Gene Exchange Research Articles

Morphological adaptation strategy of invasive plant Ambrosia trifida seed distributed along rivers is closely related to soil nutrients

Rivers are crucial in the spread of invasive plants. Invasive plants alter their seed traits to adapt to environmental changes and promote invasion. Studying the trait changes in invasive plant seeds may improve the understanding of their propagation mechanisms along the river and provide appropriate control measures. In this study, seven Ambrosia trifida populations along the Liaohe River were used as study subjects. The results showed that the seven A. trifida populations were closely related and exhibited a certain gene exchange, but the absence of evidence of directed gene flow among populations did not confirm that rivers were the medium of seed dispersal of A. trifida. Along the Liaohe River, from top to bottom, the positive view area, length, width, perimeter, and thousand seed weight of A. trifida seeds showed an increasing trend. The total nitrogen and phosphorus contents in the river water of the A. trifida population in the lower reaches of the Liaohe River were higher than those at the other sites. Furthermore, along the river, from top to bottom, the available nitrogen, total nitrogen, total potassium, available potassium, and organic matter contents in the soil in which A. trifida populations grew showed significant increasing trends. River structure, water quality, and soil nutrients had direct and indirect effects on seed morphology. Soil total nitrogen, available potassium, and organic matter had significant positive effects on seed positive view area and perimeter, suggesting that the maternal effect played a critical role in shaping seed morphology. Our analysis showed that soil nutrients along the river may be the primary driver that governs changes in A. trifida seed traits.

Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken

Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.

Tire wear particles enhance horizontal gene transfer of antibiotic resistance genes in aquatic ecosystems

Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10−3 at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of MP pollution in various aquatic ecosystems.

Mucopolysaccharidosis type I: founder effect of the p.P533R mutation in North Africa

BackgroundMucopolysaccharidosis type I is a lysosomal storage disease resulting from a deficiency in alpha-L-iduronidase (IDUA), which causes the accumulation of partially degraded dermatan sulfate and heparan sulfate. This retrospective study, spanning eight years, analyzed data from 45 MPSI patients. The report aimed to explore the potential origin of the p.P533R mutation in the Maghrebin population by constructing a single-nucleotide polymorphism haplotype around the IDUA gene, in order to propose a molecular proof of a founder effect of the MPSI/p.P533R allele.Patients and methodsAll of the studied patients were from Libya (2), Mauritania (1) Morocco (21) and Tunisia (21) with first cousins being the most frequent union. The diagnosis of MPSI patients often involves the combination of urinary screening, leukocyte IDUA activity determination, and DNA molecular analysis. In our study, to identify the common p.P533R mutation, we performed both DNA sequencing and tetra-primer ARMS PCR assay. Additionally, Haploview was used to determine the specific haplotype that cosegregates with the p.P533R mutation. Controls were genotyped to ensure that all the SNPs were in Hardy–Weinberg equilibrium.ResultsIn the present report we confirmed the very strong impact of consanguinity on the incidence of MPSI disease. Furthermore, studied families of mixed ancestry shared common and specific haplotype, which was observed in studied populations, suggesting the presence of a founder effect in the North Africa.ConclusionThe p.P533R missense mutation was identified in each patient originated from Libya, Mauritania, Morocco and Tunisia. Furthermore, these MPSI patients exhibited the same IDUA haplotype. The occurrence of a shared AAGGGTG haplotype, among North African populations may be attributed to substantial historical gene exchange between these groups, likely stemming from migration, inter-ethnic marriage, or other forms of interaction throughout history.

Analyzing Antibiotic Resistance in Bacteria from Wastewater in Pakistan Using Whole-Genome Sequencing.

