Evolution Of Species Research Articles

Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae

Aroideae is an important subfamily of the Araceae family and contains many plants with medicinal and edible value. It is difficult to identify and classify Aroideae species accurately on the basis of morphology alone because of their polymorphic phenotypic traits. The chloroplast genome (CPG) is useful for studying on plant taxonomy and phylogeny, and the analysis of codon usage bias (CUB) in CPGs provides further insights into the intricate phylogenetic relationships among Aroideae. The results showed that the codon third position of the chloroplast genome coding sequence in Aroideae was rich in A and T, with a GC content of 37.91%. The ENC-plot and PR2-plot revealed that the codon usage bias of Aroideae was influenced by multiple factors, with natural selection as the dominant factor. Thirteen to twenty optimal codons ending in A/T were identified in 61 Aroideae species. Additionally, the comparative analysis of CPGs revealed that two single copy regions and non-coding regions were variable in Aroideae. Eight highly divergent regions (Pi > 0.064) were identified (ndhF, rpl32, ccsA, ndhE, ndhG, ndhF-rpl32, ccsA-ndhD, and ndhE-ndhG) , in which ndhE have the potential to serve as a reliable DNA marker to discriminate chloroplasts in Aroideae subfamily. Furthermore, the maximum likelihood-based phylogenetic trees constructed from complete chloroplast genomes and protein-coding sequences presented similar topologies. Principal component clustering analysis based on relative synonymous codon usage values (RSCUs) revealed that Calla was clearly deviated from Montrichardia and Anubias, and that Alocasia was closer to Colocasieae than to Arisaemateae. These findings suggest that the use of RSCU for clustering analysis could offer new theoretical support for species classification and evolution. Our research could provide a theoretical foundation for the chloroplast genetic engineering, taxonomy, and phylogenetic relationships of Aroideae chloroplasts.

Species evolution: cryptic species and phenotypic noise with a particular focus on fungal systematics

The evolution of a species can be understood in the context of two major concepts—the cryptic species concept and the phenotypic noise concept. The former represents morphologically indistinguishable but genetically distinct evolutionary lineages, while the latter represents the phenotypic variations of an isogenic population. Although the concept of cryptic species currently represents a general topic, its effect on other aspects of biology, such as biodiversity, ecology, evolutionary biology, and taxonomy, is still unclear. In particular, cryptic species cause complications and prevent the development of a clear taxonomy. The phenotypic noise concept or phenotypic plasticity generally refers to the various expressions of phenotypes in different environments. Hence, the cryptic species concept refers to genetic variations, while the phenotypic noises concept is about non-genetic variations. Although both concepts are opposites, they each contribute significantly to the evolutionary process of an organism. Despite the extensive research studies and publications discussing those two concepts in separate accounts, a concise account that combines and compares both concepts are generally lacking. Nevertheless, these are essential to understand the evolutionary process clearly. This review addresses the available literature on this topic, intending to provide a general and overall discussion on both the cryptic species concept and the phenotypic noise concept and their effect on evolution, ecology, biodiversity, and taxonomy with a special focus on fungal systematics. hence, several fungal case studies representing the two concepts are presented, compared, and discussed for a better understanding.

