude Gansu zokors (E. cansus) are sympatrically distributed in the grassland ecosystems of the Qinghai-Tibet Plateau (QTP). Together, they provide a model for the study of the role of introgression in the adaptation of low-altitude subterranean rodents to high altitudes.ResultsApplying low-coverage whole-genome resequencing and population genetics analyses, we identified evidence of adaptive introgression from plateau zokors into Gansu zokors, which likely facilitated the adaptation of the latter to the high-altitude environment of the QTP. We identified positively selected genes with functions related to energy metabolism, cardiovascular system development, calcium ion transport, and response to hypoxia which likely made critical contributions to adaptation to the plateau environment in both plateau zokors and high-altitude populations of Gansu zokors.ConclusionsIntrogression of genes associated with hypoxia adaptation from plateau zokors may have played a role in the adaptation of Gansu zokors to the plateau environment. Our study provides new insights into the understanding of adaptive evolution of species on the QTP and the importance of introgression in the adaptation of species to high-altitude environments.

Comparative analysis of codon usage bias in the chloroplast genomes of eighteen Ampelopsideae species (Vitaceae)

BackgroundThe tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family.ResultsThe base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35–61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species.ConclusionThe codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies.

In-situ manganese-aluminum-iron biochar derived from waste flocs for enhanced peroxymonosulfate oxidation: Role of Fe/Mn drives active species based on aluminum adsorption and synergistic promoted electron transfer

Conventional coagulation or enhanced coagulation water treatment produced mass floc sludge, which contained plenty of metals and organic matter. Floc sludge disposal and resource recycling was vital relevance and urgently needed. Here, we reported on the waste flocs recycling through in-situ manganese-aluminum-iron biochar (MAFBC) synthesized via one-step pyrolysis using potassium permanganate (KMnO4) oxidation- aluminum-iron composite flocculant coagulation for humic acid removal floc sludge as raw material. Compared with ex-situ loaded or similar types of biochar, MAFBC showed faster and efficient activation effect of peroxymonosulfate (PMS) to degrade tetracycline (TC). TC was rapidly removed within 1 min in MAFBC/PMS system with degradation rate constant Kobs was 1.825 min−1, which mainly attributed to the multiple promoting effects of manganese-aluminum-iron. Aluminum oxides facilitated TC adsorption and synergistic Fe/Mn further significantly promoted electron transfer on the surface of the MAFBC. Additionally, bimetallic structure of Fe/Mn and the CO functional group on MAFBC accelerated the formation of reactive species. The redox cycles of Fe2+/Fe3+ and Mn2+/Mn3+/Mn4+ promoted the formation of free radicals OH and SO4−. Moreover, O2– and 1O2 also assumed an important role for TC removal during active species evolution drived by Fe/Mn. This research provides a new perspective for in-situ design of economical and stable metal carbon-based water treatment activator, and make contributions to the utilization of waste flocs in water treatment.

Reconciling cosmological tensions with inelastic dark matter and dark radiation in a U(1) D framework

We propose a novel and comprehensive particle physics framework that addresses multiple cosmological tensions observed in recent measurements of the Hubble parameter, S 8, and Lyman-α forest data. Our model, termed `SIDR+z t ' (Self Interacting Dark Radiation with transition redshift), is based on an inelastic dark matter (IDM) scenario coupled with dark radiation, governed by a U(1) D gauge symmetry. This framework naturally incorporates cold dark matter (DM), strongly interacting dark radiation (SIDR), and the interactions between these components. The fluid-like behavior of the dark radiation component which originates from the self-quartic coupling of the U(1) D breaking scalar can suppress the free-streaming effects. Simultaneously, the interacting DM-DR system can attenuate the matter power spectrum at small scales. The inelastic nature of DM provides a distinct temperature dependence for the DM-DR interaction rate determined by the mass-splitting between the inelastic dark fermions which is crucial for resolving the Ly-α discrepancies. We present a cosmologically consistent analysis of the model by solving the relevant Boltzmann equations to obtain the energy density and number density evolution of different species of the model. The DR undergoes two “steps” of increased energy density when the heavier dark species freeze out and become non-relativistic, transferring their entropy to the dark radiation and enhancing ΔN eff. The analysis showcases the model's potential to uphold the Big Bang Nucleosynthesis (BBN) prediction of ΔN eff but dominantly producing additional contributions prior to recombination, while simultaneously achieving correct relic density of DM though an hybrid of freeze-in and non-thermal production.

Phenotypic, Metabolic and Genetic Adaptations of the Ficus Species to Abiotic Stress Response: A Comprehensive Review.