Background: Wastewater is a major source of Antibiotic-Resistant Bacteria (ARB) and a hotspot for the exchange of Antibiotic-Resistant Genes (ARGs). The occurrence of Carbapenem-Resistant Bacteria (CRB) in wastewater samples is a major public health concern. Objectives: This study aimed to analyze Antibiotic resistance in bacteria from wastewater sources in Pakistan. Methods: We analyzed 32 bacterial isolates, including 18 Escherichia coli, 4 Klebsiella pneumoniae, and 10 other bacterial isolates using phenotypic antibiotic susceptibility assay and whole-genome sequencing. This study identified the ARGs, plasmid replicons, and integron genes cassettes in the sequenced isolates. One representative isolate was further sequenced using Illumina and Oxford nanopore sequencing technologies. Results: Our findings revealed high resistance to clinically important antibiotics: 91% of isolates were resistant to cefotaxime, 75% to ciprofloxacin, and 62.5% to imipenem, while 31% showed non-susceptibility to gentamicin. All E. coli isolates were resistant to cephalosporins, with 72% also resistant to carbapenems. Sequence analysis showed a diverse resistome, including carbapenamases (blaNDM-5, blaOXA-181), ESBLs (blaCTX-M-15, blaTEM), and AmpC-type β-lactamases (blaCMY). Key point mutations noticed in the isolates were pmrB_Y358N (colistin) and ftsI_N337NYRIN, ftsI_I336IKYRI (carbapenem). The E. coli isolates had 11 different STs, with ST410 predominating (28%). Notably, the E. coli phylogroup A isolate 45EC1, (ST10886) is reported for the first time from wastewater, carrying blaNDM-5, blaCMY-16, and pmrB_Y358N with class 1 integron gene cassette of dfrA12-aadA2-qacEΔ1 on a plasmid-borne contig. Other carbapenamase, blaNDM-1 and blaOXA-72, were detected in K. pneumoniae 22EB1 and Acinetobacter baumannii 51AC1, respectively. The integrons with the gene cassettes encoding antibiotic resistance, and the transport and bacterial mobilization protein, were identified in the sequenced isolates. Ten plasmid replicons were identified, with IncFIB prevalent in 53% of isolates. Combined Illumina and Oxford nanopore sequencing revealed blaNDM-5 on an IncFIA/IncFIC plasmid and is identical to those reported in the USA, Myanmar, and Tanzania. Conclusions: These findings highlight the environmental prevalence of high-risk and WHO-priority pathogens with clinically important ARGs, underscoring the need for a One Health approach to mitigate ARB isolates.

Molecular characterization of a novel putative pathogen, Streptococcus nakanoensis sp. nov., isolated from sputum culture.

The genus Streptococcus encompasses a wide range of bacteria with more than 60 species. Recently, there has been a notable increase in reports of novel species of α-Streptococcus based on genomic analysis data. However, limited information exists regarding the pathogenicity of these species. In this study, a quinolone-resistant α-hemolytic Streptococcus strain, MTG105, was isolated from a patient with pneumonia. Genetic analysis revealed that this species was a novel species closely related to S. pseudopneumoniae. In an infection assay using organotypic lung tissue models, MTG105 induced epithelial damage comparable to that caused by S. pneumoniae and S. pseudopneumoniae, strongly suggesting its potential as a pathogenic α-Streptococcus. The natural transformation abilities of Streptococcus species facilitate gene exchange within the same genus, leading to the emergence of species with increasingly diverse genome structures. Therefore, the identification of this species underscores the importance of monitoring the emergence of novel species exhibiting virulence and/or multidrug resistance.

Antibiotic-Resistance Genes and Mobile Genetic Elements in Free-DNA with Transformational Capacity are Present in the Cantaloupe Melon Production Environment

ABSTRACT Bacterial free DNA (fDNA) may be a template for genetic exchange of antibiotic resistance genes (fARG), facilitated by mobile genetic elements (MGE). We analyzed for the presence of fARGs in cantaloupe melon, farmworker´s hands, and irrigation water samples; and if these fARGs, containing the ampicillin resistance gene (ampC), could transform ampicillin-sensitive Acinetobacter baumannii. Fourteen ARGs and five MGEs were identified in the fDNA from a total of 201 samples. Ninety-one percent of the hand rinses, 74% of the cantaloupe melon rinses, and 62% of the water samples contained at least one of the groups of genes analyzed. The genes most frequently found were ampC, 50%. Of the MGE genes analyzed, int1 was the most often detected (24%). ARG and MGE genes were more prevalent in farmworker’s hands. The fDNA, containing the ampC, transformed the ampicillin-sensitive A. baumannii (efficiency of 10−7). fDNA can facilitate the spread of antibiotic resistance among the agricultural microbiota.