Karyotyping: Basics and Application in Forestry

Karyotyping is the method of assessing an organism's chromosomal number and structure, is essential for comprehending the genetic composition of species, especially those used in forestry. This method provides important insights into the genetic diversity, evolution, breeding, and conservation of trees and other forest species by examining their chromosomal features. Karyotypes explain how many chromosomes each organism has and how they appear under a light microscope. Length of the chromosome, centromere location, banding pattern, sex-chromosome variations, and other physical traits can also be determined by karyotyping. At traditional level, by using light microscope, we can study chromosomes but to generate chromosomal data, sophisticated methods like fluorescence in-situ hybridization (FISH) and genomic in-situ hybridization (GISH) can be employed. From taxonomical classification to identify different types of abnormalities, karyotyping is important. There is a lack of study related to karyotyping in forestry species. This study summarizes the basics of karyotyping and the work related to it, has been done in forestry species. This review article deals with the importance of karyotyping such as how they contribute to the conservation biology of the forestry species, how it helps in the development of taxonomical identification marker and identification in different types of chromosomal abnormalities. It also covers how karyotyping can be done. From traditional methods i.e use of microscopes to the merge of different recent developments in the area of karyotyping helps not only in enrichment of cytogenetics data but also substitute the genomics and transcriptomics in the area of genetic diversity studies. Basics of karyotyping, different types of banding techniques, protocols of some of the techniques, its methodological developments, and its various applications in forestry have also been discussed in this review. Application of karyotyping in different forestry species is limited. With the advancement of imaging techniques and other genetic tools, biodiversity and forests can be managed sustainably.

Evolution and expression of TLR5a and TLR5b in lamprey (Lampetra japonica)

The lamprey serves as a key model organism for studying the origin and evolution of species, embryonic development, and the immune system. The immune system primarily relies on pattern recognition receptors, including Toll-like receptors (TLRs), with Toll-like receptor 5 (TLR5) having a particularly complex evolutionary history. Currently, although TLR5 is being identified in an expanding array of taxonomic groups, a comprehensive study on its evolutionary aspects is yet to be conducted. In this study, we identified Lj-TLR5a and Lj-TLR5b in Lampetra japonica and examined their distribution across various tissues in this species. Furthermore, we conducted preliminary investigations into their immune functions and discovered that, as primitive genes, they are highly sensitive to various pathogens. Upon recognizing flagellar proteins, both Lj-TLR5a and Lj-TLR5b work together; however, these TLRs may function independently in response to other stimuli. Subsequently, we performed comprehensive structural and evolutionary analyses of the TLR5 family, incorporating TLR5 data from various species at different evolutionary stages. Our findings revealed that TLR5a and TLR5b in lamprey are in a relatively primitive evolutionary state. Meanwhile, TLR5L differentiated during the early stages of evolution and exhibits a pseudogenic trend throughout this evolutionary process; notably, this TLR is currently preserved only in certain amphibian and reptile species. In cartilaginous fish, only one type of TLR5 is usually retained, whereas bony fish typically possess both TLR5 and TLR5S. TLR5S has a relatively simple structure, likely arising from repetitive whole-genome events in bony fishes. Among bony fishes, flesh-finned fish were found to retain only one TLR5, which eventually evolved into the TLR5 found in quadrupeds. In summary, this study provides significant insights into the origin and evolution of the TLR5 family by analyzing the evolutionary status and immune functions of Lj-TLR5a and Lj-TLR5b in Japanese lampreys.

Identification of the shortest species-specific oligonucleotide sequences.

Despite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying the shortest species-specific nucleotide sequences offers insights into species evolution and holds potential practical applications in agriculture, wildlife conservation, and healthcare. We propose a new method for sequence analysis termed nucleic "quasi-primes," the shortest occurring sequences in each of 45,076 organismal reference genomes, present in one genome and absent from every other examined genome. In the human genome, we find that the genomic loci of nucleic quasi-primes are most enriched for genes associated with brain development and cognitive function. In a single-cell case study focusing on the human primary motor cortex, nucleic quasi-prime genes account for a significantly larger proportion of the variation based on average gene expression. Nonneuronal cell types, including astrocytes, endothelial cells, microglia perivascular-macrophages, oligodendrocytes, and vascular and leptomeningeal cells, exhibit significant activation of quasi-prime-containing gene associations related to cancer, whereas simultaneously suppressing quasi-prime-containing genes are associated with cognitive, mental, and developmental disorders. We also show that human disease-causing variants, eQTLs, mQTLs, and sQTLs are 4.43-fold, 4.34-fold, 4.29-fold, and 4.21-fold enriched at human quasi-prime loci, respectively. These findings indicate that nucleic quasi-primes are genomic loci linked to the evolution of species-specific traits, and in humans, they provide insights in the development of cognitive traits and human diseases, including neurodevelopmental disorders.