The Ficus genus, having radiated from the tropics and subtropics to the temperate zone worldwide, is the largest genus among woody plants, comprising over 800 species. Evolution of the Ficus species results in genetic diversity, global radiation and geographical differentiations, suggesting adaption to diverse environments and coping with stresses. Apart from familiar physiological changes, such as stomatal closure and alteration in plant hormone levels, the Ficus species exhibit a unique mechanism in response to abiotic stress, such as regulation of leaf temperature and retention of drought memory. The stress-resistance genes harbored by Ficus result in effective responses to abiotic stress. Understanding the stress-resistance mechanisms in Ficus provides insights into the genetic breeding toward stress-tolerant crop cultivars. Following upon these issues, we comprehensively reviewed recent progress concerning the Ficus genes and relevant mechanisms that play important roles in the abiotic stress responses. These highlight prospectively important application potentials of the stress-resistance genes in Ficus.

Evolution of Cu and Zn speciation in agricultural soil amended by digested sludge over time and repeated crop growth

Metals such as Zn and Cu present in sewage sludge applied to agricultural land can accumulate in soils and potentially mobilise into crops. Sequential extractions and X-ray absorption spectroscopy results are presented that show the speciation changes of Cu and Zn sorbed to anaerobic digestion sludge after mixing with soils over three consecutive 6-week cropping cycles, with and without spring barley (Hordeum vulgare). Cu and Zn in digested sewage sludge are primarily in metal sulphide phases formed during anaerobic digestion. When Cu and Zn spiked sludge was mixed with the soil, about 40% of Cu(I)-S phases and all Zn(II)-S phases in the amended sludge were converted to other phases (mainly Cu(I)-O and outer sphere Zn(II)-O phases). Further transformations occurred over time, and with crop growth. After 18 weeks of crop growth, about 60% of Cu added as Cu(I)-S phases was converted to other phases, with an increase in organo-Cu(II) phases. As a result, Cu and Zn extractability in the sludge-amended soil decreased with time and crop growth. Over 18 weeks, the proportions of Cu and Zn in the exchangeable fraction decreased from 36% and 70%, respectively, in freshly amended soil, to 28% and 59% without crop growth, and to 24% and 53% with crop growth. Overall, while sewage sludge application to land will probably increase the overall metal concentrations, metal bioavailability tends to reduce over time. Therefore, safety assessments for sludge application in agriculture should be based on both metal concentrations present and their specific binding strength within the amended soil.

Peering through the hedge: Multiple datasets yield insights into the phylogenetic relationships and incongruences in the tribe Lilieae (Liliaceae)

The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and “ghost introgression” likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.

Molybdenum triggers the bifunctional mechanism of oxygen evolution reaction of Fe34-xNi25Co25MoxB8P8 amorphous alloy with boosted catalytic activity

High-valence metals (such as, Mo, W, Zr and Nb) have recently been reported that promote oxygen evolution reaction (OER) activity of the 3d-transition metal electrocatalysts. These high-valence metals play a key role on surface self-reconstruction process and stabilizing the low-valence active sites. However, further understand their effect on the OER mechanism is challenging, especially in amorphous electrocatalysts with complicated structure. Here, we integrate high-valence Mo with 3d metals (Fe, Co and Ni), fabricating Fe34-xCo25Ni25MoxP8B8 amorphous electrocatalysts by the melt-spinning method. We employ in-situ Raman spectroscopy to characterize the species evolution during OER, and find that the higher OER performance is originated from a bifunctional mechanism involves two catalytic sites (NiOOH and FeOOH) enabled by high-valence Mo dissolution. Benefit from this, the Fe34-xCo25Ni25MoxP8B8 with Mo show higher OER performance compared with Fe34-xCo25Ni25MoxP8B8 without Mo. For 3d-metal OER electrocatalyst, this study provides a new understanding on the effect of high-valence metals.

“The Logic of Monsters:” Pere Alberch and the Evolutionary Significance of Experimental Teratology