Genetic diversity and population structure of superior shea trees (Vitellaria paradoxa subsp. paradoxa) using SNP markers for the establishment of a core collection in Côte d'Ivoire.

The shea tree is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool. However, the genetic structure of its population is not well studied, especially in Côte d'Ivoire. In this study, 333 superior shea tree genotypes conserved in situ in Côte d'Ivoire were collected and genotyped with the aim of investigating its genetic diversity and population structure to facilitate suitable conservation and support future breeding efforts to adapt to climate change effects. A total of 7,559 filtered high-quality single nucleotide polymorphisms (SNPs) were identified using the genotyping by sequencing technology. The gene diversity (HE) ranged between 0.1 to 0.5 with an average of 0.26, while the polymorphism information content (PIC) value ranged between 0.1 to 0.5 with an average of 0.24, indicating a moderate genetic diversity among the studied genotypes. The population structure model classified the 333 genotypes into three genetic groups (GP1, GP2, and GP3). GP1 contained shea trees that mainly originated from the Poro, Tchologo, and Hambol districts, while GP2 and GP3 contained shea trees collected from the Bagoué district. Analysis of molecular variance (AMOVA) identified 55% variance within populations and 45% variance within individuals, indicating a very low genetic differentiation (or very high gene exchange) between these three groups (FST = 0.004, gene flow Nm = 59.02). Morphologically, GP1 displayed spreading tree growth habit, oval nut shape, higher mean nut weight (10.62g), wide leaf (limb width = 4.63cm), and small trunk size (trunk circumference = 133.4cm). Meanwhile, GP2 and GP3 showed similar morphological characteristics: erect and spreading tree growth habit, ovoid nut shape, lower mean nut weight (GP2: 8.89g; GP3: 8.36g), thin leaf (limb width = 4.45cm), and large trunk size ( GP2: 160.5cm, GP3: 149.1cm). A core set of 100 superior shea trees, representing 30% of the original population size and including individuals from all four study districts, was proposed using the "maximum length sub-tree function" in DARwin v. 6.0.21. These findings provide new knowledge of the genetic diversity and population structure of Ivorian shea tree genetic resources for the design of effective collection and conservation strategies for the efficient use of inbreeding.

Phylogeography and population genomics of the critically endangered aquatic plant Caldesia grandis in China

Caldesia grandis, a critically endangered aquatic species, is predominantly found in the mid-low mountainous swamps of subtropical China. This study assessed the genetic diversity and population structure of the species using RAD-seq data, explored its phylogeography across the extant nine populations based on five plastid DNA (ptDNA) regions, and conducted niche modeling analysis. We found low genetic diversity (HE = 0.180, Ho = 0.222, and π = 0.197) and genetic differentiation among populations (Fst = 0.089), which was likely due to genetic drift in small populations and frequent inter-population contact during the Quaternary period. Although RAD-seq analysis did not reveal a clear population structure, two distinct clades, comprising western and eastern populations, were identified using five ptDNA haplotypes. Molecular dating and niche modeling suggested that the uplift of the Luoxiao Mts may have contributed to the divergence of the eastern and western clades (ca. 1.51 Ma)during the Pleistocene, which also supports the hypothesis that the Nanling Mts acted as a refugium for C. grandis. Additionally, the repeated glacial periods of the Quaternary, accompanied by contraction and expansion of suitable habitats, likely facilitated gene exchange among populations, influencing the current distribution pattern in subtropical China. Our results suggested that each ptDNA haplotype should be treated as an independent unit for conservation purposes, and ex-situ efforts should be prioritized to conserve C. grandis in China.

Genetic diversity of populations of East Siberian ende

Based on nucleotide polymorphism of cpDNA intergenic spacers psbA-trnH, trnL-trnF, and trnS-trnG, we studied the genetic diversity and population structure of a mountain species Oxytropis vasskovskyi Jurtz., endemic to East Siberia. The populations were characterized by medium and high haplotype (0.524–1.000) and low nucleotide (0.0003–0.0008) diversity. Variability distribution analysis showed a moderate level of diff erentiation; the interpopulation component accounted for about 44% of the total genetic variation in O. vasskovskyi. We observed demographic expansion for three of fi ve O. vasskovskyi populations. The haplotypes of the fi ve studied populations form a single complex in the genealogical network, which is probably due to their common origin, relatively recent divergence and incomplete lineage sorting, as well as the existing gene exchange between populations. Thus, in four of the fi ve studied populations, a low level of nucleotide diversity and the absence of nucleotide substitutions were determined, which indicates the need to use certain measures to protect all known habitats, conduct regular monitoring of their state and search for new locations of the species.