Developing pangenomes for large and complex plant genomes and their representation formats.

The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations. This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies. Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species' genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction. This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity.

8000 Years of morphometric evolution of sheep, goat and pig in the northwestern Mediterranean basin

Understanding how domestic mammal species evolved through time provides insight into the artificial and natural selection processes that have shaped the diversity of domestic animals. The focus of this article is the morphometric evolution of sheep, goats and suids in the Northwestern Mediterranean Basin over the last 8000 years, employing a 2D geometric morphometrics protocol applied to the third lower molars. Using a comprehensive dataset comprising 2798 archaeological specimens from 176 sites in Southern France and Spanish Catalonia, along with 1303 modern specimens, we aim to identify and contrast the environmental and anthropic factors influencing species evolution linked to past husbandry practices. Each of these three taxa follows its own evolutionary trajectory, exhibiting variations over time and across different regions. Notably, reduction in the centroid size of sheep molars between the Neolithic and the early Iron Age could potentially be associated with an increased demand for meat and/or shifts in male-to-female ratios. A clear geographical structuring of caprines between the Neolithic and Antiquity is observed, likely influenced by a combination of factors including artificial selection, environmental changes and socio-economic dynamics, as corroborated by previous studies. Moreover, a reduction in molar size during the Middle Ages is observed across all three species, possibly linked to extensive agropastoral practices. Furthermore, divergent processes of breed improvement and standardization are identified in pigs and caprines. This study highlights the complex nature of morphological variations in domestic species, emphasising the multifactorial influences involved. It underscores the importance of interdisciplinary approaches in understanding the factors contributing to morphological transformations over time.

Comparative Chloroplast Genomes and Phylogenetic Relationships of True Mangrove Species Brownlowia tersa and Brownlowia argentata (Malvaceae)

Brownlowia tersa and Brownlowia argentata are two true mangroves in the genus Brownlowia in Malvaceae, and they are a near-threatened and a data-deficient species, respectively. However, the genomic resources of Brownlowia have not been reported for studying their phylogeny and evolution. Here, we report the chloroplast genomes of B. tersa and B. argentata based on stLFR data that were 159,478 and 159,510 base pairs in length, respectively. Both chloroplast genomes contain 110 unique genes and one infA pseudogene. Sixty-eight RNA-editing sites were detected in 26 genes in B. argentata. A comparative analysis with related species showed similar genome sizes, genome structures, and gene contents as well as high sequence divergence in non-coding regions. Abundant SSRs and dispersed repeats were identified. Five hotspots, psbI-trnS, trnR-atpA, petD-rpoA, rpl16-rps3, and trnN-ndhF, were detected among four species in Brownlowioideae. One hotspot, rps14-psaB, was observed in the two Brownlowia species. Additionally, phylogenetic analysis supported that the Brownlowia species has a close relationship with Pentace triptera. Moreover, rpoC2 was a candidate gene for adaptive evolution in the Brownlowia species compared to P. triptera. Thus, these chloroplast genomes present valuable genomic resources for further evolutionary and phylogenetic studies of mangroves and plant species in Malvaceae.

Chromosome-level de novo genome unveils the evolution of Gleditsia sinensis and thorns development.

Gleditsia sinensis Lam. (G. sinensis) as an important species within the Leguminosae family, has been utilized in Chinese medicine for centuries, and its thorns serve as a chief medicinal ingredient. The absence of a comprehensive genome database has hindered its in-depth research. In this investigation, a chromosome-level de novo genome assembly of G. sinensis 'Yulin No.1' was achieved, which harbors a 786.13 Mb sized genome with 36,408 protein-coding genes and experiences two WGD events. The comparative and evolutionary analysis unveiled the close phylogenetic relationship between G. sinensis and eight other Leguminosae species. The WGCNA and gene family analysis further indicated that GsinMYB was involved in the development of thorns. This investigation offered a high-level genome of G. sinensis, facilitating comparisons in Leguminosae species evolution and functional elucidation. It also provided key insights for further research on the molecular regulation mechanisms of thorn development in plants and the molecular breeding of G. sinensis.