This paper offers an historical introduction to Pere Alberch's evolutionary thought and his contributions to Evo-Devo, based on his unique approach to experimental teratology. We will take as our point of reference the teratogenic experiments developed by Alberch and Emily A. Gale during the 1980s, aimed at producing monstrous variants of frogs and salamanders. We will analyze his interpretation of the results of these experiments within the framework of the emergence of evolutionary developmental biology (or “Evo-Devo”). The aim is understand how Alberch interpreted teratological anomalies as highly revealing objects of study for understanding the development of organic form, not only in an ontogenetic sense—throughout embryonic development—but also phylogenetically—throughout the evolution of species. Alberch's interpretation of monsters reflects the influence of a long tradition of non-Darwinian evolutionary thought, which began in the nineteenth century and was continued in the twentieth century by people such as Richard Goldschmidt, Conrad H. Waddington, and Stephen Jay Gould. They all proposed various non-gradualist models of evolution, in which embryonic development played a central role. Following this tradition, Alberch argued that, in order to attain a correct understanding of the role of embryological development in evolution, it was necessary to renounce the gradualist paradigm associated with the Darwinian interpretation of evolution, which understood nature as a continuum. According to Alberch, the study of monstrous abnormalities was of great value in understanding how certain epigenetic restrictions in development could give rise to discontinuities and directionality in morphological transformations throughout evolution.

Regulating the evolution of interfacial species via B, N-codoped Pt sites for oxygen reduction electrocatalysis

The sluggish kinetics of the oxygen reduction reaction (ORR) poses significant limitations to the widespread application of the ORR in advanced energy systems. Here, we present a composite catalyst consisting of Pt nanoparticles immobilized on 3D B, N-doped graphene oxide (Pt/GO-BCN). Through X-ray absorption fine structure spectroscopy and synchrotron radiation infrared spectroscopy analyses, we discovered that the codoping of B and N significantly regulates the electronic structure of graphene and enhances the interaction between Pt nanoparticles and the supports. The electronic state-optimized 3D support promotes the uniform distribution of Pt nanoparticles with small size, forming a low-resistance interfacial environment to accelerate the cleavage of the *OOH species during the reaction process. The ORR activity and selectivity of Pt/GO-BCN significantly surpass those of commercial Pt/C catalysts, and excellent durability under long-term operation is achieved. These results provide a new avenue for the design of advanced Pt-based catalysts.

Maize mutant screens: from classical methods to new CRISPR-based approaches.

Mutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site-directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR-Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.

The widespread vulnerability of Hydra oligactis to tumourigenesis confirms its value as a model for studying the effects of tumoural processes on the ecology and evolution of species

Tumoural processes, ubiquitous phenomena in multicellular organisms, influence evolutionary trajectories of all species. To gain a holistic understanding of their impact on species' biology, suitable laboratory models are required. Such models are characterised by a widespread availability, ease of cultivation, and reproducible tumour induction. It is especially important to explore, through experimental approaches, how tumoural processes alter ecosystem functioning. The cnidarian Hydra oligactis is currently emerging as a promising model due to its development of both transmissible and non-transmissible tumours and the wide breadth of experiments that can be conducted with this species (at the individual, population, mechanistic, and evolutionary levels). However, tumoural hydras are, so far, only documented in Europe, and it is not clear if the phenomenon is local or widespread. In this study we demonstrate that Australian hydras from two independent river networks develop tumours in the laboratory consisting of interstitial stem cells and display phenotypic alterations (supernumerary tentacles) akin to European counterparts. This finding confirms the value of this model for ecological and evolutionary research on host-tumour interactions.

Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny

The chloroplast (cp.) genome, also known as plastome, plays crucial roles in plant survival, adaptation, and evolution. The stable genetic structure of cp. genomes provides an ideal system for investigating species evolution. We sequenced three complete cp. genome sequences of Capsicum species and analyzed them using sequences of various Capsicum species retrieved from the NCBI database. The cp. genome of Capsicum species maintains a well-preserved quadripartite structure consisting of two inverted repeats (IRs) flanked by a large single copy (LSC) region and a small single copy (SSC) region. The sizes of cp. genome sequences ranged from 156,583 bp (C. lycianthoides) to 157,390 bp (C.pubescens). A total of 127–132 unique genes, including 83–87 protein-coding, 36–37 tRNA, and eight rRNA genes, were predicted. Comparison of cp. genomes of 10 Capsicum species revealed high sequence similarity in genome-wide organization and gene arrangements. Fragments of trnT-UGU/trnL-UAA, ccsA, ndhD, rps12, and ycf1 were identified as variable regions, and nucleotide variability of LSC and SSC was higher than that of IR. Phylogenetic speciation analysis showed that the major domesticated C. annuum species were the most extensively divergent species and closely related to C. tovarii and C. frutescens. Analysis of divergent times suggested that a substantial range of speciation events started occurring ~ 25.79 million years ago (Mya). Overall, comparative analysis of cp. genomes of Capsicum species not only offers new insights into their genetic variation and phylogenetic relationships, but also lays a foundation for evolutionary history, genetic diversity, conservation, and biological breeding of Capsicum species.