Population genetics analysis of Diospyrosmun A.Chev. ex Lecomte (Ebenaceae) based on EST-SSR markers derived from a novel transcriptome.

Diospyrosmun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D.mun's genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D.mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D.mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D.mun in Vietnam. In this study, the transcriptomes of D.mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D.mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D.mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D.mun.

Water chlorination increases the relative abundance of an antibiotic resistance marker in developing sourdough starters.

Proper development of sourdough starters is critical for making tasty and healthy bread. Although many factors contributing to sourdough development have been studied, the effect of water chlorination on the bacterial communities in sourdough has been largely ignored. Researchers used sequencing techniques to investigate this effect and found that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, they discovered that water chlorination could increase the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic resistance genes in spoilage and pathogenic bacteria. This suggests that water chlorination could favor the growth of key spoilage bacteria and compromise the quality and safety of the bread. These findings emphasize the importance of considering water quality when developing sourdough starters for the best possible bread.

Genetic polymorphisms of common sandflies in selected areas of Henan Province based on DNA barcoding

To characterize the species of common sandflies in Henan Province using DNA barcoding with cytochrome c oxidase subunit I (COI) gene as the molecular marker, and to analyze the genetic polymorphisms of sandflies, so as to provide insights into visceral leishmaniasis prevention and control in Henan Province. Sandfly specimens were sampled from 13 sandflies surveillance sites from 2021 to 2023 in Anyang City, Zhengzhou, Luoyang and Xuchang cities (Zhengzhou-Luoyang-Xuchang areas) where visceral leishmaniasis cases were reported and in Jiaozuo and Xinxiang cities (Jiaozuo-Xinxiang areas) without visceral leishmaniasis cases reported. Genomic DNA was extracted from a single sandfly, and COI gene was amplified. The amplification product was subjected to bidirectional sequencing. Following sequence assembly, the species of sandflies was characterized through sequence alignment using the BLAST tool. The intra-specific and inter-specific genetic distances of sandflies were estimated among different areas using the software Mega 11, and phylogenetic trees were created. The polymorphisms of nucleotide sequences in the sandflies COI gene were estimated using the software DnaSP. The fixation index (FST) of different geographical isolates of sandflies was calculated using the Arlequin software, and the gene flow value (Nm) was used to measure the gene flow in the sandflies populations. In addition, the population genetic structure of different geographical populations of Phlebotomus chinensis was analyzed using the STRUCTURE software. A total of 978 sandflies were collected from 13 sandflies surveillance sites in Zhengzhou-Luoyang-Xuchang areas, Jiaozuo-Xinxiang areas and Anyang City of Henan Province from 2021 to 2023, and 475 sandflies were randomly sampled for subsequent detections. A total of 304 Ph. chinensis, 162 Se. squamirostris and 9 Se. bailyi were identified based on molecular biological detection of the COI gene, and Se. bailyi was reported for the first time in Henan Province. The intraspecific genetic distances of sandflies were 0.000 to 0.040, and the inter-specific genetic distances ranged from 0.133 to 0.161. Phylogenetic analysis revealed that each of the three sandfly species was clustered into a clade. The genetic polymorphisms of Ph. chinensis populations varied among different areas, with the highest haplotype diversity (0.966 ± 0.007) and the greatest nucleotide diversity (0.011) in Zhengzhou-Luoyang-Xuchang areas, and the lowest haplotype diversity (0.720 ± 0.091) and nucleotide diversity (0.004) in Anyang City. The dominant haplotype of Ph. chinensis populations was Pch_Hap_2 in Anyang City and Jiaozuo-Xinxiang areas, with moderate genetic differentiation (0.05 < FST < 0.15) and frequent gene exchange (Nm value > 1) between Ph. chinensis populations sampled from Anyang City, and Jiaozuo-Xinxiang areas. Population genetic structure analysis showed that the dominant component of Ph. chinensis populations was K5 in Anyang City and Jiaozuo-Xinxiang areas. No obvious dominant haplotype was observed in Ph. chinensis populations sampled from Zhengzhou-Luoyang-Xuchang areas, which had very high genetic differentiation (FST > 0.25) and little gene exchange (Nm value < 1) with Ph. chinensis populations from Anyang City, and Jiaozuo-Xinxiang areas, with K3 as the dominant component. In addition, there was no significant difference in the genetic polymorphism level among Se. squamirostris populations from the three areas. There are Ph. chinensis, Se. squamirostris and Se. bailyi in Henan Province, and S. bailyi is recorded for the first time in Henan Province by molecular biological assays. There are different levels of genetic differentiation and gene exchange among P. chinensis populations in different areas of Henan Province.