Genome-wide microsatellite characterization and their marker development and transferability in Broussonetia Species

BackgroundBroussonetia papyrifera, B. monoica, and B. kaempferi belong to the genus Broussonetia (Moraceae). These three species hold significant economic and research values. However, few molecular markers have been effectively utilized for resource development and molecular genetic breeding of these species. Sequencing of their genomes allowed us to develop genomic markers (e.g. simple sequence repeats (SSRs)) and construct a high-density physical map.ResultsA total of 369,557, 332,627, and 276,245 SSRs were identified in 13 high-quality assembled pseudochromosomes and their unassembled scaffolds for B. papyrifera, B. monoica, and B. kaempferi, respectively. Among the identified genomic SSRs across the three species, short repeat sequences were more abundant, while long repeat sequences constituted a smaller proportion. Additionally, the predominant repeat motifs in the SSRs of the three Broussonetia species were composed of ‘A’ and ‘T’ repeats. Using B. papyrifera genome as a reference, 4,419 common SSRs were identified among these three species, while 2,048 SSRs were specific to B. kaempferi, and 4,285 SSRs were specific to B. monoica. Distribution analysis indicated a notable similarity in the distribution patterns of SSRs across the pseudochromosomes of these three species. Furthermore, of the identified SSRs, 28%, 31%, and 24% were mapped to genes in B. papyrifera, B. kaempferi, and B. monoica, respectively. Genic-mapped SSRs may regulate biological processes by influencing gene activity and protein function. To verify SSRs polymorphism, we selected 30 ones from 10,752 potentially polymorphic SSRs loci for PCR amplification among these three species, all of which were successfully amplified and exhibited polymorphism across these three species.ConclusionsThese findings are helpful for further research on the origin, evolution, and migration of Broussonetia species and also laid the foundation for the precise identification, systematic evaluation, and efficient utilization of the germplasm resources of Broussonetia species.

A dusty dawn: galactic dust buildup at z ≳ 5

ABSTRACT Over the last decade, the Atacama large millimeter array has revealed massive, dusty star-forming galaxies at $z\gtrsim 5$, and the JWST is primed to uncover even more information about them. These observations need dust evolution theory to provide context and are excellent benchmarks to test this theory. Here, we investigate the evolution of galactic dust budget at cosmic dawn using a suite of cosmological zoom-in simulations of moderately massive, high-redshift ($M_{*}\gtrsim 10^9\, \, {\rm M}_{\odot }$; $z\gtrsim 5$) galaxies from the Feedback in Realistic Environments project, the highest resolution ($m_{\rm b} \approx 7100\, \, {\rm M}_{\odot }$) of such simulations to date. Our simulations incorporate a dust evolution model that accounts for the dominant sources of dust production, growth and destruction and follows the evolution of specific dust species, allowing it to replicate a wide range of present-day observations. We find, similar to other theoretical works, that dust growth via gas-dust accretion is the dominant producer of dust mass for these massive, $z\gtrsim 5$ galaxies. However, our fiducial model produces $M_{\rm dust}$ that fall ${\gtrsim }1$ dex below observations at any given $M_{*}$ (typical uncertainties are ${\sim }1$ dex), which we attribute to reduced accretion efficiencies caused by a combination of low galactic metallicities and extremely bursty star formation. Modest enhancements (i.e. within observational/theoretical uncertainties) to accretion and SNe ii dust creation raise $M_{\rm dust}$ by ${\lesssim }1$ dex, but this still falls below observations which assume $T_{\rm dust}\sim 25$ K. One possibility is that inferred dust masses for $z\gtrsim 4$ galaxies are overestimated, and recent observational/analytical works that find $T_{\rm dust}\sim 50$ K along with metallicity constraints tentatively support this.

Targeted migration mechanisms of nitrogen-containing pollutants during chemical looping co-gasification of coal and microalgae.

The chemical looping co-gasification of nitrogen-containing algal biomass and coal could effectively realize the high-value utilization of gasification products, but the mechanism of conversion of nitrogen-containing pollutants is not clear. In this work, the effects of the different ratios of microalgae on the co-gasification process were first explored, and the results showed that the 40 % coal + 60 % microalgae blending had the best synergistic effect, with a comprehensive synergistic index (CSI) of 1.35 as the maximum value. The effects of temperature, the ratio of OCs to feed (O/C) and steam flow rate on the evolution of nitrogen-containing species in the co-gasification products were explored based on the optimal mixing ratio, and the results showed that elevating the reaction temperature promotes the generation of nitrogen oxide precursors, and an appropriate amount of steam could inhibit the generation of NOx. The nitrogen in coke mainly came from the Maillard reaction between carbonyl (-CO) compounds and amino (-NH2) compounds and its main forms are pyridine nitrogen (N-5) and pyrrole nitrogen (N-6). Based on the nitrogen accumulation forms in the products of each phase, the mechanism of nitrogen transport and conversion in the chemical looping co-gasification of coal and microalgae (CM-CLCG) process was proposed. This study provides a reference for the synergistic utilization of coal and biomass and the control process of nitrogen-containing pollutants.

Changes in microbiome composition during ontogeny and dispersal of the coral boring sponge Thoosa mismalolli

Dispersal is an important life history trait that plays a key role in the demography and evolution of species. We employed a combined approach of DNA sequencing and transmission electron microscopy to examine the changes in the microbiome during the ontogeny and dispersal of the coral-excavating sponge Thoosa mismalolli. The results show that sponge can acquired their associated bacteria via both vertical (VT) and horizontal transmission (HT). Adult sponges, brooding larvae, and early free-swimming sponge larvae harbor a similar high-diversity microbial assemblage, dominated by Proteobacteria and Chloroflexi, which change throughout the larval dispersal phase. Larvae collected offshore showed a reorganization of their microbiome with a significant reduction of the dominance of inherited bacteria (Proteobacteria and Chloroflexi), and an enrichment of environmentally derived bacteria taxa (Bacteroidetes, Tenericutes, and Firmicutes). TEM confirmed a substantial change in cell structure and microbial composition, attributed to symbionts’ massive phagocytosis. This research provides information on microbiome dynamics through the sponge ontogeny and sheds on their possible role in the dispersal capacity of their larvae.

Investigating the decomposition mechanism of DNAN/DNB cocrystal explosive under high temperature using ReaxFF/lg molecular dynamics simulations.

DNAN/DNB cocrystals, as a newly developed type of energetic material, possess superior safety and thermal stability, making them a suitable alternative to traditional melt-cast explosives. Nonetheless, an exploration of the thermal degradation dynamics of the said cocrystal composite has heretofore remained uncharted. Consequently, we engaged the ReaxFF/lg force field modality to delve into the thermal dissociation processes of the DNAN/DNB cocrystal assembly across a spectrum of temperatures, encompassing 2500, 2750, 3000, 3250, and 3500K. We analyzed the evolution of species, preliminary disintegration processes, and fluctuations in the quantification of terminal outcomes were examined. The findings suggest that 2,4-dinitroanisole (DNAN) undergoes a thorough phase of disassembly within a timespan of 218ps, while 1,3-dinitrobenzene (DNB) completely decomposed within 228ps, demonstrating that DNAN has lower thermal stability than DNB, but with no significant difference. The thermal dissociation of DNAN/DNB cocrystals at elevated temperatures reveals a triad of potential reaction sequences. Primordially, the denitration of DNAN transpires, succeeded by the denitration of DNB, culminating in the nitro-isomerization of the latter. This sequence implies that the nitro moieties within DNB possess inferior thermal resilience compared to their counterparts within the DNAN cocrystal matrix. An examination of the six resultant end products suggests a predominance of H2O, NO2, and H2 in comparison to the other byproducts, which may be indicative of the pyrolytic transformations occurring during the disassembly process. This study first constructed the supercell model of DNAN/DNB eutectic crystal using the Materials Studio software and optimized the geometric structure of the model through the conjugate gradient algorithm. Then, the Nosé-Hoover method was used for NPT-MD simulation to further relax the model. Subsequently, molecular dynamics simulations were carried out using the LAMMPS software and the ReaxFF/lg force field. Simulation parameters were set, and NPT ensemble molecular dynamics simulations were performed at different temperatures. The simulation results were analyzed to reveal the thermal decomposition mechanism of DNAN/DNB eutectic crystal.