Genetic diversity of the Ruditapes decussatus and evidence of its hybridization with the alien R. philippinarum in the Western Mediterranean Sea

The introduction of alien species in marine ecosystems is often driven by the increasing demand of fishery resources. This is the case of the Manila clam (R. philippinarum), imported in Europe from Japan since the 1970s, to meet the growing demand for clams that the native species, the grooved carpet shell clam (Ruditapes decussatus), could not satisfy. Alien species introduction could threaten the genetic diversity and integrity of the native clam, also causing hybridization (i.e., gene flow from one species into the gene pool of another). Since R. philippinarum recently spread in a few important Mediterranean coastal areas, a combined approach based on morphological characteristics, length differences of two nuclear species-specific markers (ITS2, 5SrDNA) and the sequence of the mitochondrial gene cytochrome c oxidase subunit I (COI), was used to investigate the presence of hybrids in six Mediterranean wetlands (Sardinia, Italy). Eight individuals morphologically identified as R. decussatus were hybrids, having sequences specific to both R. decussatus and R. philippinarum in their nuclear DNA (ITS2 and 5SrDNA). Most of these individuals were found to be post-first generation (F1) hybrids indicating that F1-hybrids may be fertile. Secondly, to study the genetic diversity of R. decussatus in the Sardinian wetlands as well as in its whole distribution area, >380 new COI sequences from the eastern Atlantic Ocean and Mediterranean Sea were analysed along with those available from public databases. Mitochondrial COI data revealed variable haplotype and nucleotide diversities in different areas, which were not dependent on sample sizes. The aquaculture breeding activities and clam transplantation between different countries, along with the long pelagic larval dispersal and the commercial import of other bivalve species might have promoted gene exchange between different sites and thus higher diversity levels in a few wild populations. Our research, evaluating the genetic makeup of wild and hatchery stocks and clarifying the degree of hybridization, can contribute to develop further recommendations for conserving the genetic integrity of R. decussatus.

Genetic structure and gene flow among populations of willow (Salix species)

The newly developed Salix hybrids were assessed for genetic diversity using ISSR (Inter Simple Sequence Repeats) molecular markers. The results revealed 88.08 polymorphism, 0.53 polymorphism information content, 4.70 effective multiplex ratio, 2.54 marker index, and 7.18 resolving power from the amplified primers. Clones of the Salix matsudana (MAT) population recorded a maximum mean number of effective alleles (1.42), Shannon information index (0.38), gene diversity (0.25), and percentage of polymorphic loci (82.24 %). The AMOVA (Analysis of molecular variance) results revealed a moderate genetic divergence with a genetic variation of 88 per cent within populations and 12 per cent among the populations. The highest value of total diversity (0.28) and gene diversity (0.24) was recorded between S. matsudana (MAT) and S. tetrasperma (TETRA) populations, while there was more gene flow between S. matsudana (MAT) and S. tetrasperma (TETRA) populations (5.86). The clustering pattern obtained through STRUCTURE software showed two main gene pools and a mixture of 6–7 gene pools to confirm the hybrids based on ISSR marker data. S. matsudana and S. tetrasperma clones showed the highest gene diversity due to their proximity from their original locations, resulting in the least amount of gene exchange among populations. Molecular characterization using ISSR markers was extremely useful for studying the genetic diversity among the willow hybrids and high genetic variability should be utilized for breeding purposes in the future.