Oxygen Vacancy-Mediated Microflower-like Bi5O7I for Reactive Oxygen Species Generation through Piezo-Photocoupling Effect.

Photocatalytic reactive oxygen species (ROS) evolution with Bi5O7I still suffers from sluggish charge carrier dynamics and limited light absorption. Herein, abundant oxygen vacancies (OVs) were introduced into the microflower-like Bi5O7I, and its ROS generation toward organic dye degradation under the synergistic effect of visible light and ultrasound irradiation was investigated. Benefiting from the broadened visible-light absorption range, stronger piezoresponse, and higher carrier transport efficiency in OV-enriched Bi5O7I (2-PEG-Bi5O7I), both its photocatalytic and piezocatalytic degradations were improved. More importantly, its piezo-photocatalytic degradation performance was greater than the sum of the corresponding photocatalysis and piezocatalysis, indicating a strong coupling effect. In addition, the piezo-photocatalytic yield of •O2- with 2-PEG-Bi5O7I was 1.5 times higher than that with Bi5O7I, and it was also 4.3 and 3.1 times higher than its single photocatalysis and piezocatalysis, respectively. Interestingly, no noticeable •OH was detected in the case of visible-light irradiation, while the piezocatalytic and piezo-photocatalytic yields of •OH were 3.6 and 5.3 μmol g-1 h-1, respectively, with OV-enriched Bi5O7I, surpassing the pristine Bi5O7I as well. This work advances the coupling effect between photocatalysis and piezocatalysis as a new strategy for efficient ROS generation and also discloses the positive role of oxygen vacancies in improving multiresponsive catalysis.

GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish.

The shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield and ornamental value. This study applies our GRAMMAR-Lambda method to perform a genome-wide association study analysis on loci related to head size in catfish. Compared with traditional GWAS methods, the GRAMMAR-Lambda method offers higher computational efficiency, statistical power, and stability, especially in complex population structures. This research identifies many candidate genes closely related to cranial morphology in terms of head length, width, and depth in catfish, including bmpr1bb, fgfrl1b, nipbl, foxp2, and pax5, etc. Based on the results of gene-gene interaction analysis, we speculate that there may be frequent genetic interactions between chromosome 19 and chromosome 29 in bone development. Additionally, many candidate genes, gene families, and mechanisms (such as SOCE mechanisms) affecting skeletal development and morphology have been identified. These findings contribute to our understanding of the genetic architecture of head size and will support marker-assisted breeding in aquaculture, also reflecting the potential application of the GRAMMAR-Lambda method in genetic studies of complex traits.