Effects of Personality and Behavioral Syndromes on Competition for Social Hierarchical Status in Anemonefish Amphiprion clarkii.

In this study, the behavioral ethogram of Amphiprion clarkii during the growth phase prior to sexual differentiation was summarized based on behavioral observations in three social environments. These behaviors can be classified into four categories: in addition to normal behaviors, the other three categories of behaviors-threatening, agonistic, and appeasing behaviors-represent different intentions in interactions with other individuals. Subsequently, the personalities of each individual were assessed by testing their reactions to intruders. These individuals mainly exhibited two distinct personality types: bold-aggressive and shy-submissive. In pairing experiments, the interactive behaviors of the anemonefish were observed in pairing combinations of different body sizes and personalities. The impact of personality on the establishment of a stable social hierarchy was confirmed by significant differences in the success rates of different pairing combinations, with the frequency of appeasing behaviors being the main factor influencing the success rate. Our results suggested that in natural waters, when juvenile individuals migrate among host anemones, shy-submissive individuals are more likely to be accepted due to their appeasing behaviors towards larger individuals, thus avoiding the risk of being attacked and bitten, and benefiting the survival of the individual. Conversely, bold-aggressive individuals are more likely to be driven away to another host anemone due to their unwillingness to settle for a lower-ranked status, thereby contributing to population dispersal and increasing opportunities for gene exchange between populations.

Genetic diversity and population structure of Thymallus sp. in China based on morphological and molecular markers

Thymallus sp. is a native fish species distributed in the Irtysh River Basin in China. Unfortunately, environmental damage and overfishing have led to a significant decline in Arctic grayling resources, pushing them towards endangerment. However, there is a lack of comprehensive genetic information regarding the wild populations of Thymallus sp., which poses challenges for the development of effective conservation strategies for their genetic resources. In response, this study collected 180 samples from six major tributaries within the Irtysh River Basin. It conducted a thorough investigation of Thymallus sp.'s morphological and genetic variations using morphometric measurements and microsatellite markers. The results showed that the morphological differences among the six populations were relatively minor, and none of the morphological traits reached the subspecies level or higher. Genetic analysis showed that all six populations of Thymallus sp. possessed high genetic diversity, with genetic variations among populations accounting for only 6.30 % of the total variation, suggesting that the current status of the germplasm resources was relatively good. However, due to overfishing, which had led to a decline in the number of effective breeding groups, some inbreeding has occurred within populations. Moreover, the construction of dams has hindered gene exchange, leading to a certain tendency towards genetic differentiation within the populations. This was evidenced by the clustering of Burqin and Haba into one genetic group, while Kuirt, Kayit, Kalaerzis, and Crane were classified into another genetic group. This study offers an important reference for the management and conservation of Thymallus sp. populations in the Irtysh River Basin.

Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence

IntroductionGene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored. ObjectiveThe present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence. MethodsWe collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000 years. We characterized their metagenomes, and identified DNA viruses within these metagenomes. ResultsOur findings reveal a significant shift in viral community composition after 50 years of land reclamation, but soil viral diversity reached a stable phase approximately 300 years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer. ConclusionThese findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.

Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China

Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense.

Genetic diversity of the critically endangered Blue‐crowned laughingthrush (Garrulax courtoisi)

AbstractTo evaluate the genetic quality and provide available management strategies for Blue‐crowned laughingthrush (BCLT), fifteen polymorphic microsatellite loci were developed and applied. The genetic diversity of wild individuals was indicated to be higher than the two captive populations. The average number of alleles (5.50 ± 0.317), the number of effective alleles (3.417 ± 0.222), observed heterozygosity (0.828 ± 0.04), and genetic differentiation index (0.028 ± 0.007) of 64 wild individuals showed high genetic diversity despite drastic bottleneck and low genetic differentiation. The number of effective migrants (22.737 ± 8.318) indicated the intriguing wintering grounds may be surrounded by the breeding sites where the syncheimadia occurred in Wuyuan. Efficient conservation, winter flocking, and cooperative breeding may facilitate gene exchange and inclusive fitness. We recommend that monitoring concentrated distribution areas for BCLT should be strengthened, and geographical barriers, interference types, and the inner mechanism of distribution patterns should be further explored.