Comparative insights into genomic variability and adaptation in the chloroplast genomes of Salvia japonica and Salvia rosmarinus

Chloroplast genomes provide important information about phylogenetics, plant evolution, and adaptive processes. This study examines the chloroplast genomes of Salvia japonica and Salvia rosmarinus. We conducted structural and functional annotations to identify significant variations in gene content and organization. We found that S. rosmarinus has fewer photosystem II (psb) genes and a greater abundance of hypothetical genes (ycf). This may help maintain genomic stability while facilitating species evolution. There are big differences in insertion-deletion events (indels) and single nucleotide polymorphisms (SNPs) in important gene families, like NADH dehydrogenase and ribosomal proteins. We determined this organizational difference by applying Principal Component Analysis (PCA) to the genomes of the two species, which belong to different and distinct gene categories. Sequence alignment revealed gaps and inconsistencies in genes related to RNA polymerase and photosynthesis. The fact that S. japonica and S. rosmarinus have a lot of different genes and may have adapted to live in different environments suggests that they have had different evolutionary paths. These results give us important information about how Salvia species have evolved and give us a way to think about how chloroplast genomes change in different ecological settings. This study provides a basis for understanding the evolution of the chloroplast genome in the genus Salvia. This study has been significant in clarifying the role of photosynthetic and hypothetical genes in controlling environmental responses. Future study must use transcriptome and ecological data to enhance our understanding of the impact of genetic variants on functionality.

Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis.

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae.

The formation, maintenance, and loss of island biodiversity.

Due to the unique geographical features of large numbers, isolated by water and diverse formation histories, islands have become natural laboratories for ecological and evolutionary research. Islands have a high proportion of endemic species and disharmony in representing the species compared with that in the continent, which provides a good opportunity to explore the formation of island biodiversity. In this review, we focuse on island ecosystems and describes the progress of research in island biogeography in recent years from three aspects: formation, maintenance, and loss of island biodiversity. First, we take several representative island systems in the world as examples to introduce the formation mechanism of island biodiversity from species dispersal and immigration, population establishment and selection, species evolution and adaptive radiation. Based on the Equilibrium Theory of Island Biogeography, we then review the species-area relationship and species-isolation relationship and focus on the research progress in community assembly, including Diamond's rule, nestedness pattern, the framework of community structure of island biota, and species interactions on islands. We also discuss the high extinction risks of island species threatened from natural and human disturbances, especially from the impact of habitat loss and change, climate change, alien species invasion and the synergistic effect of these factors on the loss of island biodiversity. Finally, based on the status of island biodiversity, we summarized the current conservation practices for island biodiversity and possible research frontiers in island biogeographic studies.

Quantitative Approach for Determining Reproductive Life-History Strategies of Parasitic Plants: A Case Study in Balanophora.

Parasitic plants are a diverse and unique polyphyletic assemblage of flowering plants that survive by obtaining resources via direct vascular connections to a host plant. Ecologically important in their native ecosystems, these typically cryptic plants remain understudied and fundamental knowledge of the biology, ecology, and evolution of most species is lacking. This gap limits our understanding of ecosystems and conservation management. We established a multistep protocol to conduct the first investigation of the reproductive life history of root parasite genus Balanophora, testing the hypotheses of perenniality, cryptic perenniality, and plasticity across five geographically isolated populations in Taiwan. A review of 123 Balanophora publications found contradictory determinations, including no determination (87%), perennial (9%), annual (1%), biennial (1%), or a combination (2%). No primary study investigated the question, and no determination was accompanied by reference. Between 2021 and 2024, we tested a hypothesis of perenniality (109 individuals, 135 patches) and cryptic perenniality (73 host samples), monitored population dynamics (whole population), and potential for endophytic/dormant haustorial tissue (101 roots) across five isolated populations of Balanophora fungosa ssp. fungosa in Taiwan. Our results support semelparous annuality. After reproduction, individuals senesce and die, and the following year's population is recruited from newly germinated individuals which together develop in size and number during a vegetative growth period, undergo reproduction, and then themselves senesce and die. Each cycle is completed within a 12-month period. Synthesis: Our study provides the first quantitative determination of a semelparous annual reproductive life-history strategy for any species of Balanophora. This determination is important in our progress toward better understanding the species-and parasitic plants in general-as well as ecological roles within ecosystems and conservation management. Our study further provides a template for future work to expand life-history strategy determination across cryptic root parasitic plants.